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- EMDB-11972: Overall map of a transcribing RNA polymerase II-U1 snRNP complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-11972
TitleOverall map of a transcribing RNA polymerase II-U1 snRNP complex with 145-nt RNA
Map data
SampleThe transcribing RNA polymerase II-U1 snRNP complex with 145-nt RNA
  • RNA polymerase II
  • Nucleic acidsNucleic acid
  • U1 snRNP
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 8
  • DNA-directed RNA polymerase subunit betaPolymerase
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 2
  • RPB12
  • (nucleic-acidNucleic acid) x 4
  • (U1 small nuclear ribonucleoprotein ...) x 2
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • Small nuclear ribonucleoprotein-associated protein
  • (ligand) x 2
Function / homology
Function and homology information


negative regulation of protein refolding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / regulation of ATPase activity / regulation of mRNA polyadenylation / methylosome / histone mRNA metabolic process / negative regulation of chaperone-mediated autophagy / snRNA binding ...negative regulation of protein refolding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / regulation of ATPase activity / regulation of mRNA polyadenylation / methylosome / histone mRNA metabolic process / negative regulation of chaperone-mediated autophagy / snRNA binding / hair cycle / nuclear-transcribed mRNA catabolic process, exonucleolytic / telomerase holoenzyme complex / U1 snRNP binding / pICln-Sm protein complex / U4 snRNP / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / P granule / small nuclear ribonucleoprotein complex / spliceosomal tri-snRNP complex / telomerase RNA binding / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / SMN-Sm protein complex / import into nucleus / protein methylation / mRNA export from nucleus in response to heat stress / commitment complex / U2 snRNP / U2-type catalytic step 2 spliceosome / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / regulation of RNA splicing / U12-type spliceosomal complex / spliceosomal complex assembly / RNA polymerase II activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / U2-type prespliceosome / spliceosomal snRNP assembly / sno(s)RNA-containing ribonucleoprotein complex / U1 snRNP / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / precatalytic spliceosome / positive regulation of translational initiation / U5 snRNP / RNA polymerase I complex / mRNA cleavage / RNA polymerase III complex / RNA polymerase II, core complex / euchromatin => GO:0000791 / termination of RNA polymerase II transcription / U4/U6 x U5 tri-snRNP complex / U1 snRNA binding / translation initiation factor binding / core promoter sequence-specific DNA binding / catalytic step 2 spliceosome / spliceosomal complex / positive regulation of RNA splicing / RNA splicing / ribonucleoside binding / promoter-specific chromatin binding / P-body / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / microtubule cytoskeleton / transcription by RNA polymerase II / mRNA splicing, via spliceosome / transcription-coupled nucleotide-excision repair / single-stranded DNA binding / single-stranded RNA binding / ribonucleoprotein complex / nucleic acid binding / transcription initiation from RNA polymerase II promoter / nuclear body / nuclear speck / transcription, DNA-templated / protein dimerization activity / mRNA binding / nucleotide binding / nucleolus / enzyme binding / RNA binding / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 3 / RNA polymerase, N-terminal / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase Rpb4/RPC9, core ...DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 3 / RNA polymerase, N-terminal / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase Rpb4/RPC9, core / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase, subunit omega/K/RPB6 / RNA polymerase Rpb7-like , N-terminal / RNA polymerase subunit RPB4/RPC9 / RNA polymerase, Rpb8 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / S1 domain / Small nuclear ribonucleoprotein Sm D2 / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / Zinc finger, TFIIS-type / LSM domain, eukaryotic/archaea-type / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase, alpha subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA recognition motif domain / DNA-directed RNA polymerase, subunit N/Rpb10 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, conserved site / Small nuclear ribonucleoprotein G / Nucleotide-binding alpha-beta plait domain superfamily / RNA polymerase subunit RPB10 / RNA-binding domain, S1 / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / RNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA polymerase, subunit H/Rpb5, conserved site / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / Small ribonucleoprotein associated, SmB/SmN / Sm-like protein Lsm6/SmF / DNA-directed RNA polymerase, subunit 2 / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / Nucleic acid-binding, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase