SMTL ID : 7mei.1

Composite structure of EC+EC

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-1-1-mer

Ligands

16 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain C: C.110, C.148, G.166, C.167 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.110, C:C.148, C:C.167 ZN.2: 5 residues within 4Å: Chain C: C.67, Q.68, C.70, H.80 Chain D: I.1172 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.67, C:C.67, C:C.70, 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.6: 4 residues within 4Å: Chain E: C.86, C.88, 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.7: 6 residues within 4Å: Chain K: C.7, D.9, C.10, C.29, T.31, C.32 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:C.7, K:C.10, K:C.29, K:T.31, K:C.32 ZN.8: 6 residues within 4Å: Chain K: C.75, C.78, S.80, C.103, S.105, C.106 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:C.75, K:C.78, K:C.103, K:S.105, K:C.106 ZN.9: 5 residues within 4Å: Chain L: C.7, S.9, 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.10: 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 ZN.11: 4 residues within 4Å: Chain P: C.107, C.110, C.148, C.167 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.107, P:C.110, P:C.148, P:C.167 ZN.12: 5 residues within 4Å: Chain P: C.67, Q.68, C.70, C.77, H.80 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:C.67, P:C.67, P:C.70, P:C.77, P:H.80 ZN.14: 5 residues within 4Å: Chain Q: C.1163, C.1166, T.1170, C.1182, C.1185 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:C.1163, Q:C.1166, Q:C.1182 ZN.15: 4 residues within 4Å: Chain R: C.86, C.88, C.92, C.95 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.86, R:C.88, R:C.92, R:C.95 ZN.16: 4 residues within 4Å: Chain X: C.7, C.10, C.29, C.32 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:C.7, X:C.10, X:C.29, X:C.32 ZN.17: 4 residues within 4Å: Chain X: C.75, K.77, C.78, C.106 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:C.75, X:C.78, X:C.106 ZN.18: 4 residues within 4Å: Chain Y: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:C.7, Y:C.10, Y:C.45, Y:C.46 ZN.19: 6 residues within 4Å: Chain 0: C.31, A.32, C.34, C.48, D.50, C.51 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:C.31, 0:C.48, 0:D.50, 0:C.51

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain C: D.481, D.483, D.485 Chain O: U.15, C.16 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.481, C:D.483, C:D.483, C:D.485 MG.4: 3 residues within 4Å: Chain C: N.1393, T.1394, G.1395 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.1394 MG.13: 3 residues within 4Å: Chain P: L.860, T.1394, G.1395 No protein-ligand interaction detected (PLIP) MG.20: 5 residues within 4Å: Chain 1: A.9, U.10 Chain P: D.481, D.483, D.485 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:D.481, P:D.481, P:D.483, P:D.483, P:D.485

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, C. et al., Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. Mol.Cell (2022)

Release Date

2022-03-02

Peptides

DNA-directed RNA polymerase subunit: CP
DNA-directed RNA polymerase subunit beta: DQ
DNA-directed RNA polymerase II subunit RPB3: ER
DNA-directed RNA polymerase II subunit RPB4: FS
DNA-directed RNA polymerases I, II, and III subunit RPABC1: GT
DNA-directed RNA polymerases I, II, and III subunit RPABC2: HU
DNA-directed RNA polymerase II subunit RPB7: IV
DNA-directed RNA polymerases I, II, and III subunit RPABC3: JW
DNA-directed RNA polymerase II subunit RPB9: KX
DNA-directed RNA polymerases II subunit RPABC5: LY
DNA-directed RNA polymerase II subunit RPB11: MZ
DNA-directed RNA polymerases II subunit RPABC4: N0
Transcription initiation factor IIF subunit alpha: 2
Transcription initiation factor IIF subunit beta: 3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
a

P
A

D
b

Q
B

E
c

R
C

F
d

S
D

G
e

T
E

H
f

U
F

I
g

V
G

J
h

W
H

K
i

X
I

L
j

Y
J

M
k

Z
K

N
l

0
L

2
Q

3
M

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

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 II subunit RPABC5

DNA-directed RNA polymerase II subunit RPB11

DNA-directed RNA polymerases II subunit RPABC4

Transcription initiation factor IIF subunit alpha

Transcription initiation factor IIF subunit beta

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