SMTL ID : 3j0k.1

Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 1 residues within 4Å: Chain A: D.481 No protein-ligand interaction detected (PLIP)

9 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.2: 6 residues within 4Å: Chain A: C.107, M.108, C.110, C.148, G.166, C.167 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.107, A:C.110, A:C.148, A:C.167 ZN.3: 4 residues within 4Å: Chain A: C.67, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.67, A:C.70, A:C.77, A:H.80 ZN.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.5: 5 residues within 4Å: Chain B: C.1163, I.1165, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1163, B:C.1166, B:C.1182, B:C.1185 ZN.6: 5 residues within 4Å: Chain C: C.86, C.88, H.91, C.92, C.95 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.86, C:C.86, C:C.88, C:C.92 ZN.7: 5 residues within 4Å: Chain I: C.7, R.8, C.10, C.29, C.32 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.7, I:C.10, I:C.29, I:C.32 ZN.8: 4 residues within 4Å: Chain I: C.75, C.78, C.103, C.106 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.75, I:C.78, I:C.103, I:C.106 ZN.9: 5 residues within 4Å: Chain J: C.7, S.9, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.45, J:C.46 ZN.10: 4 residues within 4Å: Chain L: C.7, C.10, C.24, C.27 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:C.7, L:C.10, L:C.24, L:C.27, L:C.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bernecky, C. et al., Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. Plos Biol. (2011)

Release Date

2011-10-19

Peptides

DNA-directed RNA polymerase II largest subunit: A
DNA-directed RNA polymerase II 140 kDa polypeptide: B
DNA-directed RNA polymerase II 45 kDa polypeptide: C
DNA-directed RNA polymerase II 32 kDa polypeptide: D
DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide: E
DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide: F
DNA-directed RNA polymerase II 19 kDa polypeptide: G
DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide: H
DNA-directed RNA polymerase II subunit 9: I
DNA-directed RNA polymerases I/II/III subunit 10: J
DNA-directed RNA polymerase II 13.6 kDa polypeptide: K
DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

DNA-directed RNA polymerase II largest subunit

DNA-directed RNA polymerase II 140 kDa polypeptide

DNA-directed RNA polymerase II 45 kDa polypeptide

DNA-directed RNA polymerase II 32 kDa polypeptide

DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide

DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide

DNA-directed RNA polymerase II 19 kDa polypeptide

DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide

DNA-directed RNA polymerase II subunit 9

DNA-directed RNA polymerases I/II/III subunit 10

DNA-directed RNA polymerase II 13.6 kDa polypeptide

DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide

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