SMTL ID : 5xog.1

RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

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

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.67, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.67, A:C.70, A:C.77, A:H.80 ZN.2: 4 residues within 4Å: Chain A: C.107, C.110, C.148, C.168 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.107, A:C.110, A:C.148, A:C.168 ZN.5: 4 residues within 4Å: Chain B: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1163, B:C.1166, B:C.1182, B:C.1185 ZN.6: 4 residues within 4Å: Chain C: C.85, C.87, C.91, C.94 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.85, C:C.87, C:C.91, C:C.94 ZN.7: 4 residues within 4Å: Chain I: C.75, C.78, C.103, C.106 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.75, I:C.78, I:C.103, I:C.106 ZN.8: 4 residues within 4Å: Chain I: C.7, C.10, C.29, C.32 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.7, I:C.29, I:C.32 ZN.9: 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.10: 4 residues within 4Å: Chain L: C.33, C.36, C.50, C.53 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.33, L:C.36, L:C.50, L:C.53 ZN.11: 5 residues within 4Å: Chain P: C.28, C.31, C.52, C.55, Q.57 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.28, P:C.31, P:C.52, P:C.55

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.482, D.484, D.486 Chain M: U.17 Ligands: APC.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.482, A:D.482, A:D.484, A:D.484, A:D.486

1 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.4: 11 residues within 4Å: Chain A: R.447, P.449, N.480, D.482, D.484 Chain B: R.766, R.1020 Chain M: U.17 Chain N: T.22, A.23 Ligands: MG.3 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.447, A:R.447, A:N.480 Salt bridges: B:R.766, B:R.1020

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ehara, H. et al., Structure of the complete elongation complex of RNA polymerase II with basal factors. Science (2017)

Release Date

2017-08-16

Peptides

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: B
RNA polymerase II third largest subunit B44, part of central core: C
RNA polymerase II subunit B32: D
RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III: E
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III: F
RNA polymerase II subunit: G
RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III: H
DNA-directed RNA polymerase subunit: I
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III: J
RNA polymerase II subunit B12.5: K
RNA polymerase subunit ABC10-alpha: L
Transcription elongation factor 1 homolog: P
Spt4/5 complex component: Q

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

P
M

Q
W

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

RNA polymerase II third largest subunit B44, part of central core

RNA polymerase II subunit B32

RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III

RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III

RNA polymerase II subunit

RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III

DNA-directed RNA polymerase subunit

RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III

RNA polymerase II subunit B12.5

RNA polymerase subunit ABC10-alpha

Transcription elongation factor 1 homolog

Spt4/5 complex component

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