9BH5

High-resolution C. elegans 80S ribosome structure - class 1

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

A high resolution C. elegans ribosome structure

Sehgal, E., Serrao, V.H.B., Arribere, J.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3A [auth AD]247Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P48152 (Caenorhabditis elegans)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1B [auth AB]257Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5C [auth AC]272Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS4D [auth AE]259Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q9N3X2 (Caenorhabditis elegans)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS17I [auth AR]130Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for O01692 (Caenorhabditis elegans)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Plectin/S10 N-terminal domain-containing proteinJ [auth AK]149Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for O01869 (Caenorhabditis elegans)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal Protein, Small subunitK [auth AW]130Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13L [auth AS]154Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19M [auth AT]146Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS26N [auth Aa]117Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for O45499 (Caenorhabditis elegans)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein 1-ribosomal protein eS31 fusion proteinO [auth Af]163Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P37165 (Caenorhabditis elegans)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2P [auth AA]276Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P46769 (Caenorhabditis elegans)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11Q [auth AO]152Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS8R [auth AI]208Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7S [auth AF]210Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P49041 (Caenorhabditis elegans)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS12T [auth AM]140Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS21U [auth AV]88Caenorhabditis elegansMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15V [auth AN]151Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS25W [auth AZ]117Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P52821 (Caenorhabditis elegans)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14X [auth Ad]56Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P90983 (Caenorhabditis elegans)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS24Y [auth AY]131Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q1XFY9 (Caenorhabditis elegans)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10Z [auth AU]117Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q8WQA8 (Caenorhabditis elegans)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS6AA [auth AG]246Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q9NEN6 (Caenorhabditis elegans)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS27BA [auth Ab]83Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q9TXP0 (Caenorhabditis elegans)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19CA [auth AP]151Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q9XVP0 (Caenorhabditis elegans)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS28DA [auth Ac]65Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q95Y04 (Caenorhabditis elegans)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like domain-containing proteinEA [auth Ae]130Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q18231 (Caenorhabditis elegans)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12FA [auth AX]143Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q19877 (Caenorhabditis elegans)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17GA [auth AL]155Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q20206 (Caenorhabditis elegans)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4HA [auth AJ]189Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q20228 (Caenorhabditis elegans)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9IA [auth AQ]144Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q22054 (Caenorhabditis elegans)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS7JA [auth AH]194Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q23312 (Caenorhabditis elegans)
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30KA [auth CF]244Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for O01802 (Caenorhabditis elegans)
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL20LA [auth CS]180Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14MA [auth CV]140Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P48158 (Caenorhabditis elegans)
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3NA [auth CB]401Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P50880 (Caenorhabditis elegans)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL22OA [auth CU]130Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13PA [auth CL]207Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P91128 (Caenorhabditis elegans)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2QA [auth CA]260Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8RA [auth CG]265Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16SA [auth CI]214Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13TA [auth CO]202Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4UA [auth CC]345Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29VA [auth Ch]123Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P34662 (Caenorhabditis elegans)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL6WA [auth CE]217Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P47991 (Caenorhabditis elegans)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL42XA [auth Co]105Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P48166 (Caenorhabditis elegans)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL33YA [auth Cf]124Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P49180 (Caenorhabditis elegans)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL36ZA [auth Ci]104Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL39AB [auth Cl]51Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL15BB [auth CN]204Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15CB [auth Ca]145Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL43DB [auth Cp]91Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL14EB [auth CM]135Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL30FB [auth Cc]115Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6GB [auth CH]189Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24HB [auth CY]142Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL19IB [auth CR]198Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29JB [auth Cb]62Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL18KB [auth CQ]188Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL21LB [auth CT]161Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P34334 (Caenorhabditis elegans)
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18MB [auth CD]293Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL27NB [auth CZ]136Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22OB [auth CP]187Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
eL41PB [auth Cn]22Caenorhabditis elegansMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL34QB [auth Cg]110Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL38RB [auth Ck]70Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-ribosomal protein eL40 fusion proteinSB [auth Cm]128Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL31TB [auth Cd]122Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL32UB [auth Ce]134Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL24VB [auth CW]159Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37WB [auth Cj]92Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5BXB [auth CJ]196Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23BYB [auth CX]146Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains LengthOrganismImage
5S rRNAE [auth A7]119Caenorhabditis elegans
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Entity ID: 6
MoleculeChains LengthOrganismImage
5.8S rRNAF [auth A8]153Caenorhabditis elegans
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Entity ID: 7
MoleculeChains LengthOrganismImage
18S rRNAG [auth B2]1,754Caenorhabditis elegans
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Entity ID: 8
MoleculeChains LengthOrganismImage
28S rRNAH [auth A5]3,510Caenorhabditis elegans
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Entity ID: 78
MoleculeChains LengthOrganismImage
tRNAAC [auth DB],
ZB [auth DA]		76Caenorhabditis elegans
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Entity ID: 79
MoleculeChains LengthOrganismImage
mRNABC [auth DC]10Caenorhabditis elegans
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3HE
Query on 3HE
Download Ideal Coordinates CCD File 
DC [auth A5]4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione
C15 H23 N O4
YPHMISFOHDHNIV-FSZOTQKASA-N
SPD
Query on SPD
Download Ideal Coordinates CCD File 
CC [auth A5]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4.1
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM131012

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release