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- PDB-3jaq: Structure of a partial yeast 48S preinitiation complex in open co... -

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Entry
Database: PDB / ID: 3jaq
TitleStructure of a partial yeast 48S preinitiation complex in open conformation
Components
  • 18S rRNA18S ribosomal RNA
  • Met-tRNAi
  • RACK1Receptor for activated C kinase 1
  • eIF1
  • eIF1A
  • eIF2 alpha
  • eIF2 beta
  • eIF2 gamma
  • eIF3a
  • eIF3b
  • eIF3c
  • eIF3g
  • eIF3i
  • eL41
  • eS1
  • eS10
  • eS12
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • eS27
  • eS28
  • eS30
  • eS31
  • eS4
  • eS6
  • eS7
  • eS8
  • mRNAMessenger RNA
  • uS10
  • uS11
  • uS12
  • uS13
  • uS14
  • uS15
  • uS17
  • uS19
  • uS2
  • uS3
  • uS4
  • uS5
  • uS7
  • uS8
  • uS9
KeywordsTRANSLATION / Eukaryotic translation initiation / 48S / small ribosome subunit / 40S / 43S
Function / homologyEukaryotic translation initiation factor 3 subunit G, N-terminal / WD40-repeat-containing domain superfamily / Ribosomal protein S10 domain / Ribosomal protein S2, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Eukaryotic translation initiation factor 3 subunit I / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily ...Eukaryotic translation initiation factor 3 subunit G, N-terminal / WD40-repeat-containing domain superfamily / Ribosomal protein S10 domain / Ribosomal protein S2, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Eukaryotic translation initiation factor 3 subunit I / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / eIF3G, RNA recognition motif / eIF3B, RNA recognition motif / RNA-binding domain superfamily / Ribosomal protein S8 superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 40S Ribosomal protein S10 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / S27a-like superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S26e superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S19e domain superfamily / RNA-binding S4 domain superfamily / Winged helix DNA-binding domain superfamily / Ribosomal protein S11 superfamily / SUI1 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S17e-like superfamily / 30s ribosomal protein S13, C-terminal / Translation initiation factor 2, alpha subunit, C-terminal / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein S2, conserved site / Translation initiation factor 1A (eIF-1A), conserved site / Ribosomal S11, conserved site / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / WD40-repeat-containing domain / Ribosomal protein S6e, conserved site / WD40 repeat, conserved site / Translation initiation factor 2, alpha subunit, middle domain superfamily / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S15P / RNA-binding domain, S1 / Ribosomal protein S4/S9 / Ribosomal protein S19 conserved site / Ubiquitin conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein S17, conserved site / Ubiquitin / Elongation factor Tu GTP binding domain / Ribosomal protein S4/S9 N-terminal domain / Translation initiation factor IF2/IF5, zinc-binding / Ribosomal protein S7 signature. / S25 ribosomal protein / Plectin/S10 domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S30 / Ribosomal protein L41 / Eukaryotic translation initiation factor 2 alpha subunit / KH domain / Ribosomal S13/S15 N-terminal domain / RS4NT (NUC023) domain / Eukaryotic translation initiation factor eIF2A / Initiation factor eIF2 gamma, C terminal / Eukaryotic translation initiation factor 3 subunit G / 40S ribosomal protein S4 C-terminus / Ribosomal_S17 N-terminal / Ribosomal protein S8 signature. / Domain found in IF2B/IF5 / Ribosomal protein S24e signature. / Ribosomal protein S13 signature. / Ribosomal protein S4 signature. / Ribosomal protein S19e signature. / Ribosomal protein S5 signature. / Ribosomal protein S6e signature. / Ribosomal protein S3 signature. / Ribosomal protein S4e signature. / Ribosomal protein S11 signature. / Ribosomal protein S15 signature. / Ribosomal protein S9 signature.
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
Kluyveromyces lactis (yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 6 Å resolution
AuthorsLlacer, J.L. / Hussain, T. / Ramakrishnan, V.
CitationJournal: Mol. Cell / Year: 2015
Title: Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex.
Authors: Jose L Llácer / Tanweer Hussain / Laura Marler / Colin Echeverría Aitken / Anil Thakur / Jon R Lorsch / Alan G Hinnebusch / V Ramakrishnan
Abstract: Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and ...Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. The PIC, in an open conformation, attaches to the 5' end of the mRNA and scans to locate the start codon, whereupon it closes to arrest scanning. We present single particle cryo-electron microscopy (cryo-EM) reconstructions of 48S PICs from yeast in these open and closed states, at 6.0 Å and 4.9 Å, respectively. These reconstructions show eIF2β as well as a configuration of eIF3 that appears to encircle the 40S, occupying part of the subunit interface. Comparison of the complexes reveals a large conformational change in the 40S head from an open mRNA latch conformation to a closed one that constricts the mRNA entry channel and narrows the P site to enclose tRNAi, thus elucidating key events in start codon recognition.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 18, 2015 / Release: Aug 12, 2015
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 12, 2015Structure modelrepositoryInitial release
1.1Sep 2, 2015Structure modelDatabase references
1.2Jul 18, 2018Structure modelAdvisory / Data collection / Otherem_software / pdbx_database_status / pdbx_validate_polymer_linkage_em_software.image_processing_id / _em_software.name / _pdbx_database_status.pdb_format_compatible