subunit, RPB6/omega / DNA-directed RNA polymerase subunit/transcription factor S / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase, insert domain / HRDC-like superfamily / LSM domain superfamily / DNA-directed RNA polymerase, RBP11-like dimerisation domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 3 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 2 / Pol II subunit B9, C-terminal zinc ribbon / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein Sm D3 / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein D1 / snRNP70, RNA recognition motif / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RNA polymerase Rpb1, funnel domain superfamily / U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / RPB5-like RNA polymerase subunit superfamily / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA-binding domain superfamily / RPB6/omega subunit-like superfamily / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb1, domain 7 superfamily / DNA-directed RNA polymerase subunit Rpb5-like / RNA polymerase Rpb1, domain 3 superfamily
Small nuclear ribonucleoprotein F / DNA-directed RNA polymerase II subunit RPB9 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / U1 small nuclear ribonucleoprotein A / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB3 ...Small nuclear ribonucleoprotein F / DNA-directed RNA polymerase II subunit RPB9 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / U1 small nuclear ribonucleoprotein A / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB3 / U1 small nuclear ribonucleoprotein 70 kDa / DNA-directed RNA polymerase II subunit E / RNA polymerase II subunit K / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase II subunit D / DNA-directed RNA polymerase subunit beta / Small nuclear ribonucleoprotein-associated protein
Biological speciesSus scrofa domesticus (domestic pig) / synthetic construct (others) / Homo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZhang S / Aibara S / Vos SM / Agafonov DE / Luehrmann R / Cramer P
Funding support4 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 830-2018
European Research Council (ERC)882357
H2020 Marie Curie Actions of the European Commission894862
German Research Foundation (DFG)EXC 2067/1-390729940
CitationJournal: Science / Year: 2021
Title: Structure of a transcribing RNA polymerase II-U1 snRNP complex.
Authors: Suyang Zhang / Shintaro Aibara / Seychelle M Vos / Dmitry E Agafonov / Reinhard Lührmann / Patrick Cramer /
Abstract: To initiate cotranscriptional splicing, RNA polymerase II (Pol II) recruits the U1 small nuclear ribonucleoprotein particle (U1 snRNP) to nascent precursor messenger RNA (pre-mRNA). Here, we report ...To initiate cotranscriptional splicing, RNA polymerase II (Pol II) recruits the U1 small nuclear ribonucleoprotein particle (U1 snRNP) to nascent precursor messenger RNA (pre-mRNA). Here, we report the cryo-electron microscopy structure of a mammalian transcribing Pol II-U1 snRNP complex. The structure reveals that Pol II and U1 snRNP interact directly. This interaction positions the pre-mRNA 5' splice site near the RNA exit site of Pol II. Extension of pre-mRNA retains the 5' splice site, leading to the formation of a "growing intron loop." Loop formation may facilitate scanning of nascent pre-mRNA for the 3' splice site, functional pairing of distant intron ends, and prespliceosome assembly. Our results provide a starting point for a mechanistic analysis of cotranscriptional spliceosome assembly and the biogenesis of mRNA isoforms by alternative splicing.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionNov 23, 2020-
Header (metadata) releaseJan 13, 2021-
Map releaseJan 13, 2021-
UpdateJan 27, 2021-
Current statusJan 27, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b0y
  • Surface level: 3.8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11972.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.05 Å/pix.
x 400 pix.
= 420. Å
1.05 Å/pix.
x 400 pix.
= 420. Å
1.05 Å/pix.
x 400 pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 3.8 / Movie #1: 3.8
Minimum - Maximum-24.010733 - 41.496452
Average (Standard dev.)1.1204568e-12 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z420.000420.000420.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-24.01141.4960.000

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Supplemental data

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Segmentation: #1

Fileemd_11972_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Unsharpened map

Fileemd_11972_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map 1

Fileemd_11972_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map 2

Fileemd_11972_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire The transcribing RNA polymerase II-U1 snRNP complex with 145-nt RNA

EntireName: The transcribing RNA polymerase II-U1 snRNP complex with 145-nt RNA
Number of components: 31

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Component #1: protein, The transcribing RNA polymerase II-U1 snRNP complex with...

