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Entry Information
Entry status
(1)
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
Entries
Macromolecules
Compounds
Protein families
...
Entries 1 to 10 of 131
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Cryo-EM structure of the human 80S ribosome with 4 um Tigecycline
In situ human top-back di-ribosome structure (Composite map)
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
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
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
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
In situ human hibernating class2 80S ribosome
dormant ribosome with eIF5A, eEF2 and SERBP1
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
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
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
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
Cryo-EM structure of the human 40S ribosome with PDCD4 and eIF3G
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
PDBe complex ID:
PDB-CPX-272442 (Preferred)
search this ID
...
Entries 1 to 10 of 131