8HFR

NPC-trapped pre-60S particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Nuclear export of pre-60S particles through the nuclear pore complex.

Li, Z.Chen, S.Zhao, L.Huang, G.Xu, H.Yang, X.Wang, P.Gao, N.Sui, S.F.

(2023) Nature 618: 411-418

  • DOI: https://doi.org/10.1038/s41586-023-06128-y
  • Primary Citation of Related Structures:  
    8HBN, 8HFR

  • PubMed Abstract: 

    The nuclear pore complex (NPC) is the bidirectional gate that mediates the exchange of macromolecules or their assemblies between nucleus and cytoplasm 1-3 . The assembly intermediates of the ribosomal subunits, pre-60S and pre-40S particles, are among the largest cargoes of the NPC and the export of these gigantic ribonucleoproteins requires numerous export factors 4,5 . Here we report the cryo-electron microscopy structure of native pre-60S particles trapped in the channel of yeast NPCs. In addition to known assembly factors, multiple factors with export functions are also included in the structure. These factors in general bind to either the flexible regions or subunit interface of the pre-60S particle, and virtually form many anchor sites for NPC binding. Through interactions with phenylalanine-glycine (FG) repeats from various nucleoporins of NPC, these factors collectively facilitate the passage of the pre-60S particle through the central FG repeat network of the NPC. Moreover, in silico analysis of the axial and radial distribution of pre-60S particles within the NPC shows that a single NPC can take up to four pre-60S particles simultaneously, and pre-60S particles are enriched in the inner ring regions close to the wall of the NPC with the solvent-exposed surface facing the centre of the nuclear pore. Our data suggest a translocation model for the export of pre-60S particles through the NPC.


