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Entry
Database: EMDB / ID: EMD-0441
TitleConformational switches control early maturation of the eukaryotic small ribosomal subunit
Map data
Sample5' ETS particle:
(nucleic-acidNucleic acid) x 3 / Utp17 / Utp8 / Utp15 / Utp9 / Utp5 / Utp10 / Utp4 / Utp1 / Utp6 ...(nucleic-acidNucleic acid) x 3 / Utp17 / Utp8 / Utp15 / Utp9 / Utp5 / Utp10 / Utp4 / Utp1 / Utp6 / Utp12 / Utp13 / Utp18 / Utp21 / Sof1 / Utp7 / Imp3 / Mpp10 / Bud21 / Nop56 / Nop58 / Nop1.1 / Snu13NHP2L1 / Rrp9 / Utp24 / Unidentified fragment
Function / homology
Function and homology information


t-UTP complex / sno(s)RNA processing / Pwp2p-containing subcomplex of 90S preribosome / RNA fragment catabolic process / histone-glutamine methyltransferase activity / box C/D RNA 3'-end processing / Mpp10 complex / rRNA methyltransferase activity / rRNA 2'-O-methylation / septum digestion after cytokinesis ...t-UTP complex / sno(s)RNA processing / Pwp2p-containing subcomplex of 90S preribosome / RNA fragment catabolic process / histone-glutamine methyltransferase activity / box C/D RNA 3'-end processing / Mpp10 complex / rRNA methyltransferase activity / rRNA 2'-O-methylation / septum digestion after cytokinesis / rRNA modification / regulation of transcription by RNA polymerase I / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of RNA binding / rDNA heterochromatin / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D RNP complex / snRNA binding / positive regulation of transcription by RNA polymerase I / protein localization to nucleolus / U4 snRNA binding / histone glutamine methylation / U3 snoRNA binding / Cul4-RING E3 ubiquitin ligase complex / sno(s)RNA-containing ribonucleoprotein complex / tRNA export from nucleus / precatalytic spliceosome / 90S preribosome / preribosome, small subunit precursor / O-methyltransferase activity / rRNA methylation / snoRNA binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / U4/U6 x U5 tri-snRNP complex / small-subunit processome / ribosomal small subunit biogenesis / maturation of LSU-rRNA / Cajal body / establishment of cell polarity / endoribonuclease activity / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA processing / mRNA splicing, via spliceosome / Transferases; Transferring one-carbon groups; Methyltransferases / tRNA binding / rRNA binding / mRNA binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Tetratricopeptide-like helical domain superfamily / Quinoprotein alcohol dehydrogenase-like superfamily / Small-subunit processome, Utp21 / Sof1-like protein / Small-subunit processome, Utp12 / rRNA-processing protein Fcf1/Utp23 / HAT (Half-A-TPR) repeat ...Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Tetratricopeptide-like helical domain superfamily / Quinoprotein alcohol dehydrogenase-like superfamily / Small-subunit processome, Utp21 / Sof1-like protein / Small-subunit processome, Utp12 / rRNA-processing protein Fcf1/Utp23 / HAT (Half-A-TPR) repeat / BP28, C-terminal domain / RNA-binding S4 domain / PIN domain / Nop domain / H/ACA ribonucleoprotein complex, subunit Nhp2, eukaryote / Ribosomal protein S4/S9, N-terminal / WD40 repeat / Fibrillarin / BING4, C-terminal domain / NOP5, N-terminal / PIN-like domain superfamily / U3 small nucleolar RNA-associated protein 15, C-terminal / Anaphase-promoting complex subunit 4, WD40 domain / Ribosomal protein S4/S9 / U3 small nucleolar RNA-associated protein 10, N-terminal / HEAT, type 2 / Fibrillarin, conserved site / G-protein beta WD-40 repeat / WD40 repeat, conserved site / U3 small nucleolar RNA-associated protein 8 / NOSIC / Ribosomal protein L7Ae/L8/Nhp2 family / WD40-repeat-containing domain / Armadillo-type fold / WD40/YVTN repeat-like-containing domain superfamily / U3 small nucleolar RNA-associated protein 6 / Small-subunit processome, Utp13 / U3 snoRNA associated / Helix hairpin bin domain superfamily / Periodic tryptophan protein 2 / S-adenosyl-L-methionine-dependent methyltransferase / Nop, C-terminal domain / WD repeat-containing protein WDR46/Utp7 / U3 small nucleolar RNA-associated protein 10 / Ribosomal RNA-processing protein Rrp9-like / RNA-binding S4 domain superfamily / WD40-repeat-containing domain superfamily / Nop domain superfamily / 50S ribosomal protein L30e-like
