Uniprot accession / id : P97461  OR   Uniprot accession / id : P46782  OR   Uniprot accession / id : A0A024R4Q8
 
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Entry Information
Entry status  (1)
REL
(131)
 
Experimental methods  (2)
Electron Microscopy
(130)
X-ray diffraction
(1)
 
Authors  (390)
Beckmann R
(46)
Cheng J
(45)
Berninghausen O
(35)
Ameismeier M
(30)
Thoms M
(22)
Buschauer R
(18)
Denk T
(16)
Kratzat H
(15)
Becker T
(14)
Li Y
(14)
Mackens-Kiani T
(14)
Natchiar SK
(12)
Wang M
(12)
Frohlich T
(9)
Fröhlich T
(9)
Hayn M
(9)
Hirschenberger M
(9)
Kirchhoff F
(9)
Koepke L
(9)
Myasnikov AG
(9)
Sparrer KMJ
(9)
Straub JH
(9)
Sturzel CM
(9)
Stürzel CM
(9)
Yokoyama T
(9)
Cate JHD
(8)
Chang ST
(8)
Fischer N
(8)
Huang Z
(8)
Li W
(8)
Li X
(8)
Montabana E
(8)
Petrychenko V
(8)
Rodnina MV
(8)
Ward FR
(8)
Wei Z
(8)
Yi S-H
(8)
Yi SH
(8)
Yong X
(8)
Dullea RG
(7)
Hurt E
(7)
Klaholz BP
(7)
Kutay U
(7)
Lau B
(7)
Liras S
(7)
McClure KF
(7)
Shirouzu M
(7)
Altman RB
(6)
Ban N
(6)
Blanchard SC
(6)
Fraser CS
(6)
Green R
(6)
Holm M
(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)
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)
Chaker-Margot M
(3)
Chao JA
(3)
Chen FX
(3)
Diaz-Lopez I
(3)
Diehl FF
(3)
Díaz-López I
(3)
 
More...
 
Homo / hetero assembly  (1)
hetero
(131)
 
Assembly composition  (1)
RNA/protein complex
(131)
 
Assembly polymer count  (35)
37-mer
(12)
83-mer
(11)
36-mer
(10)
35-mer
(9)
86-mer
(9)
80-mer
(8)
85-mer
(8)
81-mer
(7)
38-mer
(6)
84-mer
(6)
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)
31-mer
(1)
48-mer
(1)
49-mer
(1)
52-mer
(1)
72-mer
(1)
74-mer
(1)
75-mer
(1)
87-mer
(1)
89-mer
(1)
92-mer
(1)
hexadecamer
(1)
octadecamer
(1)
 
Resolution distribution
1.5 - 2
(4)
2.0 - 2.5
(9)
2.5 - 3
(45)
3.0 - 3.5
(38)
3.5 - 4
(26)
4.0 - 4.5
(5)
4.5 - 5
(2)
5.5 - 6
(1)
6.0 - 6.5
(1)
 
Release year distribution
2010 - 2015
(5)
2015 - 2020
(56)
2020 - 2025
(103)
2025 - 2030
(10)
 
Journal  (17)
Nature
(26)
Nat Struct Mol Biol
(17)
Science
(15)
Nat Commun
(14)
Nucleic Acids Res
(11)
Mol Cell
(9)
To be published
(8)
Cell
(5)
Cell Rep
(5)
EMBO J
(5)
Cell Res
(3)
Elife
(3)
PLoS Biol
(3)
Cancer Discov
(2)
Front Mol Biosci
(2)
J Biochem
(2)
bioRxiv
(1)
 
Macromolecules
Organism superkingdom  (1)
Eukaryota
(131)
 
Organism name  (3)
Homo sapiens
(126)
Mus musculus
(4)
Oryctolagus cuniculus
(1)
 
Molecule name  (4)
40S ribosomal protein S5
(131)
Small ribosomal subunit protein uS7
(131)
Small ribosomal subunit protein uS7, N-terminally processed
(131)
40S ribosomal protein S5, N-terminally processed
(127)
 
