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- PDB-3j80: CryoEM structure of 40S-eIF1-eIF1A preinitiation complex -

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Entry
Database: PDB / ID: 3j80
TitleCryoEM structure of 40S-eIF1-eIF1A preinitiation complex
Components
  • 18S rRNA18S ribosomal RNA
  • RACK1Receptor for activated C kinase 1
  • eIF1
  • eIF1AEIF1AX
  • eL41
  • eS1
  • eS10
  • eS12
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • eS27
  • eS28
  • eS30
  • eS31
  • eS4
  • eS6
  • eS7
  • eS8
  • uS10
  • uS11
  • uS12
  • uS13
  • uS14
  • uS15
  • uS17
  • uS19
  • uS2
  • uS3
  • uS4
  • uS5
  • uS7
  • uS8
  • uS9
KeywordsRIBOSOME / small ribosome subunit / eukaryotic translation initiation
Function / homology
Function and homology information


formation of translation initiation ternary complex / regulation of fungal-type cell wall biogenesis / conjugation with cellular fusion / translation reinitiation / multi-eIF complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / formation of translation preinitiation complex / formation of cytoplasmic translation initiation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) ...formation of translation initiation ternary complex / regulation of fungal-type cell wall biogenesis / conjugation with cellular fusion / translation reinitiation / multi-eIF complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / formation of translation preinitiation complex / formation of cytoplasmic translation initiation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / regulation of cellular response to stress / invasive growth in response to glucose limitation / GDP-dissociation inhibitor activity / rRNA export from nucleus / preribosome, small subunit precursor / mRNA destabilization / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / G-protein alpha-subunit binding / DNA-(apurinic or apyrimidinic site) endonuclease activity / ribosomal small subunit export from nucleus / ribosomal small subunit binding / regulation of translational fidelity / small-subunit processome / protein kinase A catalytic subunit binding / translation initiation factor binding / translation initiation factor activity / positive regulation of protein autophosphorylation / maintenance of translational fidelity / positive regulation of translational fidelity / translational termination / protein kinase C binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small ribosomal subunit rRNA binding / protein tag / rRNA processing / cytoplasmic stress granule / cytoplasmic translation / cytosolic large ribosomal subunit / regulation of G2/M transition of mitotic cell cycle / ribosome binding / double-stranded RNA binding / cytosolic small ribosomal subunit / small ribosomal subunit / protein localization / ribosome / rRNA binding / structural constituent of ribosome / translation / G protein-coupled receptor signaling pathway / protein kinase binding / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm
40S ribosomal protein S11, N-terminal / Ribosomal protein S4/S9 / WD40 repeat, conserved site / Ubiquitin conserved site / Ubiquitin domain / Ribosomal protein S17, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site ...40S ribosomal protein S11, N-terminal / Ribosomal protein S4/S9 / WD40 repeat, conserved site / Ubiquitin conserved site / Ubiquitin domain / Ribosomal protein S17, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S15P / Ribosomal protein S6e, conserved site / Ribosomal protein S19/S15, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein S2, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / Ribosomal protein S8e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S8 superfamily / K homology domain-like, alpha/beta / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S5, N-terminal / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Ribosomal protein S6, eukaryotic / Ribosomal protein S21e / Ribosomal protein L2, domain 2 / WD40/YVTN repeat-like-containing domain superfamily / WD40-repeat-containing domain / Ribosomal protein S3, conserved site / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Translation initiation factor 1A (eIF-1A), conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S21e, conserved site / 40S ribosomal protein S4, C-terminal domain / WD40-repeat-containing domain superfamily / S15/NS1, RNA-binding / Ribosomal protein S7e / Ribosomal protein S24e / Ribosomal protein S12/S23 / Ribosomal protein S8 / Ribosomal S3Ae family / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S3, C-terminal domain / KH domain / KOW motif / Ribosomal family S4e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S8e / Ribosomal protein S26e / Ribosomal protein S4/S9 N-terminal domain / S4 domain / Plectin/S10 domain / Ribosomal protein S17 / Ribosomal_S17 N-terminal / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S15 / Ribosomal protein S11 / Ribosomal protein S9/S16 / Ribosomal S17 / Ribosomal protein S13/S18 / S25 ribosomal protein / Ribosomal protein S27 / Winged helix-like DNA-binding domain superfamily / Ribosomal protein S26e superfamily / Winged helix DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / SUI1 domain superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / 40S Ribosomal protein S10 / in:ipr038111: / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S28e / S27a-like superfamily / 40S ribosomal protein S29/30S ribosomal protein S14 type Z
KLLA0B01474p / KLLA0A07194p / KLLA0A10483p / KLLA0B01562p / KLLA0B08173p / 40S ribosomal protein S4 / KLLA0F07843p / 40S ribosomal protein S24 / 40S ribosomal protein S7 / 40S ribosomal protein S26 ...KLLA0B01474p / KLLA0A07194p / KLLA0A10483p / KLLA0B01562p / KLLA0B08173p / 40S ribosomal protein S4 / KLLA0F07843p / 40S ribosomal protein S24 / 40S ribosomal protein S7 / 40S ribosomal protein S26 / KLLA0D08305p / KLLA0D10659p / 40S ribosomal protein S29 / 40S ribosomal protein S27 / KLLA0E12277p / 40S ribosomal protein S0 / 40S ribosomal protein S8 / KLLA0E23673p / 40S ribosomal protein S6 / 40S ribosomal protein S12 / KLLA0F09812p / 40S ribosomal protein S1 / KLLA0F18040p / KLLA0F25542p / Ubiquitin-40S ribosomal protein S27a / Eukaryotic translation initiation factor 1A / 40S ribosomal protein S28 / Eukaryotic translation initiation factor eIF-1 / 40S ribosomal protein S14 / 60S ribosomal protein L41-A / KLLA0B11231p / 40S ribosomal protein S22 / 40S ribosomal protein S25 / 40S ribosomal protein S21 / 40S ribosomal protein S30 / 40S ribosomal protein S16
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Kluyveromyces lactis (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsHussain, T. / Llacer, J.L. / Fernandez, I.S. / Savva, C.G. / Ramakrishnan, V.
CitationJournal: Cell / Year: 2014
Title: Structural changes enable start codon recognition by the eukaryotic translation initiation complex.
Authors: Tanweer Hussain / Jose L Llácer / Israel S Fernández / Antonio Munoz / Pilar Martin-Marcos / Christos G Savva / Jon R Lorsch / Alan G Hinnebusch / V Ramakrishnan /
Abstract: During eukaryotic translation initiation, initiator tRNA does not insert fully into the P decoding site on the 40S ribosomal subunit. This conformation (POUT) is compatible with scanning mRNA for the ...During eukaryotic translation initiation, initiator tRNA does not insert fully into the P decoding site on the 40S ribosomal subunit. This conformation (POUT) is compatible with scanning mRNA for the AUG start codon. Base pairing with AUG is thought to promote isomerization to a more stable conformation (PIN) that arrests scanning and promotes dissociation of eIF1 from the 40S subunit. Here, we present a cryoEM reconstruction of a yeast preinitiation complex at 4.0 Å resolution with initiator tRNA in the PIN state, prior to eIF1 release. The structure reveals stabilization of the codon-anticodon duplex by the N-terminal tail of eIF1A, changes in the structure of eIF1 likely instrumental in its subsequent release, and changes in the conformation of eIF2. The mRNA traverses the entire mRNA cleft and makes connections to the regulatory domain of eIF2?, eIF1A, and ribosomal elements that allow recognition of context nucleotides surrounding the AUG codon.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name

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Structure visualization

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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2: 18S rRNA
A: uS2
B: eS1
C: uS5
E: eS4
G: eS6
H: eS7
I: eS8
J: uS4
L: uS17
N: uS15
O: uS11
V: eS21
W: uS8
X: uS12
Y: eS24
a: eS26
b: eS27
e: eS30
D: uS3
F: uS7
K: eS10
M: eS12
P: uS19
Q: uS9
R: eS17
S: uS13
T: eS19
U: uS10
Z: eS25
c: eS28
d: uS14
f: eS31
g: RACK1
h: eL41
i: eIF1A
j: eIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,208,132107
Polymers1,206,30737
Non-polymers1,82570
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 35 types, 35 molecules ABCEGHIJLNOVWXYabeDFKMPQRSTUZc...