U3 small nucleolar RNA-associated protein 21 / U3 small nucleolar RNA-associated protein 15 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 13 / Nucleolar protein 56 / Ribosomal RNA-processing protein 9 / U3 small nucleolar RNA-associated protein 4 / Bud site selection protein 21 / U3 small nucleolar RNA-associated protein 12 / NET1-associated nuclear protein 1 ...U3 small nucleolar RNA-associated protein 21 / U3 small nucleolar RNA-associated protein 15 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 13 / Nucleolar protein 56 / Ribosomal RNA-processing protein 9 / U3 small nucleolar RNA-associated protein 4 / Bud site selection protein 21 / U3 small nucleolar RNA-associated protein 12 / NET1-associated nuclear protein 1 / U3 small nucleolar RNA-associated protein 5 / U3 small nucleolar RNA-associated protein 18 / U3 small nucleolar RNA-associated protein 6 / U3 small nucleolar RNA-associated protein 8 / U3 small nucleolar RNA-associated protein MPP10 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein 7 / 13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 9 / Protein SOF1 / U3 small nucleolar ribonucleoprotein protein IMP3 / Periodic tryptophan protein 2 / rRNA 2'-O-methyltransferase fibrillarin / Nucleolar protein 58
Biological speciesSaccharomyces cerevisiae BY4741 (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsHunziker M / Barandun J / Klinge S
Funding support United States, Switzerland, 2 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director1DP2GM123459 United States
Swiss National Science Foundation155515 Switzerland
CitationJournal: Elife / Year: 2019
Title: Conformational switches control early maturation of the eukaryotic small ribosomal subunit.
Authors: Mirjam Hunziker / Jonas Barandun / Olga Buzovetsky / Caitlin Steckler / Henrik Molina / Sebastian Klinge /
Abstract: Eukaryotic ribosome biogenesis is initiated with the transcription of pre-ribosomal RNA at the 5' external transcribed spacer, which directs the early association of assembly factors but is absent ...Eukaryotic ribosome biogenesis is initiated with the transcription of pre-ribosomal RNA at the 5' external transcribed spacer, which directs the early association of assembly factors but is absent from the mature ribosome. The subsequent co-transcriptional association of ribosome assembly factors with pre-ribosomal RNA results in the formation of the small subunit processome. Here we show that stable rRNA domains of the small ribosomal subunit can independently recruit their own biogenesis factors in vivo. The final assembly and compaction of the small subunit processome requires the presence of the 5' external transcribed spacer RNA and all ribosomal RNA domains. Additionally, our cryo-electron microscopy structure of the earliest nucleolar pre-ribosomal assembly - the 5' external transcribed spacer ribonucleoprotein - provides a mechanism for how conformational changes in multi-protein complexes can be employed to regulate the accessibility of binding sites and therefore define the chronology of maturation events during early stages of ribosome assembly.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionDec 13, 2018-
Header (metadata) releaseFeb 20, 2019-
Map releaseJun 19, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0203
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0203
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6nd4
  • Surface level: 0.0203
  • 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_0441.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.6 Å/pix.
x 360 pix.
= 576. Å
1.6 Å/pix.
x 360 pix.
= 576. Å
1.6 Å/pix.
x 360 pix.
= 576. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6 Å
Density
Contour LevelBy AUTHOR: 0.0203 / Movie #1: 0.0203
Minimum - Maximum-0.04939924 - 0.09136246
Average (Standard dev.)0.0001420385 (±0.001903109)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 576.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.61.61.6
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z576.000576.000576.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0490.0910.000

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Supplemental data

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Additional map: unsharpened map

Fileemd_0441_additional.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire 5' ETS particle

EntireName: 5' ETS particle / Number of components: 29

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Component #1: protein, 5' ETS particle

ProteinName: 5' ETS particle / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast)

