4V8Y

Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 5.1 of the entry. See complete history. 


Literature

Molecular architecture of a eukaryotic translational initiation complex.

Fernandez, I.S., Bai, X.C., Hussain, T., Kelley, A.C., Lorsch, J.R., Ramakrishnan, V., Scheres, S.H.W.

(2013) Science 342: 1240585-1240585

  • DOI: https://doi.org/10.1126/science.1240585
  • Primary Citation of Related Structures:  
    4V8Y, 4V8Z

  • PubMed Abstract: 

    The last step in eukaryotic translational initiation involves the joining of the large and small subunits of the ribosome, with initiator transfer RNA (Met-tRNA(i)(Met)) positioned over the start codon of messenger RNA in the P site. This step is catalyzed by initiation factor eIF5B. We used recent advances in cryo-electron microscopy (cryo-EM) to determine a structure of the eIF5B initiation complex to 6.6 angstrom resolution from <3% of the population, comprising just 5143 particles. The structure reveals conformational changes in eIF5B, initiator tRNA, and the ribosome that provide insights into the role of eIF5B in translational initiation. The relatively high resolution obtained from such a small fraction of a heterogeneous sample suggests a general approach for characterizing the structure of other dynamic or transient biological complexes.

    • Organizational Affiliation: 

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, CB2 0QH, United Kingdom.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S26-AA [auth A0]119Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S27-AB [auth A1]82Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S28-AC [auth A2]67Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S29-AD [auth A3]56Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S30-AE [auth A4]63Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUITIN-40S RIBOSOMAL PROTEIN S31F [auth A5]152Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-LIKE PROTEING [auth A6]319Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
SUPPRESSOR PROTEIN STM1H [auth A7]273Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S0-AI [auth AA]252Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S1-AJ [auth AB]255Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S2K [auth AC]254Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S3L [auth AD]240Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S4-AM [auth AE]261Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S5N [auth AF]225Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S6-AO [auth AG]236Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S7-AP [auth AH]190Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S8-AQ [auth AI]200Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S9-AR [auth AJ]197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
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40S RIBOSOMAL PROTEIN S10-AS [auth AK]105Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S11-AT [auth AL]156Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S12U [auth AM]143Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S13V [auth AN]151Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S14-AW [auth AO]137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S15X [auth AP]142Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S16-AY [auth AQ]143Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S17-AZ [auth AR]136Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S18-AAA [auth AS]146Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S19-ABA [auth AT]144Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S20CA [auth AU]121Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S21-ADA [auth AV]87Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S22-AEA [auth AW]130Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S23-AFA [auth AX]145Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S24-AGA [auth AY]135Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S25-AHA [auth AZ]108Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L2-BIA [auth BA]253Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L3JA [auth BB]386Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L4-AKA [auth BC]361Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L5LA [auth BD]296Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L6-AMA [auth BE]175Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L7-ANA [auth BF]243Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L8-AOA [auth BG]255Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L9-APA [auth BH]191Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L10QA [auth BI]220Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
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60S RIBOSOMAL PROTEIN L11-ARA [auth BJ]173Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L11-ASA [auth BK]174Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L13-ATA [auth BL]198Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L14-BUA [auth BM]137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L15-AVA [auth BN]203Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L16-AWA [auth BO]198Saccharomyces cerevisiaeMutation(s): 20 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L17-AXA [auth BP]183Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L18-AYA [auth BQ]185Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L19-BZA [auth BR]188Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L20-BAB [auth BS]172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L21-ABB [auth BT]159Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L22-ACB [auth BU]120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L23-ADB [auth BV]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L24-AEB [auth BW]155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L25FB [auth BX]141Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L26-AGB [auth BY]126Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L27-AHB [auth BZ]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L28IB [auth Ba]148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L29JB [auth Bb]58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L30KB [auth Bc]104Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L31-ALB [auth Bd]112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L32MB [auth Be]129Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L33-ANB [auth Bf]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L34-AOB [auth Bg]120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L35-BPB [auth Bh]119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L36-AQB [auth Bi]99Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L37-ARB [auth Bj]87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L38SB [auth Bk]77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L39TB [auth Bl]50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUITIN-60S RIBOSOMAL PROTEIN L40UB [auth Bm]128Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L41-BVB [auth Bn]25Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L42-AWB [auth Bo]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ACIDIC RIBOSOMAL PROTEIN P0XB [auth Bq]312Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
60S ACIDIC RIBOSOMAL PROTEIN P1YB [auth Br]47Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
60S ACIDIC RIBOSOMAL PROTEIN P2ZB [auth Bs]46Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L1AC [auth By],
FC [auth CL]		229Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION INITIATION FACTOR 5BHC [auth CP]339Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.5.3
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP
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NR [auth CP]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
OHX
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AE [auth B2]
AF [auth B2]
AG [auth B2]
AH [auth B2]
AI [auth B2]
osmium (III) hexammine
H12 N6 Os
OWCQTVJQFLTQTE-UHFFFAOYSA-N
ZN
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JC [auth A0]
MC [auth A1]
NC [auth A3]
PD [auth Bj]
QD [auth Bm]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
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AD [auth AG]
AL [auth B2]
AM [auth B2]
AN [auth B2]
AO [auth B2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-04-22
    Changes: Other
  • Version 2.0: 2017-08-02
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 3.0: 2018-04-18
    Changes: Atomic model, Data collection, Database references, Other, Source and taxonomy
  • Version 4.0: 2024-06-19
    Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence
  • Version 5.0: 2024-06-26
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary
  • Version 5.1: 2024-10-16
    Changes: Structure summary