SMTL ID : 5iyd.1

Human core-PIC in the initial transcribing state (no IIS)

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

1 x A- G- U- C- G- C: RNA(Non-covalent)

A-G-U-C-G-C.1: 21 residues within 4Å: Chain A: R.460, D.497, D.499 Chain B: Q.468, E.516, K.934, K.942 Chain M: S.56, N.57, K.59, A.60, T.61, K.62 Chain V: G.34, C.35, G.36, A.37, C.38, T.39, G.40 Ligands: MG.2 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.497, G.498, D.499 Ligands: A-G-U-C-G-C.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.497, A:D.497 MG.3: 5 residues within 4Å: Chain A: D.495, F.496, D.497 Chain B: E.791, D.792 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.792

11 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.4: 5 residues within 4Å: Chain A: R.61, Q.62, R.70, C.71, Q.72 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Q.62, A:R.70, A:C.71 ZN.5: 6 residues within 4Å: Chain A: C.111, F.112, C.114, C.154, C.184, Q.188 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.111 ZN.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.7: 3 residues within 4Å: Chain B: A.1126, C.1137, R.1138 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.1137, B:R.1138 ZN.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.9: 5 residues within 4Å: Chain I: F.16, C.17, Q.18, N.22, L.24 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:C.17, I:C.17 ZN.10: 4 residues within 4Å: Chain I: C.89, H.91, K.92, A.116 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:H.91 ZN.11: 5 residues within 4Å: Chain J: R.6, K.12, I.13, V.14, G.15 No protein-ligand interaction detected (PLIP) ZN.12: 4 residues within 4Å: Chain L: R.37, E.38, C.39 Chain M: K.226 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:E.38 ZN.13: 5 residues within 4Å: Chain M: P.19, D.20, A.21, I.22, E.36 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.20 ZN.14: 4 residues within 4Å: Chain Q: P.130, V.131, C.132, S.133 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:V.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, Y. et al., Near-atomic resolution visualization of human transcription promoter opening. Nature (2016)

Release Date

2016-05-18

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 polymerase II subunit RPB5: E
DNA-directed RNA polymerase II subunit RPB6: F
DNA-directed RNA polymerase II subunit RPB7: G
DNA-directed RNA polymerase II subunit RPB8: H
DNA-directed RNA polymerase II subunit RPB9: I
DNA-directed RNA polymerase II subunit RPB10: J
DNA-directed RNA polymerase II subunit RPB11-a: K
DNA-directed RNA polymerase II subunit RPB12: L
Transcription initiation factor IIB: M
Transcription initiation factor IIA subunit 1: N
Transcription initiation factor IIA subunit 2: O
TATA-box-binding protein: P
General transcription factor IIE subunit 1: Q
Transcription initiation factor IIE subunit beta: R
General transcription factor IIF subunit 1: S
General transcription factor IIF subunit 2: T

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

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

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 polymerase II subunit RPB5

DNA-directed RNA polymerase II subunit RPB6

DNA-directed RNA polymerase II subunit RPB7

DNA-directed RNA polymerase II subunit RPB8

DNA-directed RNA polymerase II subunit RPB9

DNA-directed RNA polymerase II subunit RPB10

DNA-directed RNA polymerase II subunit RPB11-a

DNA-directed RNA polymerase II subunit RPB12

Transcription initiation factor IIB

Transcription initiation factor IIA subunit 1

Transcription initiation factor IIA subunit 2

TATA-box-binding protein

General transcription factor IIE subunit 1

Transcription initiation factor IIE subunit beta

General transcription factor IIF subunit 1

General transcription factor IIF subunit 2

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