SMTL ID : 6gyl.1

Structure of a yeast closed complex with distorted DNA (core CCdist)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.107, C.110, C.148, C.167, Q.171 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.107, A:C.110, A:C.148, A:C.167 ZN.2: 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: 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.5: 4 residues within 4Å: Chain C: C.86, C.88, 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.6: 5 residues within 4Å: Chain I: C.7, C.10, C.29, T.31, 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.7: 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.8: 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.9: 6 residues within 4Å: Chain L: C.31, C.34, S.36, C.48, K.49, C.51 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.31, L:C.34, L:C.48, L:C.51 ZN.10: 4 residues within 4Å: Chain M: C.24, C.27, C.45, C.48 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.24, M:C.27, M:C.45, M:C.48 ZN.11: 4 residues within 4Å: Chain U: C.124, C.127, C.149, C.152 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:C.124, U:C.127, U:C.149, U:C.152

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.481, D.483, D.485 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.481, A:D.485, A:D.485

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dienemann, C. et al., Promoter Distortion and Opening in the RNA Polymerase II Cleft. Mol. Cell (2019)

Release Date

2018-12-05

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
Transcription initiation factor IIB: M
TATA-box-binding protein: O
Transcription initiation factor IIF subunit alpha: P
Transcription initiation factor IIF subunit beta: Q
Transcription initiation factor IIA large subunit,Transcription initiation factor IIA large subunit: S
Transcription initiation factor IIA subunit 2: T
Transcription initiation factor IIE subunit alpha,Tfa1,Tfa1: U
Transcription initiation factor IIE subunit beta: V

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

M
M

O
O

P
Q

Q
R

S
U

T
V

U
W

V
X

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

Transcription initiation factor IIB

TATA-box-binding protein

Transcription initiation factor IIF subunit alpha

Transcription initiation factor IIF subunit beta

Transcription initiation factor IIA large subunit,Transcription initiation factor IIA large subunit

Transcription initiation factor IIA subunit 2

Transcription initiation factor IIE subunit alpha,Tfa1,Tfa1

Transcription initiation factor IIE subunit beta

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