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- PDB-6ybw: Structure of a human 48S translational initiation complex - 40S body -

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Entry
Database: PDB / ID: 6ybw
TitleStructure of a human 48S translational initiation complex - 40S body
Components
  • (40S ribosomal protein ...) x 19
  • (Eukaryotic translation initiation factor ...) x 4
  • 18S rRNA18S ribosomal RNA
  • 60S ribosomal protein L41
  • mRNAMessenger RNA
KeywordsTRANSLATION / eIF3 / ribosome / initiation complex
Function / homology
Function and homology information


positive regulation of mRNA binding / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / dosage compensation by inactivation of X chromosome / negative regulation of RNA splicing / eukaryotic 48S preinitiation complex / ubiquitin ligase inhibitor activity / laminin receptor activity / formation of cytoplasmic translation initiation complex ...positive regulation of mRNA binding / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / dosage compensation by inactivation of X chromosome / negative regulation of RNA splicing / eukaryotic 48S preinitiation complex / ubiquitin ligase inhibitor activity / laminin receptor activity / formation of cytoplasmic translation initiation complex / cytoplasmic side of rough endoplasmic reticulum membrane / negative regulation of ubiquitin protein ligase activity / regulation of translational initiation / erythrocyte homeostasis / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / fibroblast growth factor binding / stress granule assembly / poly(U) RNA binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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) / positive regulation of ubiquitin-protein transferase activity / TOR signaling / ribosomal small subunit binding / SRP-dependent cotranslational protein targeting to membrane / maturation of SSU-rRNA / negative regulation of ubiquitin-dependent protein catabolic process / small-subunit processome / polysome / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / ribosomal small subunit biogenesis / viral transcription / translation initiation factor binding / erythrocyte differentiation / laminin binding / positive regulation of cell cycle / translation initiation factor activity / translational initiation / innate immune response in mucosa / polysomal ribosome / mRNA 3'-UTR binding / positive regulation of translational fidelity / rough endoplasmic reticulum / maintenance of translational fidelity / microtubule organizing center / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of translation / response to virus / cytoplasmic ribonucleoprotein granule / neural tube closure / mRNA 5'-UTR binding / rRNA processing / cytoplasmic translation / virus receptor activity / cell body / cytosolic large ribosomal subunit / cytosolic small ribosomal subunit / ribosome binding / glucose homeostasis / small ribosomal subunit / ribonucleoprotein complex / protein N-terminus binding / antibacterial humoral response / protein stabilization / ribosome / rRNA binding / structural constituent of ribosome / antimicrobial humoral immune response mediated by antimicrobial peptide / cell differentiation / postsynaptic density / translation / cadherin binding / multicellular organism development / cell adhesion / defense response to Gram-positive bacterium / mRNA binding / synapse / positive regulation of apoptotic process / dendrite / focal adhesion / nucleolus / positive regulation of gene expression / positive regulation of cell population proliferation / protein kinase binding / negative regulation of apoptotic process / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / enzyme binding / protein-containing complex / RNA binding / DNA binding / extracellular space / extracellular exosome / zinc ion binding / membrane / nucleoplasm / plasma membrane / nucleus
Ribosomal protein S27e / Ribosomal protein S4e, central region / Ribosomal protein S30 / Ribosomal protein L41 / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / S15/NS1, RNA-binding / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / Ribosomal protein L23/L15e core domain superfamily ...Ribosomal protein S27e / Ribosomal protein S4e, central region / Ribosomal protein S30 / Ribosomal protein L41 / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / S15/NS1, RNA-binding / 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 / Eukaryotic translation initiation factor 3 subunit J / Ribosomal protein S7e / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Ribosomal protein S4, conserved site / Ribosomal protein S12/S23 / 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 S17/S11 / Ribosomal protein S15 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e / KOW / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S5, C-terminal / RNA-binding S4 domain / Ribosomal protein S24e / Ribosomal protein S11 / SUI1 domain / Ribosomal protein S4/S9, N-terminal / RNA-binding domain, S1, IF1 type / Ribosomal protein S2 / Ribosomal protein S3Ae / Ribosomal protein S6e / Translation initiation factor 1A (eIF-1A) / Ribosomal protein S17e / Ribosomal protein S8e / Ribosomal protein S26e / Ribosomal protein S4e / Ribosomal protein S5 / Proteasome component (PCI) domain / Ribosomal protein S8 / Ribosomal protein S17e, conserved site / Ribosomal S24e conserved site / Ribosomal protein S3Ae, conserved site / Winged helix-like DNA-binding domain superfamily / Ribosomal protein S2, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Eukaryotic translation initiation factor 3 subunit C / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily / Winged helix DNA-binding domain superfamily / Eukaryotic translation initiation factor 3-like domain superfamily / Ribosomal protein S17e-like superfamily / SUI1 domain superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S26e superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S4, KOW domain / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S2, flavodoxin-like domain superfamily / 40S ribosomal protein SA / Ribosomal protein S15P / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / Eukaryotic translation initiation factor SUI1
40S ribosomal protein S21 / 60S ribosomal protein L41 / 40S ribosomal protein S30 / 40S ribosomal protein S26 / 40S ribosomal protein S24 / 40S ribosomal protein S14 / 40S ribosomal protein S6 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S11 / 40S ribosomal protein S13 ...40S ribosomal protein S21 / 60S ribosomal protein L41 / 40S ribosomal protein S30 / 40S ribosomal protein S26 / 40S ribosomal protein S24 / 40S ribosomal protein S14 / 40S ribosomal protein S6 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S11 / 40S ribosomal protein S13 / 40S ribosomal protein S23 / 40S ribosomal protein S27 / 40S ribosomal protein S15a / 40S ribosomal protein S8 / 40S ribosomal protein S7 / 40S ribosomal protein S3a / Eukaryotic translation initiation factor 1A, X-chromosomal / 40S ribosomal protein S9 / Eukaryotic translation initiation factor 1 / 40S ribosomal protein S2 / 40S ribosomal protein SA / 40S ribosomal protein S17 / Eukaryotic translation initiation factor 3 subunit J / Eukaryotic translation initiation factor 3 subunit C
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBrito Querido, J. / Sokabe, M. / Kraatz, S. / Gordiyenko, Y. / Skehel, M. / Fraser, C. / Ramakrishnan, V.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Wellcome TrustWTY096570 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105184332 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM092927 United States
CitationJournal: Science / Year: 2020
Title: Structure of a human 48 translational initiation complex.
Authors: Jailson Brito Querido / Masaaki Sokabe / Sebastian Kraatz / Yuliya Gordiyenko / J Mark Skehel / Christopher S Fraser / V Ramakrishnan /
Abstract: A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to ...A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to form the 48 initiation complex (i.e., the 48). The 48 then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we used cryo-electron microscopy to determine the structure of a reconstituted human 48 The structure reveals insights into early events of translation initiation complex assembly, as well as how eIF4F interacts with subunits of eIF3 near the mRNA exit channel in the 43 The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests that downstream mRNA is unwound at least in part by being "pulled" through the 40 subunit during scanning.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release

