SMTL ID : 5fmf.1

the P-lobe of RNA polymerase II pre-initiation complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 6.00 Å

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-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain B: D.155 Chain C: D.481, D.483 Ligands: MG.5 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain C: D.481, D.483, D.485 Ligands: MG.1 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.481, C:D.481, C:D.483, C:D.483, C:D.485

9 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain B: C.136, C.139, C.164, C.167 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.136, B:C.139 ZN.3: 4 residues within 4Å: Chain C: C.107, C.110, C.148, C.167 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.107, C:C.110, C:C.148, C:C.167 ZN.4: 4 residues within 4Å: Chain C: C.67, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.67, C:C.70, C:C.77, C:H.80 ZN.6: 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.7: 5 residues within 4Å: Chain E: C.84, C.86, H.89, C.90, C.93 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.84, E:C.86, E:C.90, E:C.93 ZN.8: 4 residues within 4Å: Chain K: C.6, C.9, C.28, C.31 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.6, K:C.9, K:C.28, K:C.31 ZN.9: 4 residues within 4Å: Chain K: C.74, C.77, C.102, C.105 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.74, K:C.77, K:C.102, K:C.105 ZN.10: 4 residues within 4Å: Chain L: C.7, 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.11: 5 residues within 4Å: Chain N: C.7, C.10, S.12, C.24, C.27 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.7, N:C.10, N:C.24, N:C.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murakami, K. et al., Structure of an RNA Polymerase II Pre-Initiation Complex. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-11-25

Peptides

DNA REPAIR HELICASE RAD25, SSL2: A
TRANSCRIPTION ELONGATION FACTOR S-II, DST1: B
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1: C
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2: D
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3: E
RNA POLYMERASE II PRE-INITIATION COMPLEX, RPB4: F
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1, RPB5: G
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2, RPB6: H
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7: I
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3, RPB8: J
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9: K
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5, RPB10: L
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11: M
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4, RPB12: N
RNA POLYMERASE II PRE-INITIATION COMPLEX, TOA1: O
TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 2, TOA2: Q
TRANSCRIPTION INITIATION FACTOR IIB, SUA7: R
TATA-BOX-BINDING PROTEIN, TBP: S
TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT ALPHA, TFA1: T
TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT BETA, TFA2: U
RNA POLYMERASE II PRE-INITIATION COMPLEX, TFG1: W
TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT BETA, TFG2: X
RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 2, TFB2: Y
RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 5, TFB5: Z
DNA REPAIR HELICASE RAD3: 0

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
A

D
B

E
C

F
D

G
E

H
F

I
G

J
H

K
I

L
J

M
K

N
L

O
M

Q
O

R
P

S
Q

T
R

U
S

W
U

X
V

Y
W

Z
X

0
Y

DNA REPAIR HELICASE RAD25, SSL2

TRANSCRIPTION ELONGATION FACTOR S-II, DST1

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3

RNA POLYMERASE II PRE-INITIATION COMPLEX, RPB4

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1, RPB5

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2, RPB6

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3, RPB8

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5, RPB10

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4, RPB12

RNA POLYMERASE II PRE-INITIATION COMPLEX, TOA1

TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 2, TOA2

TRANSCRIPTION INITIATION FACTOR IIB, SUA7

TATA-BOX-BINDING PROTEIN, TBP

TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT ALPHA, TFA1

TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT BETA, TFA2

RNA POLYMERASE II PRE-INITIATION COMPLEX, TFG1

TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT BETA, TFG2

RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 2, TFB2

RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 5, TFB5

DNA REPAIR HELICASE RAD3

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