Molecule type  (1)
Protein
(131)
 
Gene names  (2)
RPS5
(127)
Rps5
(4)
 
Interacting Molecules  (337)
Small ribosomal subunit protein eS28
(131)
Small ribosomal subunit protein uS9
(130)
Small ribosomal subunit protein eS1
(129)
Small ribosomal subunit protein eS6
(129)
Small ribosomal subunit protein eS7
(129)
Small ribosomal subunit protein eS8
(129)
Small ribosomal subunit protein uS15
(129)
Small ribosomal subunit protein uS4
(129)
Small ribosomal subunit protein uS8
(129)
Small ribosomal subunit protein eS19
(128)
Small ribosomal subunit protein uS17
(128)
Small ribosomal subunit protein eS24
(127)
Small ribosomal subunit protein eS25
(127)
Small ribosomal subunit protein uS11
(127)
Small ribosomal subunit protein uS13
(127)
Small ribosomal subunit protein uS19
(127)
Small ribosomal subunit protein eS17
(126)
Small ribosomal subunit protein eS27
(126)
Small ribosomal subunit protein uS12
(123)
Small ribosomal subunit protein uS2
(123)
Small ribosomal subunit protein eS21
(122)
Small ribosomal subunit protein uS5
(122)
Small ribosomal subunit protein RACK1
(119)
Small ribosomal subunit protein eS4, X isoform
(119)
Small ribosomal subunit protein eS12
(118)
Small ribosomal subunit protein uS14
(118)
Small ribosomal subunit protein uS3
(118)
Small ribosomal subunit protein eS10
(117)
Small ribosomal subunit protein uS10
(117)
18S Ribosomal RNA
(114)
Small ribosomal subunit protein eS26
(105)
Small ribosomal subunit protein eS30
(105)
Small ribosomal subunit protein eS32
(98)
Ubiquitin-ribosomal protein eS31 fusion protein
(89)
Large ribosomal subunit protein eL19
(65)
Large ribosomal subunit protein eL14
(64)
Large ribosomal subunit protein eL15
(64)
Large ribosomal subunit protein eL18
(64)
Large ribosomal subunit protein eL20
(64)
Large ribosomal subunit protein eL21
(64)
Large ribosomal subunit protein eL22
(64)
Large ribosomal subunit protein eL24
(64)
Large ribosomal subunit protein eL28
(64)
Large ribosomal subunit protein eL30
(64)
Large ribosomal subunit protein eL31
(64)
Large ribosomal subunit protein eL32
(64)
Large ribosomal subunit protein eL33
(64)
Large ribosomal subunit protein eL34
(64)
Large ribosomal subunit protein eL36
(64)
Large ribosomal subunit protein eL37
(64)
Large ribosomal subunit protein eL38
(64)
Large ribosomal subunit protein eL43
(64)
Large ribosomal subunit protein eL8
(64)
Large ribosomal subunit protein uL13
(64)
Large ribosomal subunit protein uL14
(64)
Large ribosomal subunit protein uL18
(64)
Large ribosomal subunit protein uL22
(64)
Large ribosomal subunit protein uL24
(64)
Large ribosomal subunit protein uL29
(64)
Large ribosomal subunit protein uL3
(64)
Large ribosomal subunit protein uL30
(64)
Large ribosomal subunit protein uL4
(64)
Large ribosomal subunit protein uL5
(64)
Large ribosomal subunit protein uL6
(64)
Large ribosomal subunit protein eL13
(63)
Large ribosomal subunit protein eL39
(63)
Large ribosomal subunit protein eL6
(63)
Large ribosomal subunit protein uL15
(63)
Large ribosomal subunit protein uL23
(63)
Large ribosomal subunit protein eL27
(62)
Large ribosomal subunit protein eL29
(62)
Large ribosomal subunit protein uL2
(58)
28S ribosomal RNA
(57)
5.8S ribosomal RNA
(56)
5S ribosomal RNA
(56)
Large ribosomal subunit protein eL42
(55)
Ubiquitin-ribosomal protein eL40 fusion protein
(39)
Ribosomal protein uL16-like
(38)
Messenger RNA
(37)
Large ribosomal subunit protein uL1
(36)
Large ribosomal subunit protein uL10
(26)
Small ribosomal subunit protein eS31
(26)
tRNA
(22)
Large ribosomal subunit protein uL16
(21)
RNA-binding protein PNO1
(21)
Large ribosomal subunit protein uL11
(20)
Eukaryotic translation initiation factor 3 subunit A
(18)
Eukaryotic translation initiation factor 3 subunit C
(18)
Eukaryotic translation initiation factor 3 subunit D
(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)
Large ribosomal subunit protein eL40
(18)
Eukaryotic translation initiation factor 3 subunit B
(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)
Elongation factor 2
(16)
Pre-rRNA-processing protein TSR1 homolog
(16)
Proliferation-associated protein 2G4
(16)
 