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Assembly

Deposited unit
C: 40S ribosomal protein S4, X isoform
B: 40S ribosomal protein S11
E: 40S ribosomal protein S23
D: 40S ribosomal protein S9
G: 40S ribosomal protein S7
F: 40S ribosomal protein S30
H: 40S ribosomal protein S27
K: 40S ribosomal protein S21
J: 40S ribosomal protein S15a
M: 40S ribosomal protein S17
L: 40S ribosomal protein S2
O: 40S ribosomal protein S3a
N: 40S ribosomal protein SA
Q: 40S ribosomal protein S26
P: 40S ribosomal protein S14
S: 40S ribosomal protein S6
R: 40S ribosomal protein S8
T: 40S ribosomal protein S24
q: Eukaryotic translation initiation factor 1A, X-chromosomal
p: Eukaryotic translation initiation factor 1
I: 40S ribosomal protein S13
z: Eukaryotic translation initiation factor 3 subunit J
y: Eukaryotic translation initiation factor 3 subunit C
9: 60S ribosomal protein L41
A: 18S rRNA
7: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,154,85387
Polymers1,153,33026
Non-polymers1,52461
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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40S ribosomal protein ... , 19 types, 19 molecules CBEDGFHKJMLONQPSRTI

#1: Protein 40S ribosomal protein S4, X isoform / Ribosome / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4 / eS4