#2: Protein uS2


Mass: 28264.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CN12
#3: Protein eS1


Mass: 28971.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWD0
#4: Protein uS5


Mass: 27649.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKL3
#5: Protein eS4


Mass: 29617.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWJ2
#6: Protein eS6


Mass: 26970.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM04
#7: Protein eS7


Mass: 21735.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CTD6
#8: Protein eS8


Mass: 22642.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CMG3
#9: Protein uS4


Mass: 21587.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM18
#10: Protein uS17


Mass: 17843.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CX80
#11: Protein uS15


Mass: 16989.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CJK0
#12: Protein uS11


Mass: 14530.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P27069
#13: Protein eS21


Mass: 9797.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXT6
#14: Protein uS8


Mass: 14645.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW21
#15: Protein uS12


Mass: 16047.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: F2Z602
#16: Protein eS24


Mass: 15194.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CU44
#17: Protein eS26


Mass: 13539.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CS01
#18: Protein eS27


Mass: 8884.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CNL2
#19: Protein eS30


Mass: 7141.421 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CUH5
#20: Protein uS3


Mass: 26300.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRK7
#21: Protein uS7


Mass: 25385.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRA3
#22: Protein eS10


Mass: 12584.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CVZ5
#23: Protein eS12


Mass: 14466.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CLU4
#24: Protein uS19


Mass: 15768.522 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKV4
#25: Protein uS9


Mass: 15874.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q875N2
#26: Protein eS17


Mass: 15722.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWU3
#27: Protein uS13


Mass: 17084.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWT9
#28: Protein eS19


Mass: 15879.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXM0
#29: Protein uS10


Mass: 13337.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CIM1
#30: Protein eS25


Mass: 12002.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW78
#31: Protein eS28


Mass: 7549.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P33285
#32: Protein uS14


Mass: 6662.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CPG3
#33: Protein eS31


Mass: 17110.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P69061
#34: Protein RACK1 / Receptor for activated C kinase 1


Mass: 35830.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CNI7
#36: Protein eIF1A / EIF1AX


Mass: 17462.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P38912
#37: Protein eIF1 /


Mass: 12330.147 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P32911

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RNA chain / Protein/peptide , 2 types, 2 molecules 2h

#1: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 579545.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast)
#35: Protein/peptide eL41


Mass: 3354.243 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P0CX86

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Non-polymers , 2 types, 70 molecules

#38: Chemical...
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 67 / Source method: obtained synthetically / Formula: Mg
#39: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeParent-ID
140S-eIF1-eIF1A preinitiation complexCOMPLEX0
2Ribosome small subunitRIBOSOME1
3Eukaryotic initiation factor 11
4Eukaryotic initiation factor 1A1
Molecular weightValue: 1.2 MDa / Experimental value: NO
Buffer solutionName: 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT
pH: 6.5
Details: 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT
SpecimenConc.: 0.17 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R2/2 400 mesh copper grids with 4-5 nm thin carbon on top
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temp: 120 K / Humidity: 100 %
Details: Blot for 2.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK I)
Method: Blot for 2.5 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Oct 28, 2013
Details: Complete dataset was collected in 5 non-consecutive days
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 78000 X / Calibrated magnification: 104478 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1600 nm / Cs: 2 mm
Specimen holderSpecimen holder type: GATAN LIQUID NITROGEN
Image recordingElectron dose: 28 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 1791
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: REFMAC / Version: 5.8.0077 2014/05/16 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk
Description: (un)restrained refinement or idealisation of macromolecular structures
EM software
IDNameVersionCategory
1REFMACmodel fitting
2UCSF Chimeramodel fitting
3EMAN23D reconstruction
4RELION3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100709 / Nominal pixel size: 1.34 Å / Actual pixel size: 1.34 Å / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL / Target criteria: R-factor, FSC / Details: REFINEMENT PROTOCOL--flexible
Atomic model building
IDPDB-IDPdb chain-ID3D fitting-ID
13U5B

3u5b
PDB Unreleased entry

21
23U5C

3u5c
PDB Unreleased entry

1
RefinementDetails: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms39871 37775 70 0 77716

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