SMTL ID : 6exv.1

Structure of mammalian RNA polymerase II elongation complex inhibited by Alpha-amanitin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ILX-TRX-GLY-ILE-GLY-CSX-ASN-HYP.1: 19 residues within 4Å: Chain A: N.742, N.746, R.749, D.750, I.779, S.782, Q.783, V.787, V.788, G.789, Q.790, Q.791, N.792, H.839, G.842, G.843, E.845, H.1108 Chain B: Q.711 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Q.783, A:Q.791 Hydrogen bonds: A:N.746, A:R.749, A:S.782, A:Q.783, A:Q.790, A:Q.791, A:N.792, A:N.792, A:E.845, B:Q.711 pi-Cation interactions: A:R.749, A:R.749

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.71, T.73, C.74, C.81, H.84 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.71, A:C.74, A:C.81, A:H.84 ZN.3: 4 residues within 4Å: Chain A: C.111, C.114, C.154, C.184 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.111, A:C.114, A:C.154 ZN.5: 4 residues within 4Å: Chain B: C.1112, C.1115, C.1130, C.1133 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.1112, B:C.1115 ZN.6: 4 residues within 4Å: Chain C: C.90, F.93, C.94, C.97 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.90, C:C.94 ZN.7: 4 residues within 4Å: Chain I: C.17, N.21, N.22, M.23 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:N.22 ZN.8: 5 residues within 4Å: Chain I: C.86, C.89, C.114, C.119, H.121 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.86, I:C.89, I:C.114, I:C.119 ZN.9: 3 residues within 4Å: Chain J: C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.10, J:C.44, J:C.44, J:C.45 ZN.10: 5 residues within 4Å: Chain L: C.19, C.22, T.24, C.36, C.39 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.19, L:C.22, L:C.36, L:C.39

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.495, D.497, D.499 Chain N: C.20 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.495, A:D.495, A:D.497

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, X. et al., Cryo-EM structure of a mammalian RNA polymerase II elongation complex inhibited by alpha-amanitin. J. Biol. Chem. (2018)

Release Date

2018-03-21

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 RPB3: D
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1: E
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1: 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 POLYMERASES I, II, AND III SUBUNIT RPABC4: 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 RPB3

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1

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 POLYMERASES I, II, AND III SUBUNIT RPABC4

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

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