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#2: Protein 40S ribosomal protein S11 / / Small ribosomal subunit protein uS17 / uS17


Mass: 18321.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#3: Protein 40S ribosomal protein S23 / / Small ribosomal subunit protein uS12 / uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266
#4: Protein 40S ribosomal protein S9 / / Small ribosomal subunit protein uS4 / uS4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#5: Protein 40S ribosomal protein S7 / / Small ribosomal subunit protein eS7 / eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#6: Protein 40S ribosomal protein S30 / / Small ribosomal subunit protein eS30 / eS30


Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861
#7: Protein 40S ribosomal protein S27 / / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27 / eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#8: Protein 40S ribosomal protein S21 / / Small ribosomal subunit protein eS21 / eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#9: Protein 40S ribosomal protein S15a / / Small ribosomal subunit protein uS8 / uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#10: Protein 40S ribosomal protein S17 / / Small ribosomal subunit protein eS17 / eS17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#11: Protein 40S ribosomal protein S2 / / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5 / uS5


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#12: Protein 40S ribosomal protein S3a / / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#13: Protein 40S ribosomal protein SA / / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2 / uS2


Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#14: Protein 40S ribosomal protein S26 / / Small ribosomal subunit protein eS26 / eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#15: Protein 40S ribosomal protein S14 / / Small ribosomal subunit protein uS11 / uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#16: Protein 40S ribosomal protein S6 / / Phosphoprotein NP33 / Small ribosomal subunit protein eS6 / eS6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#17: Protein 40S ribosomal protein S8 / / Small ribosomal subunit protein eS8 / eS8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#18: Protein 40S ribosomal protein S24 / / Small ribosomal subunit protein eS24 / eS24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#21: Protein 40S ribosomal protein S13 / / Small ribosomal subunit protein uS15 / uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277

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Eukaryotic translation initiation factor ... , 4 types, 4 molecules qpzy

#19: Protein Eukaryotic translation initiation factor 1A, X-chromosomal / eIF-1A X isoform / Eukaryotic translation initiation factor 4C / eIF-4C


Mass: 16488.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF1AX, EIF1A, EIF4C / Production host: Escherichia coli (E. coli) / References: UniProt: P47813
#20: Protein Eukaryotic translation initiation factor 1 / eIF1 / A121 / Protein translation factor SUI1 homolog / Sui1iso1


Mass: 12752.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF1, SUI1 / Production host: Escherichia coli (E. coli) / References: UniProt: P41567
#22: Protein Eukaryotic translation initiation factor 3 subunit J / eIF3j / Eukaryotic translation initiation factor 3 subunit 1 / eIF-3-alpha / eIF3 p35


Mass: 29108.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF3J, EIF3S1, PRO0391 / Production host: Escherichia coli (E. coli) / References: UniProt: O75822
#23: Protein Eukaryotic translation initiation factor 3 subunit C / eIF3c / Eukaryotic translation initiation factor 3 subunit 8 / eIF3 p110


Mass: 105503.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99613

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Protein/peptide , 1 types, 1 molecules 9

#24: Protein/peptide 60S ribosomal protein L41 / / HG12 / Large ribosomal subunit protein eL41 / eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62945

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RNA chain , 2 types, 2 molecules A7

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


Mass: 603130.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#26: RNA chain mRNA / Messenger RNA


Mass: 9172.806 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 61 molecules

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


Mass: 24.305 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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
IDNameTypeEntity IDParent-IDSource
1Human 48S initiation complexRIBOSOME#1-#260MULTIPLE SOURCES
2Human 48S initiation complexRIBOSOME#1-#18, #21, #23-#251NATURAL
3Human 48S initiation complexRIBOSOME#19-#20, #221RECOMBINANT
4Human 48S initiation complexRIBOSOME#261RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
34Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Escherichia coli (E. coli)562
24synthetic construct (others)32630
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 1 sec. / Electron dose: 107 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
EM softwareName: RELION / Version: 3 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144882 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 88.69 Å2
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004856299
ELECTRON MICROSCOPYf_angle_d0.915181899
ELECTRON MICROSCOPYf_chiral_restr0.048210189
ELECTRON MICROSCOPYf_plane_restr0.00625817
ELECTRON MICROSCOPYf_dihedral_angle_d19.118118837

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