ProteinName: The transcribing RNA polymerase II-U1 snRNP complex with 145-nt RNA
Recombinant expression: No

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Component #2: protein, RNA polymerase II

ProteinName: RNA polymerase II / Recombinant expression: No
SourceSpecies: Sus scrofa domesticus (domestic pig)

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Component #3: protein, Nucleic acids

ProteinName: Nucleic acidsNucleic acid / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: synthetic construct (others)

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Component #4: protein, U1 snRNP

ProteinName: U1 snRNP / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #5: protein, DNA-directed RNA polymerase II subunit RPB1

ProteinName: DNA-directed RNA polymerase II subunit RPB1Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 217.450078 kDa
SourceSpecies: Sus scrofa domesticus (domestic pig)

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Component #6: protein, DNA-directed RNA polymerase subunit beta

ProteinName: DNA-directed RNA polymerase subunit betaPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 134.041422 kDa
SourceSpecies: Sus scrofa domesticus (domestic pig)

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Component #7: protein, DNA-directed RNA polymerase II subunit RPB3

ProteinName: DNA-directed RNA polymerase II subunit RPB3Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.439074 kDa
SourceSpecies: Sus scrofa domesticus (domestic pig)

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Component #8: protein, DNA-directed RNA polymerase II subunit D

ProteinName: DNA-directed RNA polymerase II subunit DPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.331255 kDa
SourceSpecies: Sus scrofa domesticus (domestic pig)

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Component #9: protein, DNA-directed RNA polymerase II subunit E

ProteinName: DNA-directed RNA polymerase II subunit EPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.644318 kDa
SourceSpecies: Sus scrofa domesticus (domestic pig)

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Component #10: protein, DNA-directed RNA polymerase II subunit F

ProteinName: DNA-directed RNA polymerase II subunit FPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.477001 kDa
SourceSpecies: Sus scrofa domesticus (domestic pig)

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Component #11: protein, DNA-directed RNA polymerase II subunit RPB7

ProteinName: DNA-directed RNA polymerase II subunit RPB7Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.314283 kDa
SourceSpecies: Sus scrofa domesticus (domestic pig)

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Component #12: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC3

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.162273 kDa
SourceSpecies: Sus scrofa domesticus (domestic pig)

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Component #13: protein, DNA-directed RNA polymerase II subunit RPB9

ProteinName: DNA-directed RNA polymerase II subunit RPB9Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.541221 kDa
SourceSpecies: Sus scrofa domesticus (domestic pig)

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Component #14: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC5

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.655123 kDa
SourceSpecies: Sus scrofa domesticus (domestic pig)

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Component #15: protein, DNA-directed RNA polymerase II subunit RPB11-a

ProteinName: DNA-directed RNA polymerase II subunit RPB11-aPolymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.310284 kDa
SourceSpecies: Sus scrofa domesticus (domestic pig)

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Component #16: protein, RPB12

ProteinName: RPB12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.018244 kDa
SourceSpecies: Sus scrofa domesticus (domestic pig)

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Component #17: nucleic-acid, Non-template DNA

nucleic acidName: Non-template DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DC)(DA)(DT)(DT)(DG)(DA)(DG)(DA)(DG) (DC)(DG)(DG)(DC)(DC)(DC)(DT)(DT)(DG)(DT) (DG)(DT)(DT)(DC)(DA)(DG)(DG)(DA)(DG)(DC) (DC)(DA)(DG)(DC)(DA)(DG)(DG)(DG)(DA)(DG) (DC)(DT)(DG)(DG)(DG)(DA)(DG)(DC)
MassTheoretical: 14.932533 kDa
SourceSpecies: synthetic construct (others)