  • Organizational Affiliation

    School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-AA [auth h1]120Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX84 
Go to UniProtKB:  P0CX84
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX84
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AB [auth g2]121Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P87262 
Go to UniProtKB:  P87262
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP87262
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29C [auth b3]59Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05747 
Go to UniProtKB:  P05747
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05747
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AD [auth B4]254Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX45 
Go to UniProtKB:  P0CX45
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX45
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AE [auth V5]137Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX41 
Go to UniProtKB:  P0CX41
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX41
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AF [auth O6]199Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P26784 
Go to UniProtKB:  P26784
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26784
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AG [auth f7]107Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05744 
Go to UniProtKB:  P05744
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05744
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-AH [auth F8]176Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02326 
Go to UniProtKB:  Q02326
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02326
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 2I [auth v9]486Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P53742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53742 
Go to UniProtKB:  P53742
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53742
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 1J [auth rA]647Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q02892 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02892 
Go to UniProtKB:  Q02892
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02892
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP24K [auth tB]199Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q07915 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07915 
Go to UniProtKB:  Q07915
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07915
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30L [auth cC]105Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14120 
Go to UniProtKB:  P14120
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14120
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3M [auth CD]387Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14126 
Go to UniProtKB:  P14126
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14126
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6N [auth yE]245Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12522 
Go to UniProtKB:  Q12522
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12522
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AO [auth UF]121Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05749 
Go to UniProtKB:  P05749
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05749
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AP [auth dG]113Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0C2H8 
Go to UniProtKB:  P0C2H8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C2H8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32Q [auth eH]130Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38061 
Go to UniProtKB:  P38061
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38061
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Shuttling pre-60S factor ECM1R [auth xI]212Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P39715 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39715 
Go to UniProtKB:  P39715
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39715
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein ALB1S [auth qJ]175Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P47019 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47019 
Go to UniProtKB:  P47019
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47019
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA transport regulator MTR2AA [auth FR],
CB [auth Bt],
T [auth DK]
184Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P34232 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P34232 
Go to UniProtKB:  P34232
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34232
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AU [auth LL]199Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12690 
Go to UniProtKB:  Q12690
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12690
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
YEAST 60S ribosomal protein L12-AV [auth KM]165Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX53 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX53 
Go to UniProtKB:  P0CX53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX53
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA export factor MEX67FA [auth CW],
GA [auth EX],
W [auth AN]
599Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q99257 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q99257 
Go to UniProtKB:  Q99257
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99257
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-AX [auth DO]362Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P10664 
Go to UniProtKB:  P10664
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10664
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AY [auth RP]189Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX82 
Go to UniProtKB:  P0CX82
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX82
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AZ [auth MQ]138Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36105 
Go to UniProtKB:  P36105
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36105
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-ABA [auth mS]106Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX27 
Go to UniProtKB:  P0CX27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX27
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Probable metalloprotease ARX1CA [auth pT]593Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3
UniProt
Find proteins for Q03862 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03862 
Go to UniProtKB:  Q03862
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03862
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-ADA [auth YU]127Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05743 
Go to UniProtKB:  P05743
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05743
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal export protein NMD3EA [auth vV]518Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38861 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38861 
Go to UniProtKB:  P38861
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38861
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-AHA [auth nY]92Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX25 
Go to UniProtKB:  P0CX25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX25
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AIA [auth SZ]172Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX23 
Go to UniProtKB:  P0CX23
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX23
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-AJA [auth ia]100Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05745 
Go to UniProtKB:  P05745
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05745
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AKA [auth Ib]191Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05738 
Go to UniProtKB:  P05738
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05738
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25LA [auth Xc]142Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04456 
Go to UniProtKB:  P04456
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04456
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA2MA [auth xd]261Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40078 