More...
 
Interacting ligands  (3)
MG : MAGNESIUM ION
(27)
K : POTASSIUM ION
(4)
T1C : TIGECYCLINE
(1)
 
Function and Biology
Biological function  (5)
RNA binding
(124)
mRNA binding
(124)
structural constituent of ribosome
(124)
protein binding
(120)
rRNA binding
(120)
 
Biological process  (8)
cytoplasmic translation
(124)
regulation of translational fidelity
(124)
ribosomal small subunit biogenesis
(124)
translation
(124)
ribosomal small subunit assembly
(120)
translational initiation
(120)
translation at postsynapse
(4)
translation at presynapse
(4)
 
Biological cell component  (17)
cytoplasm
(124)
cytosol
(124)
cytosolic ribosome
(124)
cytosolic small ribosomal subunit
(124)
nucleolus
(124)
nucleus
(124)
ribonucleoprotein complex
(124)
ribosome
(124)
small-subunit processome
(124)
synapse
(124)
small ribosomal subunit
(121)
extracellular exosome
(120)
focal adhesion
(120)
membrane
(120)
nucleoplasm
(120)
postsynapse
(4)
presynapse
(4)
 
Sequence and Structure classification
CATH class  (1)
Mainly Alpha
(6)
 
CATH topology  (1)
Ribosomal Protein S7
(6)
 
Pfam accession / name  (1)
PF00177 : Ribosomal_S7
(131)
 
Experimental Information
Diffraction protocol  (1)
Single wavelength
(2)
 
Diffraction radiation source type  (1)
Synchrotron
(1)
 
Diffraction source  (1)
APS BEAMLINE 24-ID-C
(1)
 
Synchrotron site  (1)
APS
(1)
 
Diffraction detector type  (1)
Pixel
(1)
 
Refinement software  (3)
PHENIX
(25)
phenix.real_space_refine
(14)
REFMAC
(2)
 
EM microscope model  (4)
FEI TITAN KRIOS
(123)
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)
(41)
FEI FALCON II (4k x 4k)
(15)
FEI FALCON III (4k x 4k)
(13)
FEI FALCON IV (4k x 4k)
(8)
GATAN K3 BIOQUANTUM (6k x 4k)
(4)
GATAN K2 QUANTUM (4k x 4k)
(2)
FEI EAGLE (4k x 4k)
(1)
GATAN K3 BIOCONTINUUM (6k x 4k)
(1)
TVIPS TEMCAM-F416 (4k x 4k)
(1)
 
