3JCT

Cryo-em structure of eukaryotic pre-60S ribosomal subunits


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 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

Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomes

Wu, S.Tutuncuoglu, B.Yan, K.Brown, H.Zhang, Y.Tan, D.Gamalinda, M.Yuan, Y.Li, Z.Jakovljevic, J.Ma, C.Lei, J.Dong, M.Q.Woolford, J.L.Gao, N.

(2016) Nature 534: 133-137

  • DOI: 10.1038/nature17942
  • Primary Citation of Related Structures:  
    3JCT

  • PubMed Abstract: 
  • Ribosome biogenesis is a highly complex process in eukaryotes, involving temporally and spatially regulated ribosomal protein (r-protein) binding and ribosomal RNA remodelling events in the nucleolus, nucleoplasm and cytoplasm. Hundreds of assembly factors, organized into sequential functional groups, facilitate and guide the maturation process into productive assembly branches in and across different cellular compartments ...

    Ribosome biogenesis is a highly complex process in eukaryotes, involving temporally and spatially regulated ribosomal protein (r-protein) binding and ribosomal RNA remodelling events in the nucleolus, nucleoplasm and cytoplasm. Hundreds of assembly factors, organized into sequential functional groups, facilitate and guide the maturation process into productive assembly branches in and across different cellular compartments. However, the precise mechanisms by which these assembly factors function are largely unknown. Here we use cryo-electron microscopy to characterize the structures of yeast nucleoplasmic pre-60S particles affinity-purified using the epitope-tagged assembly factor Nog2. Our data pinpoint the locations and determine the structures of over 20 assembly factors, which are enriched in two areas: an arc region extending from the central protuberance to the polypeptide tunnel exit, and the domain including the internal transcribed spacer 2 (ITS2) that separates 5.8S and 25S ribosomal RNAs. In particular, two regulatory GTPases, Nog2 and Nog1, act as hub proteins to interact with multiple, distant assembly factors and functional ribosomal RNA elements, manifesting their critical roles in structural remodelling checkpoints and nuclear export. Moreover, our snapshots of compositionally and structurally different pre-60S intermediates provide essential mechanistic details for three major remodelling events before nuclear export: rotation of the 5S ribonucleoprotein, construction of the active centre and ITS2 removal. The rich structural information in our structures provides a framework to dissect molecular roles of diverse assembly factors in eukaryotic ribosome assembly.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L2-AA254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2ARPL5BYFR031C-AYFR031BC
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3B387Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L4-AC362Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5D297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5RPL1RPL1AYPL131WLPI14W
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6-AE176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6ARPL17AYL16AYML073C
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7-AF244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8-AG256Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L9-AH191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Bud site selection protein 20I166Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD20YLR074C
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L11-AJ174Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11ARP39ARPL16AYPR102CP8283.14
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome-interacting protein CIC1K376Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CIC1NSA3YHR052W
UniProt
Find proteins for P38779 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38779 
Go to UniProtKB:  P38779
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38779
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L13-AL199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L14-AM138Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L15-AN204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L16-AO199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L17-AP184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18-AQ186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L19-AR189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L20-AS172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L21-AT160Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L22-AU121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L23-AV137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome assembly factor MRT4W236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MRT4YKL009WYKL160
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L25X142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L26-AY127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27-AZ136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28AA [auth a]149Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 1BA [auth b]647Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOG1YPL093WLPG15W
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30CA [auth c]105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L31-ADA [auth d]113Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L32EA [auth e]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L33-AFA [auth f]107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L34-AGA [auth g]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35-AHA [auth h]120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36-AIA [auth i]100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37-AJA [auth j]88Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L38KA [auth k]78Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39LA [auth l]51Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 2MA [auth m]486Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOG2YNR053CN3484
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Pescadillo homologNA [auth n]605Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP7RRP13YPH1YGR103W
UniProt
Find proteins for P53261 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53261 
Go to UniProtKB:  P53261
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53261
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein 15OA [auth o]220Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP15YNL110CN1954
UniProt
Find proteins for P53927 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53927 
Go to UniProtKB:  P53927
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53927
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L43-APA [auth p]92Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein NOP53QA [auth q]455Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP53YPL146CLPI2CP2610
UniProt
Find proteins for Q12080 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12080 
Go to UniProtKB:  Q12080
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12080
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA2RA [auth r]261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NSA2YER126CSYGP-ORF47
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear GTP-binding protein NUG1SA [auth s]520Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUG1YER006W
UniProt
Find proteins for P40010 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40010 
Go to UniProtKB:  P40010
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40010
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP7TA [auth t]322Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RLP7RPL7YNL002CN2014
UniProt
Find proteins for P40693 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40693 
Go to UniProtKB:  P40693
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40693
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP24UA [auth u]199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RLP24YLR009W
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein RPF2VA [auth v]344Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPF2YKR081CYKR401
UniProt
Find proteins for P36160 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36160 
Go to UniProtKB:  P36160
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36160
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
Regulator of ribosome biosynthesisWA [auth w]203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRS1YOR294W
UniProt
Find proteins for Q08746 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08746 
Go to UniProtKB:  Q08746
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08746
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome assembly protein 4XA [auth x]515Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSA4YCR072CYCR72C
UniProt
Find proteins for P25382 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25382 
Go to UniProtKB:  P25382
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25382
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6YA [auth y]245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF6CDC95YPR016CLPZ15C
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
UPF0642 protein YBL028CZA [auth z]106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YBL028CYBL0423
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Probable metalloprotease ARX1DB [auth 4]593Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARX1YDR101CYD8557.10c
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
rRNA-processing protein CGR1EB [auth 5]120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CGR1YGL029W
UniProt
Find proteins for P53188 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53188 
Go to UniProtKB:  P53188
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53188
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 53
MoleculeChainsLengthOrganismImage
RDN25-1 rRNAAB [auth 1]3,396Saccharomyces cerevisiae S288C
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 54
MoleculeChainsLengthOrganismImage
RDN58-1 rRNABB [auth 2]158Saccharomyces cerevisiae S288C
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 55
MoleculeChainsLengthOrganismImage
RDN5-2 rRNACB [auth 3]121Saccharomyces cerevisiae S288C
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 58
MoleculeChainsLengthOrganismImage
ITS2-1 miscRNAFB [auth 6]232Saccharomyces cerevisiae S288C
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2017-02-01
    Changes: Database references
  • Version 1.2: 2019-12-18
    Changes: Advisory, Data collection, Database references, Derived calculations