8XP3

Cryo-EM structure of the human 40S ribosome with LARP1 and LRRC47

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

LARP1 binds ribosomes and TOP mRNAs in repressed complexes

Saba, J.A., Huang, Z., Schole, K.L., Ye, X., Bhatt, S.D., Li, Y., Timp, W., Cheng, J., Green, R.

(2024) EMBO J 


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41A [auth Ln]25Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAC [auth SA]295Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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UniProt GroupP08865
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aD [auth SB]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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UniProt GroupP61247
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3E [auth SD]243Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformF [auth SE]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5G [auth SF]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7H [auth SH]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8I [auth SI]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10J [auth SK]165Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11K [auth SL]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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UniProt GroupP62280
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15L [auth SP]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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UniProt GroupP62841
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16M [auth SQ]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17N [auth SR]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18O [auth SS]152Homo sapiensMutation(s): 0 
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Find proteins for P62269 (Homo sapiens)
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GTEx:  ENSG00000231500 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19P [auth ST]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20Q [auth SU]119Homo sapiensMutation(s): 0 
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Find proteins for P60866 (Homo sapiens)
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GTEx:  ENSG00000008988 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21R [auth SV]83Homo sapiensMutation(s): 0 
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Find proteins for P63220 (Homo sapiens)
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GTEx:  ENSG00000171858 
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UniProt GroupP63220
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23S [auth SX]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26T [auth Sa]115Homo sapiensMutation(s): 0 
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Find proteins for P62854 (Homo sapiens)
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GTEx:  ENSG00000197728 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28U [auth Sc]69Homo sapiensMutation(s): 0 
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Find proteins for P62857 (Homo sapiens)
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GTEx:  ENSG00000233927 
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UniProt GroupP62857
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29V [auth Sd]56Homo sapiensMutation(s): 0 
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Find proteins for P62273 (Homo sapiens)
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GTEx:  ENSG00000213741 
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UniProt GroupP62273
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1W [auth Sg]317Homo sapiensMutation(s): 0 
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Find proteins for P63244 (Homo sapiens)
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GTEx:  ENSG00000204628 
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UniProt GroupP63244
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2X [auth SC]293Homo sapiensMutation(s): 0 
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Find proteins for P15880 (Homo sapiens)
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GTEx:  ENSG00000140988 
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UniProt GroupP15880
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6Y [auth SG]249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9Z [auth SJ]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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UniProt GroupP46781
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12AA [auth SM]132Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13BA [auth SN]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14CA [auth SO]151Homo sapiensMutation(s): 0 
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Find proteins for P62263 (Homo sapiens)
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GTEx:  ENSG00000164587 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aDA [auth SW]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24EA [auth SY]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25FA [auth SZ]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27GA [auth Sb]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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UniProt GroupP42677
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30HA [auth Se]59Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aIA [auth Sf]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
La-related protein 1JA [auth JD]1,096Homo sapiensMutation(s): 0 
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Find proteins for Q6PKG0 (Homo sapiens)
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PHAROS:  Q6PKG0
GTEx:  ENSG00000155506 
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UniProt GroupQ6PKG0
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-rich repeat-containing protein 47KA [auth JC]583Homo sapiensMutation(s): 0 
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Find proteins for Q8N1G4 (Homo sapiens)
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PHAROS:  Q8N1G4
GTEx:  ENSG00000130764 
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UniProt GroupQ8N1G4
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Entity ID: 2
MoleculeChains LengthOrganismImage
18S rRNAB [auth S2]1,869Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release