GL1X · GenesisL1 explorer

MolNFT v2 · #179779 · protein + DNA

TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED)

7ENA: “TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED)”. Electron microscopy at 4.07, 3 ligands (SF4, ZN, MG). MolNFT v2 #179779 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
7ENA
Type
protein + DNA
Length
21,733 residues
Chains
76
Method
electron microscopy
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
4.07
Source
Homo sapiens; Sus scrofa; SYNTHETIC CONSTRUCT
UniProt
P51948, P50613, P51946, P52657, P20226, Q00403, P35269, P13984, A0A4X1TVZ5, I3LCH3, A0A481BYI6, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1ULF2, P60899, A0A4X1UK25, A0A4X1TRS6, P21675, Q6P1X5, O00268, Q15542, P49848, Q15545, Q7Z7C8, Q16594, Q12962, Q16514, Q5VWG9, Q15544, Q15543, P29083, P29084, P32780, Q13888, Q13889, Q92759, Q6ZYL4, P19447, P18074, Q6P2C8, Q9H204, Q9NX70, Q96HR3, Q9Y3C7, Q15648, Q9NPJ6, O75586, O43513, Q96G25, Q9NWA0, Q9BTT4, Q9P086, O60244, Q96RN5, Q9NVC6, Q9BUE0, A0JLT2, Q9H944, Q13503, Q15528, O95402, O75448, Q9ULK4, Q9Y2X0
Ligands
SF4, ZN, MG

Structure

electron microscopy · resolution 4.07 · 76 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
0—protein306—P51948
8—protein299—P50613
9—protein287—P51946
DO—protein97—P52657
DP—protein177—P20226
DQ—protein122——
BA—protein255—Q00403
FA—protein134—P35269
FB—protein222—P13984
PA—protein1475——
PB—protein1134—A0A4X1TVZ5
PC—protein257—I3LCH3
PD—protein129—A0A481BYI6
PE—protein209—A0A4X1VTX4
PF—protein79—A0A4X1VEK9
PG—protein171—A0A4X1VKG7
PH—protein148—A0A4X1ULF2
PI—protein114—P60899
PJ—protein64——
PK—protein117—A0A4X1UK25
PL—protein44—A0A4X1TRS6
DA—protein600—P21675
DB—protein963—Q6P1X5
DD—protein159—O00268
DE—protein546—Q15542
DF—protein408—P49848
DG—protein145—Q15545
DH—protein209—Q7Z7C8
DI—protein120—Q16594
DJ—protein90—Q12962
DL—protein75—Q16514
Dc—protein127—Q5VWG9
Dd—protein158—O00268
De—protein539—Q15542
Df—protein403—P49848
Di—protein121—Q16594
Dj—protein95—Q12962
Dk—protein98—Q15544
Dl—protein107—Q16514
Dm—protein87—Q15543
EA—protein179—P29083
EB—protein172—P29084
1—protein433—P32780
2—protein385—Q13888
3—protein295—Q13889
4—protein457—Q92759
5—protein66—Q6ZYL4
6—protein652—P19447
7—protein732—P18074
c—protein263—Q6P2C8
e—protein102—Q9H204
b—protein115—Q9NX70
l—protein126—Q96HR3
m—protein112—Q9Y3C7
a—protein469—Q15648
d—protein158—Q9NPJ6
f—protein167—O75586
g—protein166—O43513
h—protein190—Q96G25
i—protein73—Q9NWA0
j—protein122—Q9BTT4
k—protein112—Q9P086
n—protein994—O60244
o—protein156—Q96RN5
q—protein555—Q9NVC6
r—protein206—Q9BUE0
s—protein81—A0JLT2
t—protein193—Q9H944
u—protein107—Q13503
v—protein134—Q15528
z—protein97—O95402
x—protein896—O75448
w—protein1334—Q9ULK4
p—protein406—Q9Y2X0
X—dna69——
Y—dna69——

Ligands and binding sites

  • SF4 · Iron/sulfur cluster · ligand · chains 7
  • ZN · Zinc ion · metal · 16 copies · chains 0, BA, PA, PB, PC, PI, PJ, PL, EA, 2, 1, 3
  • MG · Magnesium ion · metal · chains PA

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

Compared structures

  • Q6P1X5 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 2… · a predicted model of the same protein · chain DB against A, TM-score 0.99
  • Q9ULK4 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain w against A, TM-score 0.97
  • Q9Y2X0 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain p against A, TM-score 0.96
  • P20226 · AlphaFold monomer V2.0 prediction for tata-box-binding protein (P20226) · a predicted model of the same protein · chain DP against A, TM-score 0.96
  • P51946 · AlphaFold monomer V2.0 prediction for cyclin-H (P51946) · a predicted model of the same protein · chain 9 against A, TM-score 0.95
  • P18074 · AlphaFold monomer V2.0 prediction for general transcription and DNA repair factor iih… · a predicted model of the same protein · chain 7 against A, TM-score 0.95
  • Q9H944 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain t against A, TM-score 0.95
  • Q15542 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 5… · a predicted model of the same protein · chain DE against A, TM-score 0.94
  • P52657 · AlphaFold monomer V2.0 prediction for transcription initiation factor iia subunit 2… · a predicted model of the same protein · chain DO against A, TM-score 0.92
  • Q9BUE0 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain r against A, TM-score 0.90
  • Q15544 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 11… · a predicted model of the same protein · chain Dk against A, TM-score 0.90
  • P19447 · AlphaFold monomer V2.0 prediction for general transcription and DNA repair factor iih… · a predicted model of the same protein · chain 6 against A, TM-score 0.90

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