SMTL ID : 6gml.1

Structure of paused transcription complex Pol II-DSIF-NELF

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-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.495, D.497, D.499 Chain L: U.46 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.495, A:D.497, A:D.499, A:D.499

9 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: C.111, C.114, G.183 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.111, A:C.114 ZN.3: 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.4: 4 residues within 4Å: Chain B: C.1119, C.1122, C.1137, C.1140 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.1119, B:C.1122, B:C.1137 ZN.5: 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.6: 4 residues within 4Å: Chain G: C.17, C.20, C.39, C.42 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.17, G:C.20, G:C.39, G:C.42 ZN.7: 5 residues within 4Å: Chain G: C.86, C.89, C.114, C.119, H.121 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.86, G:C.89, G:C.119 ZN.8: 4 residues within 4Å: Chain H: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.7, H:C.10, H:C.44, H:C.45 ZN.9: 5 residues within 4Å: Chain J: C.19, C.22, T.24, C.36, E.38 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:C.22, J:C.36 ZN.10: 3 residues within 4Å: Chain R: C.20, C.23, C.37 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:C.20, R:C.23, R:C.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vos, S.M. et al., Structure of paused transcription complex Pol II-DSIF-NELF. Nature (2018)

Release Date

2018-09-05

Peptides

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: B
RNA polymerase II subunit C: C
RNA polymerase II subunit E: D
RNA polymerase II subunit F: E
DNA-directed RNA polymerases I, II, and III subunit RPABC3: F
DNA-directed RNA polymerase II subunit RPB9: G
Uncharacterized protein: H
Uncharacterized protein: I
Uncharacterized protein: J
Negative elongation factor A: N
Negative elongation factor B,Negative elongation factor B: O
Negative elongation factor C/D: P
Negative elongation factor E,Negative elongation factor E: Q
Transcription elongation factor SPT4: R
Transcription elongation factor SPT5: S
RNA polymerase II subunit D: T
RNA polymerase II subunit G: U

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
H

G
I

H
J

I
K

J
L

N
U

O
V

P
W

Q
X

R
Y

S
Z

T
D

U
G

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

RNA polymerase II subunit C

RNA polymerase II subunit E

RNA polymerase II subunit F

DNA-directed RNA polymerases I, II, and III subunit RPABC3

DNA-directed RNA polymerase II subunit RPB9

Uncharacterized protein

Uncharacterized protein

Uncharacterized protein

Negative elongation factor A

Negative elongation factor B,Negative elongation factor B

Negative elongation factor C/D

Negative elongation factor E,Negative elongation factor E

Transcription elongation factor SPT4

Transcription elongation factor SPT5

RNA polymerase II subunit D

RNA polymerase II subunit G

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