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Component #2: nucleic-acid, 5'ETS rRNA

nucleic acidName: 5'ETS rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AUGCGAAAGC AGUUGAAGAC AAGU(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)GCUUG UCGUUCGUUA UGUUUUUGUA AAUGGCCUCG UCAAACGGUG GAGAGAGUCG ...Sequence:
AUGCGAAAGC AGUUGAAGAC AAGU(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)GCUUG UCGUUCGUUA UGUUUUUGUA AAUGGCCUCG UCAAACGGUG GAGAGAGUCG CUAGGUGAUC GUCAGAUCUG CCUAGUCUCU AUACAGCGUG UUUAAUUGAC AUGGGUUGAU GCGUAUUGAG AGAUACAAUU UGGGAAGAAA UUCCCAGAGU GUGUUUCUUU UGCGUUUAAC CUGAACAGUC UCAUCGUGGG CAUCUUGCGA UUCCAUUGGU GAGCAGCGAA GGAUUUGGUG GAUUACUAGC UAAUAGCAAU CUAUUUCAAA GAAUUCAAAC UUGGGGGAAU GCCUUGUUGA AUAGCCGGUC GCAAGACUGU GAUUCUUCAA GUGUAACCUC CUCUCAAAUC AGCGAUAUCA AACGUACCAU UCCGUGAAAC ACCGGGGUAU CUGUUUGGUG GAACCUGAUU AGAGGAAACU CAAAGAGUGC UAUGGUAUGG UGACGGAGUG CGCUGGUCAA GAGUGUAAAA GCUUUUUGAA CAGAGAGCAU UUCCGGCAGC AGAGAGACCU GAAAAAGCAA UUUUUCUGGA AUUUCAGCUG UU(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)AUAAGUAU CUUCUAGCAA GAGGGAAUAG GUGGGAAAAA AAAAAAGAGA UUUCGGUUUC UUUCUUUUUU ACUGCUUGUU GCUUCUUCUU UUAAGAUAGU
MassTheoretical: 220.317 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #3: nucleic-acid, 18S rRNA 5' domain start

nucleic acidName: 18S rRNA 5' domain start / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
(N)(N)(N)(N)(N)(N)(N)(N)UG AUCCU
MassTheoretical: 3.727073 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #4: nucleic-acid, U3 snoRNA

nucleic acidName: U3 snoRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGGAUCAGGA AUCGUCACUC UUUGACUCUU CAAAAGAGCC ACUGAAUCCA ACUUGGUUGA UGAGUCCCAU AACCUUUGUA CCCAGUGAGA AACCGUAUGG CGCGAUGAUC UACCCAUGGG UGGGUACAAA UGGCAGUCUG ACAAGU
MassTheoretical: 46.932852 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #5: protein, Utp17

ProteinName: Utp17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 96.36357 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #6: protein, Utp8

ProteinName: Utp8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.062371 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #7: protein, Utp15

ProteinName: Utp15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.765289 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #8: protein, Utp9

ProteinName: Utp9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.93582 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #9: protein, Utp5

ProteinName: Utp5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.079445 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #10: protein, Utp10

ProteinName: Utp10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 200.298984 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #11: protein, Utp4

ProteinName: Utp4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 81.782867 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #12: protein, Utp1

ProteinName: Utp1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 104.097039 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #13: protein, Utp6

ProteinName: Utp6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.820391 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #14: protein, Utp12

ProteinName: Utp12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 102.690555 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #15: protein, Utp13

ProteinName: Utp13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 68.142312 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #16: protein, Utp18

ProteinName: Utp18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.49425 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #17: protein, Utp21

ProteinName: Utp21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 104.927844 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #18: protein, Sof1

ProteinName: Sof1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.888918 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #19: protein, Utp7

ProteinName: Utp7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 62.41857 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #20: protein, Imp3

ProteinName: Imp3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.928529 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #21: protein, Mpp10

ProteinName: Mpp10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 67.042492 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #22: protein, Bud21

ProteinName: Bud21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.431016 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #23: protein, Nop56

ProteinName: Nop56 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.307637 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #24: protein, Nop58

ProteinName: Nop58 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 53.13368 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #25: protein, Nop1.1

ProteinName: Nop1.1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 34.525418 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #26: protein, Snu13

ProteinName: Snu13NHP2L1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.582855 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #27: protein, Rrp9

ProteinName: Rrp9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.146969 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #28: protein, Utp24

ProteinName: Utp24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.650729 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #29: protein, Unidentified fragment

ProteinName: Unidentified fragment / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.060531 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 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: 31.25 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2750

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 52629
3D reconstructionSoftware: RELION / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 5WLC
Output model

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