Representative Structures
Representative Structures
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95%
90%
70%
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40%
30%
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Entries 1 to 10 of 131
Entries 1 to 10 of 131
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Cryo-EM structure of the human 80S ribosome with 4 um Tigecycline
Li X, Wang M, Denk T, Cheng J
Nat Commun (2024) [PMID: 38942792  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: MG    ZN    ZN    MG   
PDBe complex ID: PDB-CPX-272331 (Preferred)   search this ID
PDBe-KB: P46782    P32969    P40429    P46779    P62753    P62081    (view 72 more)
Electron Microscopy
2.2Å resolution
Released: 10 Jul 2024
Model geometry
Fit model/data
Data not analysed
8yop
8yop
8yop
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: P46782    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
80S ribosome from mouse bound to eEF2 (Class I)
Loerch S, Smith PR, Kunder N, Stanowick AD, Lou T-F, Campbell ZT
Nat Commun (2021) [PMID: 34815424  ]
Source organism: Mus musculus  
Assembly composition: RNA/protein complex
Bound ligands: GDP    MG    ZN    ZN    GDP    MG   
Modified residues: 4AC    A2M    B8N    B8Q    B8W    E7G    MLZ    OMC    OMG    5MC    6MZ    B9H    OMU    G7M    P7G    5MC    DDE    E6G    G7M    I4U    MHG    UR3    2MG    4AC    6MZ    A2M    1MA    MLZ    1MA    2MG    B8T    B9B    DDE    PSU    PSU    OMC    OMG    OMU    UR3   
PDBe complex ID: PDB-CPX-236911 (Preferred)   search this ID
PDBe-KB: P97461    Q9CY58    Q9CZX8    Q9D8E6    P62855    Q6ZWN5    (view 74 more)
Electron Microscopy
3.1Å resolution
Released: 3 Nov 2021
Model geometry
Fit model/data
Data not analysed
7ls2
7ls2
7ls2
mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state)
Holm M, Natchiar KS, Rundlet EJ, Myasnikov AG, 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    ZN    3H3    MG    MET    MET    PUT   
Modified residues: 4AC    4SU    A2M    AME    B8N    H2U    M3L    MLZ    OMC    OMG    UY1    5CT    5MC    6MZ    HIC    OMU    SAC    UY1    G7M    4SU    5MC    G7M    H2U    HY3    HY3    UR3    4AC    6MZ    A2M    MA6    SAC    1MA    HIC    MLZ    V5N    1MA    5CT    M3L    PSU    PSU    AME    MA6    OMC    OMG    OMU    UR3   
PDBe complex ID: PDB-CPX-271328 (Preferred)   search this ID
PDBe-KB: P46782    P32969    P40429    P46779    P62753    P62081    (view 67 more)
Electron Microscopy
2.29Å resolution
Released: 19 Apr 2023
Model geometry
Fit model/data
Data not analysed
8g5y
8g5y
8g5y
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: P46782    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
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: P46782    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
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: P46782    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
mRNA decoding in human is kinetically and structurally distinct from bacteria (CR state)
Holm M, Natchiar KS, Rundlet EJ, Myasnikov AG, Altman RB, Blanchard SC
Nature (2023) [PMID: 37020024  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: 3H3    K    PHE    SPD    K    MG    PHE    ANM    ANM    ZN    GSP    GSP    ZN    3H3    MG    ZIY    MET    MET    PUT    ZIY   
Modified residues: 4AC    4SU    A2M    AME    B8N    H2U    M3L    MIA    MLZ    OMC    OMG    UY1    5MC    6MZ    HIC    OMU    SAC    UY1    G7M    4SU    5MC    G7M    H2U    HY3    HY3    MLY    UR3    4AC    6MZ    A2M    MA6    MLY    SAC    1MA    HIC    MIA    MLZ    V5N    1MA    M3L    PSU    PSU    AME    MA6    OMC    OMG    OMU    UR3   
PDBe complex ID: PDB-CPX-271325 (Preferred)   search this ID
PDBe-KB: P46782    P32969    P40429    P46779    P62753    P62081    (view 70 more)
Electron Microscopy
2.54Å resolution
Released: 19 Apr 2023
Model geometry
Fit model/data
Data not analysed
8g60
8g60
8g60
Cryo-EM structure of the human 40S ribosome with PDCD4 and eIF3G
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-271866 (Preferred)   search this ID
PDBe-KB: P46782    P62753    P62081    P60866    P62979    Q53EL6    (view 30 more)
Electron Microscopy
3.2Å resolution
Released: 1 May 2024
Model geometry
Fit model/data
Data not analysed
8xxm
8xxm
8xxm
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: P46782    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
...
Entries 1 to 10 of 131
Entries 1 to 10 of 131