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MolNFT v2 · #189275 · protein + RNA

Structure of mature human mitochondrial ribosome large subunit in complex with GTPBP6 (PTC conformation 1).

7OF4: “Structure of mature human mitochondrial ribosome large subunit in complex with GTPBP6 (PTC conformation 1).”. Electron microscopy at 2.7, 3 ligands (GTP, MG, ZN). MolNFT v2 #189275 on GenesisL1: 3D structure, binding sites and…

PDB
7OF4
Type
protein + RNA
Length
9,841 residues
Chains
53
Method
electron microscopy
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
2.7
Source
Homo sapiens
UniProt
Q9BYC8, O75394, Q9BQ48, Q9NZE8, Q9P0J6, Q9BZE1, Q96DV4, Q9NYK5, Q9NQ50, Q8IXM3, O43824, Q5T653, P09001, Q9BYD3, Q9BYD2, Q7Z7H8, Q9Y3B7, Q9BYD1, Q6P1L8, Q9P015, Q9NX20, Q9NRX2, Q9H0U6, P49406, Q9BYC9, Q7Z2W9, Q9NWU5, Q16540, Q96A35, Q9P0M9, Q13084, Q9HD33, Q8TCC3, Q9Y6G3, Q8N983, Q9H9J2, Q9BRJ2, Q9H2W6, Q96GC5, Q13405, Q8N5N7, Q4U2R6, Q86TS9, Q96EL3, Q6P161, Q7Z7F7, Q9BQC6, Q14197, Q8TAE8, Q9NVS2, Q9NP92
Ligands
GTP, MG, ZN

Structure

electron microscopy · resolution 2.7 · 53 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
0—protein108—Q9BYC8
1—protein52—O75394
2—protein45—Q9BQ48
3—protein95—Q9NZE8
4—protein37—Q9P0J6
5—protein392—Q9BZE1
6—protein324—Q96DV4
7—protein287—Q9NYK5
8—protein77—Q9NQ50
9—protein117—Q8IXM3
A—rna1465——
B—rna56——
C—protein422—O43824
D—protein236—Q5T653
E—protein305—P09001
F—protein250—Q9BYD3
H—protein95—Q9BYD2
I—protein158—Q7Z7H8
J—protein140—Q9Y3B7
K—protein177—Q9BYD1
L—protein115—Q6P1L8
M—protein287—Q9P015
N—protein205—Q9NX20
O—protein152—Q9NRX2
P—protein141—Q9H0U6
Q—protein217—P49406
R—protein140—Q9BYC9
S—protein156—Q7Z2W9
T—protein166—Q9NWU5
U—protein139—Q16540
V—protein191—Q96A35
W—protein109—Q9P0M9
X—protein243—Q13084
Y—protein176—Q9HD33
Z—protein120—Q8TCC3
a—protein82—Q9Y6G3
b—protein148—Q8N983
c—protein275—Q9H9J2
d—protein208—Q9BRJ2
e—protein197—Q9H2W6
f—protein105—Q96GC5
g—protein129—Q13405
h—protein105—Q8N5N7
i—protein97—Q4U2R6
j—protein84—Q86TS9
k—protein80—Q96EL3
l—protein23—Q6P161
m—protein45—Q7Z7F7
o—protein94—Q9BQC6
p—protein127—Q14197
q—protein120—Q8TAE8
r—protein157—Q9NVS2
s—protein370—Q9NP92

Ligands and binding sites

  • GTP · Guanosine-5'-triphosphate · ligand · chains C
  • MG · Magnesium ion · metal · 89 copies · chains A, Q, T, W, o, C, E, g
  • ZN · Zinc ion · metal · 3 copies · chains 0, 4, I, r

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Compared structures

  • P49406 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L19, mitochondrial (P49406) · a predicted model of the same protein · chain Q against A, TM-score 0.99
  • Q13084 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L28, mitochondrial (Q13084) · a predicted model of the same protein · chain X against A, TM-score 0.99
  • Q6P1L8 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L14, mitochondrial (Q6P1L8) · a predicted model of the same protein · chain L against A, TM-score 0.98
  • Q8TCC3 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L30, mitochondrial (Q8TCC3) · a predicted model of the same protein · chain Z against A, TM-score 0.98
  • Q9HD33 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L47, mitochondrial (Q9HD33) · a predicted model of the same protein · chain Y against A, TM-score 0.98
  • Q9NWU5 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L22, mitochondrial (Q9NWU5) · a predicted model of the same protein · chain T against A, TM-score 0.97
  • Q13405 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L49, mitochondrial (Q13405) · a predicted model of the same protein · chain g against A, TM-score 0.97
  • Q9NZE8 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L35, mitochondrial (Q9NZE8) · a predicted model of the same protein · chain 3 against A, TM-score 0.97
  • Q8N5N7 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L50, mitochondrial (Q8N5N7) · a predicted model of the same protein · chain h against A, TM-score 0.96
  • O43824 · AlphaFold monomer V2.0 prediction for putative GTP-binding protein 6 (O43824) · a predicted model of the same protein · chain C against A, TM-score 0.94
  • Q96GC5 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L48, mitochondrial (Q96GC5) · a predicted model of the same protein · chain f against A, TM-score 0.93
  • Q8IXM3 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L41, mitochondrial (Q8IXM3) · a predicted model of the same protein · chain 9 against A, TM-score 0.93

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