8RJD | pdb_00008rjd

Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural analysis of the dynamic ribosome-translocon complex.

Lewis, A.J.O.Zhong, F.Keenan, R.J.Hegde, R.S.

(2024) Elife 13

  • DOI: https://doi.org/10.7554/eLife.95814
  • Primary Citation of Related Structures:  
    8RJB, 8RJC, 8RJD

  • PubMed Abstract: 

    The protein translocon at the endoplasmic reticulum comprises the Sec61 translocation channel and numerous accessory factors that collectively facilitate the biogenesis of secretory and membrane proteins. Here, we leveraged recent advances in cryo-electron microscopy (cryo-EM) and structure prediction to derive insights into several novel configurations of the ribosome-translocon complex. We show how a transmembrane domain (TMD) in a looped configuration passes through the Sec61 lateral gate during membrane insertion; how a nascent chain can bind and constrain the conformation of ribosomal protein uL22; and how the translocon-associated protein (TRAP) complex can adjust its position during different stages of protein biogenesis. Most unexpectedly, we find that a large proportion of translocon complexes contains RAMP4 intercalated into Sec61's lateral gate, widening Sec61's central pore and contributing to its hydrophilic interior. These structures lead to mechanistic hypotheses for translocon function and highlight a remarkably plastic machinery whose conformations and composition adjust dynamically to its diverse range of substrates.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit alpha isoform 1A [auth 1]476Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for P38377 (Canis lupus familiaris)
Explore P38377 
Go to UniProtKB:  P38377
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38377
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit betaB [auth 2]96Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for P60467 (Canis lupus familiaris)
Explore P60467 
Go to UniProtKB:  P60467
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60467
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit gammaC [auth 3]68Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for P60058 (Canis lupus familiaris)
Explore P60058 
Go to UniProtKB:  P60058
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60058
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Stress-associated endoplasmic reticulum proteinD [auth 4]66Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8I3PRN4 (Canis lupus familiaris)
Explore A0A8I3PRN4 
Go to UniProtKB:  A0A8I3PRN4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8I3PRN4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit alphaE [auth 5]286Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for P16967 (Canis lupus familiaris)
Explore P16967 
Go to UniProtKB:  P16967
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16967
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit betaF [auth 6]183Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for P23438 (Canis lupus familiaris)
Explore P23438 
Go to UniProtKB:  P23438
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23438
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit gammaG [auth 7]185Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8C0T6I4 (Canis lupus familiaris)
Explore A0A8C0T6I4 
Go to UniProtKB:  A0A8C0T6I4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8C0T6I4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit deltaH [auth 8]173Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8I3PXW2 (Canis lupus familiaris)
Explore A0A8I3PXW2 
Go to UniProtKB:  A0A8I3PXW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8I3PXW2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
CalnexinI [auth 9]593Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for P24643 (Canis lupus familiaris)
Explore P24643 
Go to UniProtKB:  P24643
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24643
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L8J [auth A]257Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TT27 (Oryctolagus cuniculus)
Explore G1TT27 
Go to UniProtKB:  G1TT27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1TT27
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent chainK [auth B]229Bos taurusMutation(s): 0 
UniProt
Find proteins for P02699 (Bos taurus)
Explore P02699 
Go to UniProtKB:  P02699
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02699
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4L [auth C]425Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SVW5 (Oryctolagus cuniculus)
Explore G1SVW5 
