SMTL ID : 4a3e.1

RNA Polymerase II initial transcribing complex with a 5nt DNA-RNA hybrid and soaked with AMPCPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

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

Ligands

1 x A- G- G- A: TRANSCRIPT RNA 5'-R(*CP*AP*GP*GP*AP)-3'(Non-covalent)

A-G-G-A.1: 18 residues within 4Å: Chain A: R.446, D.481, D.483, D.485 Chain B: G.478, Q.481, Q.776, K.979, K.987, H.1097, K.1102 Chain N: T.16, C.17, C.18, U.19, G.20 Ligands: MG.4, APC.11 Protein-ligand interaction information (PLIP) not available

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.107, 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: 5 residues within 4Å: Chain A: C.67, T.69, 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.5: 4 residues within 4Å: Chain B: C.1163, 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.88, C:C.92, C:C.95 ZN.7: 4 residues within 4Å: Chain I: C.7, 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: 5 residues within 4Å: Chain I: C.75, C.78, C.103, S.105, 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: 4 residues within 4Å: Chain J: C.7, 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.31, C.34, C.48, C.51 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.31, L:C.34, L:C.48, L:C.51

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: D.481, D.483, D.485 Ligands: A-G-G-A.1, APC.11 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.481, A:D.481, A:D.483, A:D.483, A:D.485

1 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.11: 12 residues within 4Å: Chain A: R.446, P.448, N.479, D.481, D.483 Chain B: R.766, K.987, R.1020 Chain N: T.15, T.16 Ligands: A-G-G-A.1, MG.4 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.766, B:K.987, B:S.1019, A:R.446, A:R.446, A:N.479 Salt bridges: B:R.1020, A:K.752

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheung, A.C. et al., Structural basis of initial RNA polymerase II transcription. EMBO J. (2011)

Release Date

2011-12-07

Peptides

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1: A
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2: B
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3: C
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4: D
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1: E
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2: F
RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7: G
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3: H
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9: I
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5: J
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11: K
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4: 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 SUBUNIT RPB1

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2

RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4

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