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Structure visualization

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Assembly

Deposited unit
1: Met-tRNAi
2: 18S rRNA
3: mRNA
A: uS2
B: eS1
C: uS5
D: uS3
E: eS4
F: uS7
G: eS6
H: eS7
I: eS8
J: uS4
K: eS10
L: uS17
M: eS12
N: uS15
O: uS11
P: uS19
Q: uS9
R: eS17
S: uS13
T: eS19
U: uS10
V: eS21
W: uS8
X: uS12
Y: eS24
Z: eS25
a: eS26
b: eS27
c: eS28
d: uS14
e: eS30
f: eS31
g: RACK1
h: eL41
i: eIF1A
j: eIF2 alpha
k: eIF2 gamma
l: eIF2 beta
m: eIF1
o: eIF3a
p: eIF3c
q: eIF3i
r: eIF3b
s: eIF3g
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,424,906135
Polyers1,421,98147
Non-polymers2,92588
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 3 types, 3 molecules 123

#1: RNA chain Met-tRNAi


Mass: 24713.969 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Saccharomyces cerevisiae (baker's yeast)
#2: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 573814.125 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast)
#3: RNA chain mRNA / Messenger RNA


Mass: 7746.547 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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Protein/peptide , 44 types, 44 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#4: Protein/peptide uS2


Mass: 28264.525 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CN12
#5: Protein/peptide eS1


Mass: 28971.643 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWD0
#6: Protein/peptide uS5


Mass: 27649.979 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKL3
#7: Protein/peptide uS3


Mass: 26300.535 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRK7
#8: Protein/peptide eS4


Mass: 29617.514 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWJ2
#9: Protein/peptide uS7


Mass: 25385.975 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRA3
#10: Protein/peptide eS6


Mass: 26970.391 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM04
#11: Protein/peptide eS7


Mass: 21735.297 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CTD6
#12: Protein/peptide eS8


Mass: 22642.727 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CMG3
#13: Protein/peptide uS4


Mass: 21587.049 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM18
#14: Protein/peptide eS10


Mass: 12584.377 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CVZ5
#15: Protein/peptide uS17


Mass: 17843.930 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CX80
#16: Protein/peptide eS12


Mass: 14466.398 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CLU4
#17: Protein/peptide uS15


Mass: 16989.875 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CJK0
#18: Protein/peptide uS11


Mass: 14530.655 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P27069
#19: Protein/peptide uS19


Mass: 15986.796 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKV4
#20: Protein/peptide uS9


Mass: 15874.531 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q875N2
#21: Protein/peptide eS17


Mass: 15722.216 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWU3
#22: Protein/peptide uS13


Mass: 17084.602 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWT9
#23: Protein/peptide eS19


Mass: 15879.010 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXM0
#24: Protein/peptide uS10


Mass: 13337.604 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CIM1
#25: Protein/peptide eS21


Mass: 9797.949 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXT6
#26: Protein/peptide uS8


Mass: 14645.041 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW21
#27: Protein/peptide uS12


