SMTL ID : 5ip9.1

Structure of RNA Polymerase II-TFIIF complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.90 Å

Oligo State

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

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.106, C.109, C.147, C.166 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.106, A:C.109, A:C.147, A:C.166 ZN.2: 4 residues within 4Å: Chain A: C.66, C.69, C.76, H.79 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.66, A:C.69, A:C.76, A:H.79 ZN.4: 4 residues within 4Å: Chain B: C.1162, C.1165, C.1181, C.1184 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1162, B:C.1165, B:C.1181, B:C.1184 ZN.5: 5 residues within 4Å: Chain C: C.84, C.86, H.89, C.90, C.93 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.84, C:C.86, C:C.90, C:C.93 ZN.6: 4 residues within 4Å: Chain I: C.6, C.9, C.28, C.31 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.6, I:C.9, I:C.28, I:C.31 ZN.7: 4 residues within 4Å: Chain I: C.74, C.77, C.102, C.105 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.74, I:C.77, I:C.102, I:C.105 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: 4 residues within 4Å: Chain L: C.7, C.10, C.24, C.27 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.7, L:C.10, L:C.24, L:C.27

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.480, D.482, D.484 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.482, A:D.482

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Plaschka, C. et al., Transcription initiation complex structures elucidate DNA opening. Nature (2016)

Release Date

2016-05-11

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
PHE-ILE-LYS-ARG-ASP-ARG-MET-ARG-ARG-ASN-PHE-LEU-ARG-MET-ARG: M

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
Q

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

PHE-ILE-LYS-ARG-ASP-ARG-MET-ARG-ARG-ASN-PHE-LEU-ARG-MET-ARG

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