SMTL ID : 5iy9.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

A-G-U-C-G-C.1: 22 residues within 4Å: Chain 1: G.37, C.38, G.39, A.40, C.41, T.42, G.43 Chain A: R.460, D.497, D.499 Chain B: Q.468, R.484, E.516, K.934, K.942 Chain M: S.56, N.57, K.59, A.60, T.61, K.62 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.495, D.497, D.499 Ligands: A-G-U-C-G-C.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.495, A:D.497, A:D.497, A:D.499 MG.3: 2 residues within 4Å: Chain A: A.494, D.495 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.495

10 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.71, 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.5: 4 residues within 4Å: Chain A: C.111, C.114, C.154, C.184 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.111, A:C.114, A:C.154, A:C.184 ZN.6: 4 residues within 4Å: Chain B: C.1119, C.1122, C.1137, C.1140 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1119, B:C.1122, B:C.1137, B:C.1140 ZN.7: 4 residues within 4Å: Chain C: C.88, C.90, C.94, C.97 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.88, C:C.90, C:C.94, C:C.97 ZN.8: 6 residues within 4Å: Chain I: C.17, E.19, C.20, C.39, N.41, C.42 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.17, I:C.20, I:C.39, I:C.42 ZN.9: 4 residues within 4Å: Chain I: C.86, C.89, C.114, C.119 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.86, I:C.89, I:C.114, I:C.119 ZN.10: 4 residues within 4Å: Chain J: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.44, J:C.45 ZN.11: 4 residues within 4Å: Chain L: C.19, C.22, 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 ZN.12: 7 residues within 4Å: Chain M: C.15, N.17, H.18, C.34, E.36, C.37, L.39 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.15, M:H.18, M:C.34, M:C.37 ZN.13: 4 residues within 4Å: Chain Q: C.129, C.132, C.154, C.157 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.129, Q:C.132, Q:C.154, Q:C.157

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
TFIIH basal transcription factor complex helicase XPB subunit: U
TFIIH basal transcription factor complex helicase XPD subunit: V
General transcription factor IIH subunit 2: W
General transcription factor IIH subunit 5: X
General transcription factor IIH subunit 4: Y
General transcription factor IIH subunit 3: Z

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

U
V

V
W

W
0

X
1

Y
2

Z
3

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

TFIIH basal transcription factor complex helicase XPB subunit

TFIIH basal transcription factor complex helicase XPD subunit

General transcription factor IIH subunit 2

General transcription factor IIH subunit 5

General transcription factor IIH subunit 4

General transcription factor IIH subunit 3

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