Go to UniProtKB:  G1SVW5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1SVW5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L18_c domain-containing proteinM [auth D]297Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P19949 (Oryctolagus cuniculus)
Explore P19949 
Go to UniProtKB:  P19949
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19949
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6N [auth E]291Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SKF7 (Oryctolagus cuniculus)
Explore G1SKF7 
Go to UniProtKB:  G1SKF7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1SKF7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal Protein uL30O [auth F]247Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SV32 (Oryctolagus cuniculus)
Explore G1SV32 
Go to UniProtKB:  G1SV32
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1SV32
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aP [auth G]319Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1STW0 (Oryctolagus cuniculus)
Explore G1STW0 
Go to UniProtKB:  G1STW0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1STW0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9Q [auth H]192Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SWI6 (Oryctolagus cuniculus)
Explore G1SWI6 
Go to UniProtKB:  G1SWI6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1SWI6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10R [auth I]214Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for B7NZQ2 (Oryctolagus cuniculus)
Explore B7NZQ2 
Go to UniProtKB:  B7NZQ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7NZQ2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11S [auth J]178Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TUB8 (Oryctolagus cuniculus)
Explore G1TUB8 
Go to UniProtKB:  G1TUB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1TUB8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13U [auth L]211Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TKB3 (Oryctolagus cuniculus)
Explore G1TKB3 
Go to UniProtKB:  G1TKB3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1TKB3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14V [auth M]218Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SZ12 (Oryctolagus cuniculus)
Explore G1SZ12 
Go to UniProtKB:  G1SZ12
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1SZ12
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15W [auth N]204Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T0C1 (Oryctolagus cuniculus)
Explore G1T0C1 
Go to UniProtKB:  G1T0C1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1T0C1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aX [auth O]203Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TVS8 (Oryctolagus cuniculus)
Explore G1TVS8 
Go to UniProtKB:  G1TVS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1TVS8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
uL22Y [auth P]184Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SCJ6 (Oryctolagus cuniculus)
Explore G1SCJ6 
Go to UniProtKB:  G1SCJ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1SCJ6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L18Z [auth Q]187Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TFE0 (Oryctolagus cuniculus)
Explore G1TFE0 
Go to UniProtKB:  G1TFE0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1TFE0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L19AA [auth R]196Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TYL6 (Oryctolagus cuniculus)
Explore G1TYL6 
Go to UniProtKB:  G1TYL6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1TYL6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aBA [auth S]176Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TTY7 (Oryctolagus cuniculus)
Explore G1TTY7 
Go to UniProtKB:  G1TTY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1TTY7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21CA [auth T]160Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SHQ2 (Oryctolagus cuniculus)
Explore G1SHQ2 
Go to UniProtKB:  G1SHQ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1SHQ2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL22DA [auth U]128Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TSG1 (Oryctolagus cuniculus)
Explore G1TSG1 
Go to UniProtKB:  G1TSG1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1TSG1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23EA [auth V]140Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T6D1 (Oryctolagus cuniculus)
Explore G1T6D1 
Go to UniProtKB:  G1T6D1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1T6D1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24FA [auth W]157Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE28 (Oryctolagus cuniculus)
