SMTL ID : 2vum.1

Alpha-amanitin inhibited complete RNA polymerase II elongation complex

Coordinates

PDB Format

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 ASN- HYP- ILX- TRX- GLY- ILE- GLY- CSX: AMATOXIN(Non-covalent)

ASN-HYP-ILX-TRX-GLY-ILE-GLY-CSX.1: 19 residues within 4Å: Chain A: V.719, N.723, R.726, I.756, A.759, Q.760, C.764, V.765, G.766, Q.767, Q.768, S.769, G.772, H.816, G.819, G.820, E.822, H.1085 Chain B: Q.763 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.719, A:R.726, A:I.756, A:A.759, A:Q.760 Hydrogen bonds: A:N.723, A:R.726, A:Q.760, A:Q.767, A:Q.768, A:S.769, A:E.822, A:H.1085, B:Q.763 pi-Cation interactions: A:R.726, A:R.726

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: C.107, M.108, C.110, C.148, G.166, C.167 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.107, A:C.110, A:C.148 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.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 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.75, I:C.78, I:C.106 ZN.9: 4 residues within 4Å: Chain J: C.7, C.10, C.45, C.46 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.45 ZN.10: 4 residues within 4Å: Chain L: C.31, C.34, C.48, C.51 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:C.34, L:C.48

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.481, D.483, D.485 Chain N: C.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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brueckner, F. et al., Structural Basis of Transcription Inhibition by Alpha-Amanitin and Implications for RNA Polymerase II Translocation. Nat.Struct.Mol.Biol. (2008)

Release Date

2008-06-17

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 RPABC1: E
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2: F
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7: G
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3: H
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9: I
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5: J
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11: K
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4: 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 RPABC1

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4

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