Mass: 16047.897 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: F2Z602
#28: Protein/peptide eS24


Mass: 15194.549 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CU44
#29: Protein/peptide eS25


Mass: 12002.116 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW78
#30: Protein/peptide eS26


Mass: 13539.957 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CS01
#31: Protein/peptide eS27


Mass: 8884.362 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CNL2
#32: Protein/peptide eS28


Mass: 7549.824 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P33285
#33: Protein/peptide uS14


Mass: 6662.570 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CPG3
#34: Protein/peptide eS30


Mass: 7141.421 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CUH5
#35: Protein/peptide eS31


Mass: 17110.977 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P69061
#36: Protein/peptide RACK1 / Receptor for activated C kinase 1


Mass: 35830.945 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CNI7
#37: Protein/peptide eL41


Mass: 3354.243 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P0CX86
#38: Protein/peptide eIF1A


Mass: 17462.168 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Plasmid name: pTYB2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Rosetta / References: UniProt: P38912
#39: Protein/peptide eIF2 alpha


Mass: 34763.652 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20459
#40: Protein/peptide eIF2 gamma


Mass: 57942.699 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32481
#41: Protein/peptide eIF2 beta


Mass: 31631.309 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P09064
#42: Protein/peptide eIF1 /


Mass: 12330.147 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Plasmid name: pTYB2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Rosetta / References: UniProt: P32911
#43: Protein/peptide eIF3a /


Mass: 7847.665 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Plasmid name: pCDFDuet / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Rosetta
#44: Protein/peptide eIF3c /


Mass: 7507.245 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Plasmid name: pCDFDuet / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Rosetta
#45: Protein/peptide eIF3i


Mass: 38803.375 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Plasmid name: pQlink / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Rosetta / References: UniProt: P40217
#46: Protein/peptide eIF3b /


Mass: 4287.934 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Plasmid name: pQlink / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Rosetta / References: UniProt: P06103
#47: Protein/peptide eIF3g /


Mass: 5942.615 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Plasmid name: pQlink / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Rosetta / References: UniProt: A6ZZ25

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Non-polymers , 4 types, 88 molecules

#48: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 82 / Formula: Mg / Magnesium
#49: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Formula: Zn / Zinc
#50: Chemical ChemComp-MET / METHIONINE


Mass: 149.211 Da / Num. of mol.: 1 / Formula: C5H11NO2S / Methionine
#51: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Formula: C11H18N5O13P3 / Comment: GMP-PCP (energy-carrying molecule analogue) *YM

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeParent ID
1Partial yeast 48S preinitiation complex in open conformationRIBOSOME0
240S ribosomeRIBOSOME1
3Eukaryotic initiation factor eIF1A1
4Eukaryotic initiation factor eIF11
5Eukaryotic initiation factor eIF21
6Eukaryotic initiation factor eIF31
7Met-tRNAi1
8mRNA1
Buffer solutionName: 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT
Details: 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT
pH: 6.5
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 to 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK I).
Method: Blot for 2.5 to 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Apr 28, 2014
Details: Complete dataset was collected over two 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: 59000 / Calibrated magnification: 104478 / Nominal defocus max: 1500 nm / Nominal defocus min: 4000 nm / Cs: 2.7 mm
Specimen holderSpecimen holder type: GATAN LIQUID NITROGEN
Image recordingElectron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNumber digital images: 2056
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: REFMAC / Version: 5.8.0124 2015/06/03 / 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
IDNameCategory
1Cootmodel fitting
2REFMACmodel fitting
3UCSF Chimeramodel fitting
4RELION3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C1
3D reconstructionResolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 4547 / Nominal pixel size: 1.34 / Actual pixel size: 1.34 / Details: gold-standard / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT
Atomic model buildingDetails: METHOD--Local refinement / Ref protocol: OTHER / Ref space: RECIPROCAL / Target criteria: Rfactor, FSC
Atomic model building
IDPDB-ID 3D fitting ID
13J811
23CW21
32D741
44U1E1
51YFG1
RefineDetails: Hydrogens have been added in their riding positions
Number of atoms included #LASTProtein: 50164 / Nucleic acid: 39478 / Ligand: 126 / Solvent: 0 / Total: 89768

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