Explore G1SE28 
Go to UniProtKB:  G1SE28
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1SE28
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23 N-terminal domain-containing proteinGA [auth X]156OryctolagusMutation(s): 0 
UniProt
Find proteins for G1SE76 (Oryctolagus cuniculus)
Explore G1SE76 
Go to UniProtKB:  G1SE76
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1SE76
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26HA [auth Y]145OryctolagusMutation(s): 0 
UniProt
Find proteins for G1SQH0 (Oryctolagus cuniculus)
Explore G1SQH0 
Go to UniProtKB:  G1SQH0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1SQH0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27IA [auth Z]136Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXF6 (Oryctolagus cuniculus)
Explore G1TXF6 
Go to UniProtKB:  G1TXF6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1TXF6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aJA [auth a]148Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SNY0 (Oryctolagus cuniculus)
Explore G1SNY0 
Go to UniProtKB:  G1SNY0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1SNY0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29KA [auth b]226Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SGR6 (Oryctolagus cuniculus)
Explore G1SGR6 
Go to UniProtKB:  G1SGR6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1SGR6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL30LA [auth c]115OryctolagusMutation(s): 0 
UniProt
Find proteins for G1TDL2 (Oryctolagus cuniculus)
Explore G1TDL2 
Go to UniProtKB:  G1TDL2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1TDL2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31MA [auth d]125Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SHG0 (Oryctolagus cuniculus)
Explore G1SHG0 
Go to UniProtKB:  G1SHG0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1SHG0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L32NA [auth e]135Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TUN8 (Oryctolagus cuniculus)
Explore G1TUN8 
Go to UniProtKB:  G1TUN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1TUN8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aOA [auth f]110Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SF08 (Oryctolagus cuniculus)
Explore G1SF08 
Go to UniProtKB:  G1SF08
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1SF08
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34PA [auth g]116Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXG5 (Oryctolagus cuniculus)
Explore G1TXG5 
Go to UniProtKB:  G1TXG5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1TXG5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35QA [auth h]123Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SIT5 (Oryctolagus cuniculus)
Explore G1SIT5 
Go to UniProtKB:  G1SIT5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1SIT5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36RA [auth i]105Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TTQ5 (Oryctolagus cuniculus)
Explore G1TTQ5 
Go to UniProtKB:  G1TTQ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1TTQ5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37SA [auth j]97Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for U3KPD5 (Oryctolagus cuniculus)
Explore U3KPD5 
Go to UniProtKB:  U3KPD5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU3KPD5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL38TA [auth k]70OryctolagusMutation(s): 0 
UniProt
Find proteins for G1U001 (Oryctolagus cuniculus)
Explore G1U001 
Go to UniProtKB:  G1U001
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1U001
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39-likeUA [auth l]51Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TTN1 (Oryctolagus cuniculus)
Explore G1TTN1 
Go to UniProtKB:  G1TTN1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1TTN1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
eL40VA [auth m]102Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P0DXC2 (Oryctolagus cuniculus)
Explore P0DXC2 
Go to UniProtKB:  P0DXC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DXC2
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41WA [auth n]25Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
Explore A0A087WNH4 
Go to UniProtKB:  A0A087WNH4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A087WNH4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36a-likeXA [auth o]106Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T040 (Oryctolagus cuniculus)
Explore G1T040 
Go to UniProtKB:  G1T040