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Component #18: nucleic-acid, 145-nt RNA

nucleic acidName: 145-nt RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGGCGUACAC CAUCAGGGUA CGAGCUAGCC CAUGGCGUAC ACCAUCAGGG UACGACUAGU AGAUCUCGUA CACCAUCAGG GUACGCUUGG AUCGGAAACC CGUCGGCCUC CGACAGGUAA GUAUUAACCG GAGAGGGAAC CCACU
MassTheoretical: 46.78491 kDa
SourceSpecies: synthetic construct (others)

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Component #19: nucleic-acid, Template DNA

nucleic acidName: Template DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DC)(DT)(DC)(DC)(DC)(DA)(DG)(DC)(DT) (DC)(DC)(DC)(DT)(DG)(DC)(DT)(DG)(DG)(DC) (DT)(DC)(DC)(DG)(DA)(DG)(DT)(DG)(DG)(DG) (DT)(DT)(DC)(DT)(DG)(DC)(DC)(DG)(DC)(DT) (DC)(DT)(DC)(DA)(DA)(DT)(DG)(DG)
MassTheoretical: 14.672335 kDa
SourceSpecies: synthetic construct (others)

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Component #20: nucleic-acid, U1 snRNA

nucleic acidName: U1 snRNAU1 spliceosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUACUUACCU GGCAGGGGAG AUACCAUGAU CACGAAGGUG GUUUUCCCAG GGCGAGGCUU AUCCAUUGCA CUCCGGAUGU GCUGACCCCU GCGAUUUCCC CAAAUGUGGG AAACUCGACU GCAUAAUUUG UGGUAGUGGG GGACUGCGUU CGCGCUUUCC CCUG
MassTheoretical: 52.69707 kDa
SourceSpecies: Human (human)

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Component #21: protein, U1 small nuclear ribonucleoprotein 70 kDa

ProteinName: U1 small nuclear ribonucleoprotein 70 kDa / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 51.683184 kDa
SourceSpecies: Human (human)

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Component #22: protein, U1 small nuclear ribonucleoprotein A

ProteinName: U1 small nuclear ribonucleoprotein A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.319533 kDa
SourceSpecies: Human (human)

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Component #23: protein, Small nuclear ribonucleoprotein Sm D2

ProteinName: Small nuclear ribonucleoprotein Sm D2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.551928 kDa
SourceSpecies: Human (human)

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Component #24: protein, Small nuclear ribonucleoprotein F

ProteinName: Small nuclear ribonucleoprotein F / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.734171 kDa
SourceSpecies: Human (human)

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Component #25: protein, Small nuclear ribonucleoprotein E

ProteinName: Small nuclear ribonucleoprotein E / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.817601 kDa
SourceSpecies: Human (human)

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Component #26: protein, Small nuclear ribonucleoprotein G

ProteinName: Small nuclear ribonucleoprotein G / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.508084 kDa
SourceSpecies: Human (human)

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Component #27: protein, Small nuclear ribonucleoprotein Sm D3

ProteinName: Small nuclear ribonucleoprotein Sm D3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.940308 kDa
SourceSpecies: Human (human)

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Component #28: protein, Small nuclear ribonucleoprotein-associated protein

ProteinName: Small nuclear ribonucleoprotein-associated protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.686004 kDa
SourceSpecies: Human (human)

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Component #29: protein, Small nuclear ribonucleoprotein Sm D1

ProteinName: Small nuclear ribonucleoprotein Sm D1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.310653 kDa
SourceSpecies: Human (human)

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Component #30: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #31: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.01 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 61596
3D reconstructionSoftware: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Input PDB model: 6GMH, 3PGW, 4PJO, 4PKD
Output model

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