Go to UniProtKB:  P40078
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40078
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome assembly factor MRT4PA [auth Wg]236Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P33201 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33201 
Go to UniProtKB:  P33201
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33201
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AQA [auth jh]88Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49166 
Go to UniProtKB:  P49166
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49166
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39RA [auth li]51Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04650 
Go to UniProtKB:  P04650
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04650
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-ASA [auth Hj]256Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17076 
Go to UniProtKB:  P17076
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17076
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-ATA [auth Qk]186Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX49 
Go to UniProtKB:  P0CX49
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX49
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AUA [auth Tl]160Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02753 
Go to UniProtKB:  Q02753
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02753
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Translation machinery-associated protein 16VA [auth sm]178Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q08687 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08687 
Go to UniProtKB:  Q08687
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08687
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AXA [auth No]204Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05748 
Go to UniProtKB:  P05748
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05748
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0642 protein YBL028CYA [auth zp]106Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38202 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38202 
Go to UniProtKB:  P38202
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38202
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AZA [auth Zq]136Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0C2H6 
Go to UniProtKB:  P0C2H6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C2H6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38AB [auth kr]78Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49167 
Go to UniProtKB:  P49167
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49167
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
YEAST 60S ribosomal protein L1-ABB [auth As]217Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX43 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX43 
Go to UniProtKB:  P0CX43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX43
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-ADB [auth Gu]244Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05737 
Go to UniProtKB:  P05737
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05737
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AEB [auth Pv]184Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05740 
Go to UniProtKB:  P05740
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05740
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28FB [auth aw]149Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02406 
Go to UniProtKB:  P02406
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02406
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Bud site selection protein 20GB [auth ox]166Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q08004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08004 
Go to UniProtKB:  Q08004
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08004
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-AHB [auth Jy]174Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0C0W9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0C0W9 
Go to UniProtKB:  P0C0W9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0W9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5IB [auth Ez]297Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P26321 
Go to UniProtKB:  P26321
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26321
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 37
MoleculeChains LengthOrganismImage
25S ribosomal RNANA [auth 1e]3,396Saccharomyces cerevisiae S288C
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 38
MoleculeChains LengthOrganismImage
5S ribosomal RNAOA [auth 2f]121Saccharomyces cerevisiae S288C
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 46
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAWA [auth 3n]158Saccharomyces cerevisiae S288C
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth 1e]
AD [auth 1e]
AE [auth 1e]
AF [auth 1e]
AG [auth 1e]
AC [auth 1e],
AD [auth 1e],
AE [auth 1e],
AF [auth 1e],
AG [auth 1e],
AH [auth 1e],
AI [auth 1e],
AJ [auth 1e],
AK [auth 1e],
BC [auth 1e],
BD [auth 1e],
BE [auth 1e],
BF [auth 1e],
BG [auth 1e],
BH [auth 1e],
BI [auth 1e],
BJ [auth 1e],
BK [auth 1e],
CC [auth 1e],
CD [auth 1e],
CE [auth 1e],
CF [auth 1e],
CG [auth 1e],
CH [auth 1e],
CI [auth 1e],
CJ [auth 1e],
CK [auth 1e],
DC [auth 1e],
DD [auth 1e],
DE [auth 1e],
DF [auth 1e],
DG [auth 1e],
DH [auth 1e],
DI [auth 1e],
DJ [auth 1e],
DK [auth 2f],
EC [auth 1e],
ED [auth 1e],
EE [auth 1e],
EF [auth 1e],
EG [auth 1e],
EH [auth 1e],
EI [auth 1e],
EJ [auth 1e],
EK [auth 3n],
FC [auth 1e],
FD [auth 1e],
FE [auth 1e],
FF [auth 1e],
FG [auth 1e],
FH [auth 1e],
FI [auth 1e],
FJ [auth 1e],
FK [auth 3n],
GC [auth 1e],
GD [auth 1e],
GE [auth 1e],
GF [auth 1e],
GG [auth 1e],
GH [auth 1e],
GI [auth 1e],
GJ [auth 1e],
GK [auth 3n],
HC [auth 1e],
HD [auth 1e],
HE [auth 1e],
HF [auth 1e],
HG [auth 1e],
HH [auth 1e],
HI [auth 1e],
HJ [auth 1e],
HK [auth 3n],
IC [auth 1e],
ID [auth 1e],
IE [auth 1e],
IF [auth 1e],
IG [auth 1e],
IH [auth 1e],
II [auth 1e],
IJ [auth 1e],
IK [auth 3n],
JB [auth g2],
JC [auth 1e],
JD [auth 1e],
JE [auth 1e],
JF [auth 1e],
JG [auth 1e],
JH [auth 1e],
JI [auth 1e],
JJ [auth 1e],
JK [auth 3n],
KB [auth g2],
KC [auth 1e],
KD [auth 1e],
KE [auth 1e],
KF [auth 1e],
KG [auth 1e],
KH [auth 1e],
KI [auth 1e],
KJ [auth 1e],
KK [auth No],
LB [auth B4],
LC [auth 1e],
LD [auth 1e],
LE [auth 1e],
LF [auth 1e],
LG [auth 1e],
LH [auth 1e],
LI [auth 1e],
LJ [auth 1e],
LK [auth zp],
MB [auth CD],
MC [auth 1e],
MD [auth 1e],
ME [auth 1e],
MF [auth 1e],
MG [auth 1e],
MH [auth 1e],
MI [auth 1e],
MJ [auth 1e],
NB [auth CD],
NC [auth 1e],
ND [auth 1e],
NE [auth 1e],
NF [auth 1e],
NG [auth 1e],
NH [auth 1e],
NI [auth 1e],
NJ [auth 1e],
OB [auth 1e],
OC [auth 1e],
OD [auth 1e],
OE [auth 1e],
OF [auth 1e],
OG [auth 1e],
OH [auth 1e],
OI [auth 1e],
OJ [auth 1e],
PB [auth 1e],
PC [auth 1e],
PD [auth 1e],
PE [auth 1e],
PF [auth 1e],
PG [auth 1e],
PH [auth 1e],
PI [auth 1e],
PJ [auth 1e],
QB [auth 1e],
QC [auth 1e],
QD [auth 1e],
QE [auth 1e],
QF [auth 1e],
QG [auth 1e],
QH [auth 1e],
QI [auth 1e],
QJ [auth 1e],
RB [auth 1e],
RC [auth 1e],
RD [auth 1e],
RE [auth 1e],
RF [auth 1e],
RG [auth 1e],
RH [auth 1e],
RI [auth 1e],
RJ [auth 1e],
SB [auth 1e],
SC [auth 1e],
SD [auth 1e],
SE [auth 1e],
SF [auth 1e],
SG [auth 1e],
SH [auth 1e],
SI [auth 1e],
SJ [auth 1e],
TB [auth 1e],
TC [auth 1e],
TD [auth 1e],
TE [auth 1e],
TF [auth 1e],
TG [auth 1e],
TH [auth 1e],
TI [auth 1e],
TJ [auth 1e],
UB [auth 1e],
UC [auth 1e],
UD [auth 1e],
UE [auth 1e],
UF [auth 1e],
UG [auth 1e],
UH [auth 1e],
UI [auth 1e],
UJ [auth 1e],
VB [auth 1e],
VC [auth 1e],
VD [auth 1e],
VE [auth 1e],
VF [auth 1e],
VG [auth 1e],
VH [auth 1e],
VI [auth 1e],
VJ [auth 1e],
WB [auth 1e],
WC [auth 1e],
WD [auth 1e],
WE [auth 1e],
WF [auth 1e],
WG [auth 1e],
WH [auth 1e],
WI [auth 1e],
WJ [auth 1e],
XB [auth 1e],
XC [auth 1e],
XD [auth 1e],
XE [auth 1e],
XF [auth 1e],
XG [auth 1e],
XH [auth 1e],
XI [auth 1e],
XJ [auth 1e],
YB [auth 1e],
YC [auth 1e],
YD [auth 1e],
YE [auth 1e],
YF [auth 1e],
YG [auth 1e],
YH [auth 1e],
YI [auth 1e],
YJ [auth 1e],
ZB [auth 1e],
ZC [auth 1e],
ZD [auth 1e],
ZE [auth 1e],
ZF [auth 1e],
ZG [auth 1e],
ZH [auth 1e],
ZI [auth 1e],
ZJ [auth 1e]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references