SMTL ID : 1y77.1

Complete RNA Polymerase II elongation complex with substrate analogue GMPCPP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.50 Å

Oligo State

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

Ligands

1 x DA- DA- DG- DT- DA- DC- DT: 5'-D(*AP*AP*GP*TP*AP*CP*T)-3'(Non-covalent)

DA-DA-DG-DT-DA-DC-DT.1: 13 residues within 4Å: Chain A: A.1, G.2, T.3, A.4, C.5, T.6, T.7, A.8 Chain C: A.1108, N.1110, H.1387 Chain D: D.505, K.507 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.839, C:R.1386, C:R.1386 Salt bridges: C:K.330, C:R.337

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain C: C.107, M.108, C.110, C.148, C.167 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.167 ZN.3: 4 residues within 4Å: Chain C: C.67, C.70, C.77, H.80 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:C.67, C:C.67, C:C.70, C:C.77, C:H.80 ZN.5: 4 residues within 4Å: Chain D: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.1163, D:C.1166, D:C.1182, D:C.1185 ZN.7: 5 residues within 4Å: Chain E: C.86, C.88, H.91, C.92, C.95 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.86, E:C.88, E:C.92, E:C.95 ZN.8: 4 residues within 4Å: Chain K: C.7, C.10, C.29, C.32 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.7, K:C.10, K:C.29, K:C.32 ZN.9: 5 residues within 4Å: Chain K: C.75, C.78, C.103, C.106, H.108 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:C.106 ZN.10: 4 residues within 4Å: Chain L: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.7, L:C.10, L:C.45, L:C.46 ZN.11: 4 residues within 4Å: Chain N: C.31, C.34, C.48, C.51 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.31, N:C.34, N:C.48, N:C.51

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain B: C.10 Chain C: D.481, D.483, D.485 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.481, C:D.483

1 x G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Covalent)

G2P.6: 7 residues within 4Å: Chain A: G.10 Chain C: P.448, N.479, Q.1078 Chain D: R.766, S.1019, R.1020 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:N.479, C:Q.1078, D:R.766, D:S.1019, D:R.1020, D:R.1020 Salt bridges: C:K.752, D:R.1020

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kettenberger, H. et al., Complete RNA Polymerase II Elongation Complex Structure and Its Interactions with NTP and TFIIS. Mol.Cell (2004)

Release Date

2005-01-04

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

E
C

F
D

G
E

H
F

I
G

J
H

K
I

L
J

M
K

N
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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