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MolNFT v2 · #174051 · protein + RNA

Human mitochondrial ribosome in complex with mRNA and P-site tRNA

6ZSB: “Human mitochondrial ribosome in complex with mRNA and P-site tRNA”. Electron microscopy at 4.5, 4 ligands (DOL, GTP, MG). MolNFT v2 #174051 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
6ZSB
Type
protein + RNA
Length
16,597 residues
Chains
92
Method
electron microscopy
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
4.5
Source
Homo sapiens
UniProt
Q9BYC8, O75394, Q9BQ48, Q9NZE8, Q9P0J6, Q9BZE1, Q96DV4, Q9NYK5, Q9NQ50, Q8IXM3, P82930, P82673, Q96BP2, Q9NWT8, Q96EY7, Q9Y399, Q96EL2, P82675, P82932, Q9Y2R9, P82933, P82664, P82912, O15235, O60783, P82914, Q9Y3D3, Q9Y2R5, Q9Y676, Q9Y3D5, P82921, P82650, Q9Y3D9, P82663, Q9BYN8, Q92552, Q9Y2Q9, P51398, Q92665, Q9Y291, 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, P52815
Ligands
DOL, GTP, MG, ZN

Structure

electron microscopy · resolution 4.5 · 90 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
0—protein108—Q9BYC8
1—protein53—O75394
2—protein46—Q9BQ48
3—protein95—Q9NZE8
4—protein38—Q9P0J6
5—protein393—Q9BZE1
6—protein354—Q96DV4
7—protein291—Q9NYK5
8—protein139—Q9NQ50
9—protein124—Q8IXM3
XA—rna1499——
A0—protein201—P82930
A1—protein275—P82673
A2—protein116—Q96BP2
A3—protein69—Q9NWT8
A4—protein552—Q96EY7
AA—rna924——
AB—protein218—Q9Y399
AC—protein132—Q96EL2
AD—protein343—P82675
AE—protein122—P82932
AF—protein201—Q9Y2R9
AG—protein304—P82933
AH—protein135—P82664
AI—protein136—P82912
AJ—protein108—O15235
AK—protein101—O60783
AL—protein164—P82914
AM—protein116—Q9Y3D3
AN—protein107—Q9Y2R5
AO—protein185—Q9Y676
AP—protein95—Q9Y3D5
AQ—protein85—P82921
AR—protein250—P82650
AS—protein133—Q9Y3D9
AT—protein162—P82663
AU—protein173—Q9BYN8
AV—protein349—Q92552
AW—protein97—Q9Y2Q9
AX—protein348—P51398
AY—protein113—Q92665
AZ—protein86—Q9Y291
XB—rna59——
XD—protein236—Q5T653
XE—protein304—P09001
XF—protein250—Q9BYD3
XH—protein95—Q9BYD2
XI—protein211—Q7Z7H8
XJ—protein170—Q9Y3B7
XK—protein177—Q9BYD1
XL—protein115—Q6P1L8
XM—protein287—Q9P015
XN—protein221—Q9NX20
XO—protein152—Q9NRX2
XP—protein143—Q9H0U6
XQ—protein238—P49406
XR—protein140—Q9BYC9
XS—protein160—Q7Z2W9
XT—protein166—Q9NWU5
XU—protein141—Q16540
XV—protein202—Q96A35
XW—protein111—Q9P0M9
XX—protein243—Q13084
XY—protein178—Q9HD33
XZ—protein120—Q8TCC3
a—protein97—Q9Y6G3
b—protein148—Q8N983
c—protein275—Q9H9J2
d—protein216—Q9BRJ2
e—protein217—Q9H2W6
f—protein143—Q96GC5
g—protein132—Q13405
h—protein108—Q8N5N7
i—protein97—Q4U2R6
j—protein86—Q86TS9
k—protein95—Q96EL3
l—protein80—Q6P161
m—protein60—Q7Z7F7
o—protein94—Q9BQC6
p—protein127—Q14197
q—protein164—Q8TAE8
r—protein152—Q9NVS2
r1—rna4——
r3—rna75——
s—protein370—Q9NP92
t1—protein46—P52815
t2, t3—protein30—P52815
t4, t5—protein29—P52815
t6—protein27—P52815
A—protein7——

Ligands and binding sites

  • DOL · 5-(2-diethylamino-ethanesulfonyl)-21-hydroxy-10-isopropyl-11,19-dimethyl-9,26-dioxa-3,15,28-triaza-tricyclo[23.2.1.00,255]octacosa-1(27),12,17,19,25(28)-pentaene-2,8,14,23-tetraone · ligand · chains XA, r3
  • GTP · Guanosine-5'-triphosphate · ligand · chains AX
  • MG · Magnesium ion · metal · 195 copies · chains 9, XA, XF, XM, XI, XQ, XD, o, A2, AA, AH, XE, XW, g
  • ZN · Zinc ion · metal · 7 copies · chains 0, 4, AB, AO, AP, AT, XI, r

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

Compared structures

  • Q13084 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L28, mitochondrial (Q13084) · a predicted model of the same protein · chain XX against A, TM-score 0.98
  • Q8N983 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L43, mitochondrial (Q8N983) · a predicted model of the same protein · chain b against A, TM-score 0.98
  • P82650 · AlphaFold monomer V2.0 prediction for 28S ribosomal protein S22, mitochondrial (P82650) · a predicted model of the same protein · chain AR against A, TM-score 0.97
  • Q9HD33 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L47, mitochondrial (Q9HD33) · a predicted model of the same protein · chain XY against A, TM-score 0.97
  • Q8TCC3 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L30, mitochondrial (Q8TCC3) · a predicted model of the same protein · chain XZ 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
  • Q6P1L8 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L14, mitochondrial (Q6P1L8) · a predicted model of the same protein · chain XL against A, TM-score 0.97
  • Q9NWU5 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L22, mitochondrial (Q9NWU5) · a predicted model of the same protein · chain XT against A, TM-score 0.97
  • Q9Y2R5 · AlphaFold monomer V2.0 prediction for 28S ribosomal protein S17, mitochondrial (Q9Y2R5) · a predicted model of the same protein · chain AN against A, TM-score 0.96
  • Q96EY7 · AlphaFold monomer V2.0 prediction for pentatricopeptide repeat domain-containing protein… · a predicted model of the same protein · chain A4 against A, TM-score 0.94
  • 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 0.94
  • 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 0.94

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