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1T040
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aYA [auth p]92Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SY53 (Oryctolagus cuniculus)
Explore G1SY53 
Go to UniProtKB:  G1SY53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1SY53
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28AB [auth r]137Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U7L1 (Oryctolagus cuniculus)
Explore G1U7L1 
Go to UniProtKB:  G1U7L1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1U7L1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L3DB [auth w]403Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TL06 (Oryctolagus cuniculus)
Explore G1TL06 
Go to UniProtKB:  G1TL06
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1TL06
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains LengthOrganismImage
28S rRNAT [auth K]3,543Oryctolagus cuniculus
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 52
MoleculeChains LengthOrganismImage
P-site tRNAZA [auth q]76Sus scrofa
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 54
MoleculeChains LengthOrganismImage
5S rRNABB [auth u]120Oryctolagus cuniculus
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 55
MoleculeChains LengthOrganismImage
5.8S rRNACB [auth v]156Oryctolagus cuniculus
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BJ [auth g],
DJ [auth j],
EJ [auth m],
FJ [auth o],
GJ [auth p]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth K]
AD [auth K]
AE [auth K]
AF [auth K]
AG [auth K]
AC [auth K],
AD [auth K],
AE [auth K],
AF [auth K],
AG [auth K],
AH [auth K],
AI [auth K],
AJ [auth g],
BC [auth K],
BD [auth K],
BE [auth K],
BF [auth K],
BG [auth K],
BH [auth K],
BI [auth K],
CC [auth K],
CD [auth K],
CE [auth K],
CF [auth K],
CG [auth K],
CH [auth K],
CI [auth K],
CJ [auth j],
DC [auth K],
DD [auth K],
DE [auth K],
DF [auth K],
DG [auth K],
DH [auth K],
DI [auth K],
EB [auth I],
EC [auth K],
ED [auth K],
EE [auth K],
EF [auth K],
EG [auth K],
EH [auth K],
EI [auth K],
FB [auth K],
FC [auth K],
FD [auth K],
FE [auth K],
FF [auth K],
FG [auth K],
FH [auth K],
FI [auth K],
GB [auth K],
GC [auth K],
GD [auth K],
GE [auth K],
GF [auth K],
GG [auth K],
GH [auth K],
GI [auth K],
HB [auth K],
HC [auth K],
HD [auth K],
HE [auth K],
HF [auth K],
HG [auth K],
HH [auth K],
HI [auth K],
HJ [auth u],
IB [auth K],
IC [auth K],
ID [auth K],
IE [auth K],
IF [auth K],
IG [auth K],
IH [auth K],
II [auth K],
IJ [auth u],
JB [auth K],
JC [auth K],
JD [auth K],
JE [auth K],
JF [auth K],
JG [auth K],
JH [auth K],
JI [auth K],
JJ [auth u],
KB [auth K],
KC [auth K],
KD [auth K],
KE [auth K],
KF [auth K],
KG [auth K],
KH [auth K],
KI [auth K],
KJ [auth u],
LB [auth K],
LC [auth K],
LD [auth K],
LE [auth K],
LF [auth K],
LG [auth K],
LH [auth K],
LI [auth K],
LJ [auth u],
MB [auth K],
MC [auth K],
MD [auth K],
ME [auth K],
MF [auth K],
MG [auth K],
MH [auth K],
MI [auth K],
MJ [auth u],
NB [auth K],
NC [auth K],
ND [auth K],
NE [auth K],
NF [auth K],
NG [auth K],
NH [auth K],
NI [auth K],
NJ [auth u],
OB [auth K],
OC [auth K],
OD [auth K],
OE [auth K],
OF [auth K],
OG [auth K],
OH [auth K],
OI [auth K],
OJ [auth v],
PB [auth K],
PC [auth K],
PD [auth K],
PE [auth K],
PF [auth K],
PG [auth K],
PH [auth K],
PI [auth K],
PJ [auth v],
QB [auth K],
QC [auth K],
QD [auth K],
QE [auth K],
QF [auth K],
QG [auth K],
QH [auth K],
QI [auth K],
QJ [auth v],
RB [auth K],
RC [auth K],
RD [auth K],
RE [auth K],
RF [auth K],
RG [auth K],
RH [auth K],
RI [auth K],
RJ [auth v],
SB [auth K],
SC [auth K],
SD [auth K],
SE [auth K],
SF [auth K],
SG [auth K],
SH [auth K],
SI [auth K],
SJ [auth v],
TB [auth K],
TC [auth K],
TD [auth K],
TE [auth K],
TF [auth K],
TG [auth K],
TH [auth K],
TI [auth K],
UB [auth K],
UC [auth K],
UD [auth K],
UE [auth K],
UF [auth K],
UG [auth K],
UH [auth K],
UI [auth K],
VB [auth K],
VC [auth K],
VD [auth K],
VE [auth K],
VF [auth K],
VG [auth K],
VH [auth K],
VI [auth K],
WB [auth K],
WC [auth K],
WD [auth K],
WE [auth K],
WF [auth K],
WG [auth K],
WH [auth K],
WI [auth K],
XB [auth K],
XC [auth K],
XD [auth K],
XE [auth K],
XF [auth K],
XG [auth K],
XH [auth K],
XI [auth K],
YB [auth K],
YC [auth K],
YD [auth K],
YE [auth K],
YF [auth K],
YG [auth K],
YH [auth K],
YI [auth V],
ZB [auth K],
ZC [auth K],
ZD [auth K],
ZE [auth K],
ZF [auth K],
ZG [auth K],
ZH [auth K],
ZI [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_A022_1007
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM130051
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM086487

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary