Uniprot accession / id : P35545  OR   Uniprot accession / id : P62862  OR   Uniprot accession / id : P35544  OR   Uniprot accession / id : P62861
 
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Entry Information
Entry status  (1)
REL
(126)
 
Experimental methods  (3)
Electron Microscopy
(124)
Solution NMR
(1)
X-ray diffraction
(1)
 
Authors  (391)
Beckmann R
(45)
Cheng J
(44)
Berninghausen O
(36)
Ameismeier M
(31)
Thoms M
(23)
Buschauer R
(18)
Denk T
(16)
Kratzat H
(15)
Becker T
(14)
Mackens-Kiani T
(14)
Li Y
(12)
Natchiar SK
(11)
Wang M
(10)
Frohlich T
(9)
Fröhlich T
(9)
Hayn M
(9)
Hirschenberger M
(9)
Kirchhoff F
(9)
Koepke L
(9)
Sparrer KMJ
(9)
Straub JH
(9)
Sturzel CM
(9)
Stürzel CM
(9)
Yokoyama T
(9)
Fischer N
(8)
Hurt E
(8)
Lau B
(8)
Li X
(8)
Montabana E
(8)
Myasnikov AG
(8)
Petrychenko V
(8)
Rodnina MV
(8)
Wei Z
(8)
Yi S-H
(8)
Yi SH
(8)
Yong X
(8)
Cate JHD
(7)
Chang ST
(7)
Dullea RG
(7)
Kutay U
(7)
Li W
(7)
Liras S
(7)
McClure KF
(7)
Shirouzu M
(7)
Ward FR
(7)
Altman RB
(6)
Ban N
(6)
Blanchard SC
(6)
Fraser CS
(6)
Holm M
(6)
Huang Z
(6)
Klaholz BP
(6)
Leibundgut M
(6)
Liedtke D
(6)
Natchiar KS
(6)
Peng BZ
(6)
Rundlet EJ
(6)
Sokabe M
(6)
Taunton J
(6)
Wang HY
(6)
Watson ZL
(6)
van den Heuvel J
(6)
Brito Querido J
(5)
Gordiyenko Y
(5)
Ramakrishnan V
(5)
Ye X
(5)
Zemp I
(5)
Akichika S
(4)
Best K
(4)
Green R
(4)
Irie T
(4)
Ishibashi K
(4)
Ishiguro K
(4)
Iwasaki S
(4)
Karousis ED
(4)
Ma D
(4)
Matsuzawa I
(4)
Mishima Y
(4)
Mito M
(4)
Muehlemann O
(4)
Muhlemann O
(4)
Mühlemann O
(4)
Saito H
(4)
Sakaguchi Y
(4)
Scaiola A
(4)
Schubert K
(4)
Suzuki T
(4)
Wakabayashi K
(4)
Zhao X
(4)
von Loeffelholz O
(4)
Artus-Revel CG
(3)
Bhaskar V
(3)
Bretones G
(3)
Cavadini S
(3)
Chao JA
(3)
Diaz-Lopez I
(3)
Díaz-López I
(3)
Fraser C
(3)
Gilbert W
(3)
Graff-Meyer A
(3)
 
More...
 
Homo / hetero assembly  (2)
hetero
(125)
homo
(1)
 
Assembly composition  (3)
RNA/protein complex
(124)
protein structure
(1)
protein/protein complex
(1)
 
Assembly polymer count  (35)
36-mer
(10)
37-mer
(10)
83-mer
(10)
35-mer
(9)
86-mer
(9)
85-mer
(8)
80-mer
(7)
81-mer
(7)
84-mer
(6)
38-mer
(5)
50-mer
(4)
51-mer
(4)
54-mer
(4)
34-mer
(3)
79-mer
(3)
82-mer
(3)
33-mer
(2)
53-mer
(2)
57-mer
(2)
78-mer
(2)
88-mer
(2)
171-mer
(1)
172-mer
(1)
22-mer
(1)
23-mer
(1)
26-mer
(1)
31-mer
(1)
48-mer
(1)
49-mer
(1)
52-mer
(1)
87-mer
(1)
89-mer
(1)
92-mer
(1)
dimer
(1)
monomer
(1)
 
Resolution distribution
1.5 - 2
(4)
2.0 - 2.5
(10)
2.5 - 3
(43)
3.0 - 3.5
(39)
3.5 - 4
(21)
4.0 - 4.5
(5)
4.5 - 5
(2)
6.0 - 6.5
(1)
 
Release year distribution
2010 - 2015
(6)
2015 - 2020
(53)
2020 - 2025
(99)
2025 - 2030
(8)
 
Journal  (18)
Nature
(26)
Nat Struct Mol Biol
(17)
Nat Commun
(12)
Nucleic Acids Res
(12)
Science
(12)
To be published
(9)
Mol Cell
(7)
Cell
(5)
EMBO J
(5)
Cell Rep
(4)
Cell Res
(3)
Elife
(3)
PLoS Biol
(3)
Cancer Discov
(2)
Front Mol Biosci
(2)
J Biochem
(2)
Nat Chem Biol
(1)
bioRxiv
(1)
 
Macromolecules
Organism superkingdom  (1)
Eukaryota
(126)
 
Organism name  (3)
Homo sapiens
(121)
Mus musculus
(4)
Oryctolagus cuniculus
(1)
 
Molecule name  (6)
40S ribosomal protein S30
(126)
Small ribosomal subunit protein eS30
(126)
Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
(126)
Ubiquitin-like protein FUBI
(126)
FAU ubiquitin like and ribosomal protein S30 fusion
(122)
FAU ubiquitin-like and ribosomal protein S30
(4)
 
Molecule type  (1)
Protein
(126)
 
Gene names  (2)
FAU
(122)
Fau
(4)
 
Interacting Molecules  (281)
Small ribosomal subunit protein eS1
(124)
Small ribosomal subunit protein eS6
(124)
Small ribosomal subunit protein eS7
(124)
Small ribosomal subunit protein eS8
(124)
Small ribosomal subunit protein uS15
(124)
Small ribosomal subunit protein uS4
(124)
Small ribosomal subunit protein uS8
(124)
Small ribosomal subunit protein uS17
(123)
Small ribosomal subunit protein eS24
(122)
Small ribosomal subunit protein uS11
(122)
Small ribosomal subunit protein eS27
(121)
Small ribosomal subunit protein eS28
(121)
Small ribosomal subunit protein uS7
(121)
Small ribosomal subunit protein eS19
(120)
Small ribosomal subunit protein eS25
(120)
Small ribosomal subunit protein uS13
(120)
Small ribosomal subunit protein uS19
(120)
Small ribosomal subunit protein uS2
(120)
Small ribosomal subunit protein uS9
(120)
Small ribosomal subunit protein eS21
(119)
Small ribosomal subunit protein uS5
(119)
Small ribosomal subunit protein eS17
(118)
Small ribosomal subunit protein uS12
(118)
Small ribosomal subunit protein eS4, X isoform
(115)
Small ribosomal subunit protein RACK1
(112)
Small ribosomal subunit protein uS14
(111)
Small ribosomal subunit protein uS3
(111)
Small ribosomal subunit protein eS10
(110)
Small ribosomal subunit protein uS10
(110)
Small ribosomal subunit protein eS12
(108)
18S Ribosomal RNA
(107)
Small ribosomal subunit protein eS26
(104)
Small ribosomal subunit protein eS32
(97)
Ubiquitin-ribosomal protein eS31 fusion protein
(84)
Large ribosomal subunit protein eL19
(63)
Large ribosomal subunit protein eL14
(62)
Large ribosomal subunit protein eL15
(62)
Large ribosomal subunit protein eL18
(62)
Large ribosomal subunit protein eL20
(62)
Large ribosomal subunit protein eL21
(62)
Large ribosomal subunit protein eL22
(62)
Large ribosomal subunit protein eL24
(62)
Large ribosomal subunit protein eL28
(62)
Large ribosomal subunit protein eL30
(62)
Large ribosomal subunit protein eL31
(62)
Large ribosomal subunit protein eL32
(62)
Large ribosomal subunit protein eL33
(62)
Large ribosomal subunit protein eL34
(62)
Large ribosomal subunit protein eL36
(62)
Large ribosomal subunit protein eL37
(62)
Large ribosomal subunit protein eL38
(62)
Large ribosomal subunit protein eL43
(62)
Large ribosomal subunit protein eL8
(62)
Large ribosomal subunit protein uL13
(62)
Large ribosomal subunit protein uL14
(62)
Large ribosomal subunit protein uL18
(62)
Large ribosomal subunit protein uL22
(62)
Large ribosomal subunit protein uL24
(62)
Large ribosomal subunit protein uL29
(62)
Large ribosomal subunit protein uL3
(62)
Large ribosomal subunit protein uL30
(62)
Large ribosomal subunit protein uL4
(62)
Large ribosomal subunit protein uL5
(62)
Large ribosomal subunit protein uL6
(62)
Large ribosomal subunit protein eL13
(61)
Large ribosomal subunit protein eL29
(61)
Large ribosomal subunit protein eL39
(61)
Large ribosomal subunit protein eL6
(61)
Large ribosomal subunit protein uL15
(61)
Large ribosomal subunit protein uL23
(61)
Large ribosomal subunit protein eL27
(60)
Large ribosomal subunit protein uL2
(56)
28S ribosomal RNA
(55)
5.8S ribosomal RNA
(54)
5S ribosomal RNA
(54)
Large ribosomal subunit protein eL42
(53)
Ubiquitin-ribosomal protein eL40 fusion protein
(38)
Messenger RNA
(37)
Ribosomal protein uL16-like
(36)
Large ribosomal subunit protein uL1
(35)
Large ribosomal subunit protein uL10
(26)
Small ribosomal subunit protein eS31
(24)
tRNA
(22)
Large ribosomal subunit protein uL16
(21)
Large ribosomal subunit protein uL11
(20)
Eukaryotic translation initiation factor 3 subunit C
(19)
Eukaryotic translation initiation factor 3 subunit A
(18)
Eukaryotic translation initiation factor 3 subunit E
(18)
Eukaryotic translation initiation factor 3 subunit L
(18)
Eukaryotic translation initiation factor 3 subunit M
(18)
Eukaryotic translation initiation factor 3 subunit B
(17)
Eukaryotic translation initiation factor 3 subunit D
(17)
Eukaryotic translation initiation factor 3 subunit F
(17)
Eukaryotic translation initiation factor 3 subunit H
(17)
Eukaryotic translation initiation factor 3 subunit K
(17)
Large ribosomal subunit protein eL40
(17)
RNA-binding protein PNO1
(17)
Elongation factor 2
(16)
Proliferation-associated protein 2G4
(16)
Eukaryotic translation initiation factor 1A, X-chromosomal
(15)
 
More...
 
Interacting ligands  (1)
AYE : prop-2-en-1-amine
(1)
 
Function and Biology
Biological function  (5)
structural constituent of ribosome
(116)
protein binding
(16)
RNA binding
(12)
protein tag activity
(12)
ubiquitin protein ligase binding
(12)
 
Biological process  (8)
translation
(116)
antibacterial humoral response
(16)
antimicrobial humoral immune response mediated by antimicrobial peptide
(16)
cytoplasmic translation
(16)
defense response to Gram-positive bacterium
(16)
innate immune response in mucosa
(16)
modification-dependent protein catabolic process
(12)
protein ubiquitination
(12)
 
Biological cell component  (10)
ribosome
(116)
cytoplasm
(16)
cytosol
(16)
cytosolic ribosome
(16)
cytosolic small ribosomal subunit
(16)
extracellular space
(16)
nucleus
(16)
ribonucleoprotein complex
(16)
nucleoplasm
(12)
small ribosomal subunit
(12)
 
Sequence and Structure classification
CATH class  (1)
Alpha Beta
(1)
 
CATH topology  (1)
Ubiquitin-like (UB roll)
(1)
 
Pfam accession / name  (2)
PF04758 : Ribosomal_S30
(124)
PF00240 : ubiquitin
(18)
 
Experimental Information
Diffraction protocol  (1)
Single wavelength
(2)
 
Diffraction radiation source type  (1)
Synchrotron
(1)
 
Diffraction source  (1)
SLS BEAMLINE X10SA
(1)
 
Synchrotron site  (1)
SLS
(1)
 
Diffraction detector type  (1)
Pixel
(1)
 
Refinement software  (3)
PHENIX
(26)
phenix.real_space_refine
(15)
REFMAC
(2)
 
EM microscope model  (4)
FEI TITAN KRIOS
(117)
FEI TECNAI ARCTICA
(3)
JEOL CRYO ARM 300
(3)
TFS KRIOS
(2)
 
EM detector name  (10)
GATAN K2 SUMMIT (4k x 4k)
(45)
GATAN K3 (6k x 4k)
(38)
FEI FALCON II (4k x 4k)
(14)
FEI FALCON III (4k x 4k)
(13)
FEI FALCON IV (4k x 4k)
(8)
GATAN K2 QUANTUM (4k x 4k)
(2)
GATAN K3 BIOQUANTUM (6k x 4k)
(2)
FEI EAGLE (4k x 4k)
(1)
GATAN K3 BIOCONTINUUM (6k x 4k)
(1)
TVIPS TEMCAM-F416 (4k x 4k)
(1)
 
NMR
NMR software packages  (7)
CNS
(1)
CYANA
(1)
FMC
(1)
NMRPipe
(1)
PSVS
(1)
Sparky
(1)
TALOS
(1)
 
NMR Field Strength
500.0 - 600
(1)
600.0 - 700
(1)
700.0 - 800
(1)
800.0 - 900
(1)
 
Representative Structures
Representative Structures
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95%
90%
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Entries 1 to 10 of 126
Entries 1 to 10 of 126
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In situ human top-back di-ribosome structure (Composite map)
Wei Z, Yong Z
To be published
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: MG    ZN    ZN    MG   
Modified residues: N    N   
PDBe complex ID: PDB-CPX-290437 (Preferred)   search this ID
PDBe-KB: P62861    P32969    P40429    P46779    P62753    P62081    (view 73 more)
Electron Microscopy
3.2Å resolution
Released: 19 Mar 2025
Model geometry
Fit model/data
Data not analysed
9b0q
9b0q
9b0q
mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus LSU focused refined structure)
Holm M, Natchiar KS, Rundlet EJ, Myasnikov AG, Watson ZL, Altman RB, Blanchard SC
Nature (2023) [PMID: 37020024  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: 3H3    K    SPD    K    MG    ANM    ANM    ZN    TRS    ZN    3H3    MG    MET    MET    PUT    TRS   
Modified residues: 4AC    4SU    A2M    AME    B8N    H2U    M3L    MLZ    OMC    OMG    UY1    5MC    6MZ    HIC    OMU    SAC    UY1    G7M    4SU    5MC    G7M    H2U    HY3    HY3    UR3    4AC    6MZ    A2M    MA6    SAC    1MA    HIC    MLZ    V5N    1MA    M3L    PSU    PSU    AME    MA6    OMC    OMG    OMU    UR3   
PDBe complex ID: PDB-CPX-271330 (Preferred)   search this ID
PDBe-KB: P62861    P32969    P40429    P46779    P62753    P62081    (view 66 more)
Electron Microscopy
1.67Å resolution
Released: 19 Apr 2023
Model geometry
Fit model/data
Data not analysed
8glp
8glp
8glp
dormant ribosome with eIF5A, eEF2 and SERBP1
Du M, Zeng F
Front Mol Biosci (2024) [PMID: 38698775  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: MG    ZN    ZN    MG   
PDBe complex ID: PDB-CPX-272439 (Preferred)   search this ID
PDBe-KB: P62861    P32969    P40429    P46779    P62753    P62081    (view 71 more)
Electron Microscopy
3.4Å resolution
Released: 7 Feb 2024
Model geometry
Fit model/data
Data not analysed
8y0w
8y0w
8y0w
Arbekacin-added human 80S ribosome
Tomono J, Asano K, Chiashi T, Tanaka Y, Yokoyama T
J Biochem (2024) [PMID: 38227611  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: 84G    MG    ZN    84G    ZN    MG   
Modified residues: MLZ    MLZ   
PDBe complex ID: PDB-CPX-272442 (Preferred)   search this ID
PDBe-KB: P62861    P60866    P32969    P40429    P46779    P62081    (view 70 more)
Electron Microscopy
2.57Å resolution
Released: 14 Feb 2024
Model geometry
Fit model/data
Data not analysed
8ife
8ife
8ife
In situ human Hibernating class3 80S ribosome
Wei Z, Yong X
To be published
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: MG    ZN    ZN    MG   
PDBe complex ID: PDB-CPX-290433 (Preferred)   search this ID
PDBe-KB: P62861    P32969    P40429    P46779    P62753    P62081    (view 72 more)
Electron Microscopy
2.78Å resolution
Released: 19 Mar 2025
Model geometry
Fit model/data
Data not analysed
9b0f
9b0f
9b0f
Structure of human 48S translation initiation complex upon transfer of initiator tRNA to eIF5B (48S-3)
Petrychenko V, Yi S-H, Liedtke D, Peng BZ, Rodnina MV, Fischer N
Nat Struct Mol Biol (2024) [PMID: 39289545  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: MG    ZN    GTP    NA    ZN    GTP    MG    NA   
Modified residues: A2M    B8N    OMC    OMG    5MC    6MZ    OMU    5MC    UR3    5MU    5MU    6MZ    A2M    MA6    PSU    PSU    JMH    MA6    OMC    OMG    OMU    UR3   
PDBe complex ID: PDB-CPX-249643 (Preferred)   search this ID
PDBe-KB: P62861    Q7L2H7    P62081    P62753    P60866    P62979    (view 45 more)
Electron Microscopy
3.7Å resolution
Released: 14 Aug 2024
Model geometry
Fit model/data
Data not analysed
8pj3
8pj3
8pj3
MERS-CoV Nsp1 protein bound to the Human 40S Ribosomal subunit
Devarkar SC, Xiong Y
Cell Rep (2023) [PMID: 37733586  ]
Assembly composition: RNA/protein complex
Bound ligands: MG    ZN    ZN    MG   
Assembly name: MERS-CoV 3'-5' exoribonuclease proof-reading complex and RNA (Preferred)   search this complex
PDBe complex ID: PDB-CPX-271381 (Preferred)   search this ID
PDBe-KB: P62861    P62753    P62081    P60866    P62979    P46781    (view 29 more)
Electron Microscopy
2.6Å resolution
Released: 4 Oct 2023
Model geometry
Fit model/data
Data not analysed
8t4s
8t4s
8t4s
Cryo-EM structure of the human 43S ribosome with PDCD4
Ye X, Huang Z, Li Y, Wang M, Cheng J
Cell Res (2024) [PMID: 38641729  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: MG    ZN    ZN    MG   
PDBe complex ID: PDB-CPX-271448 (Preferred)   search this ID
PDBe-KB: P62861    Q14152    Q7L2H7    P62753    P62081    P60866    (view 43 more)
Electron Microscopy
3.6Å resolution
Released: 1 May 2024
Model geometry
Fit model/data
Data not analysed
8xxn
8xxn
8xxn
In situ human hibernating class2 80S ribosome
Wei Z, Yong X
To be published
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: MG    ZN    ZN    MG   
PDBe complex ID: PDB-CPX-290432 (Preferred)   search this ID
PDBe-KB: P62861    P32969    P40429    P46779    P62753    P62081    (view 73 more)
Electron Microscopy
2.81Å resolution
Released: 19 Mar 2025
Model geometry
Fit model/data
Data not analysed
9b0r
9b0r
9b0r
Dibekacin-added human 80S ribosome
Tomono J, Asano K, Chiashi T, Tanaka Y, Yokoyama T
J Biochem (2024) [PMID: 38227611  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: 84D    MG    ZN    ZN    84D    MG   
Modified residues: MLZ    MLZ   
PDBe complex ID: PDB-CPX-272441 (Preferred)   search this ID
PDBe-KB: P62861    P60866    P32969    P40429    P46779    P62081    (view 70 more)
Electron Microscopy
2.59Å resolution
Released: 14 Feb 2024
Model geometry
Fit model/data
Data not analysed
8ifd
8ifd
8ifd
...
Entries 1 to 10 of 126
Entries 1 to 10 of 126