SMTL ID : 8uha.1

Structure of paused transcription complex Pol II-DSIF-NELF - tilted

Coordinates

PDB Format

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

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain B: C.16, L.18, C.19, L.21, C.33, L.40 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.16, B:C.19, B:C.33 ZN.3: 6 residues within 4Å: Chain G: R.61, C.71, T.73, C.74, C.81, H.84 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.71, G:T.73, G:C.81, G:H.84 ZN.4: 7 residues within 4Å: Chain G: C.111, F.113, C.114, C.154, C.184, R.186, Q.188 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.111, G:C.114, G:C.154 ZN.5: 6 residues within 4Å: Chain H: C.1119, C.1122, I.1124, C.1137, R.1138, G.1139 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.1119, H:C.1122, H:C.1137, H:R.1138 ZN.6: 6 residues within 4Å: Chain C: K.718 Chain I: C.88, T.89, C.90, C.94, C.97 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.88, I:C.90, I:C.94 ZN.7: 6 residues within 4Å: Chain O: C.17, E.19, C.20, N.21, N.22, C.39 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:C.17, O:C.20 ZN.8: 7 residues within 4Å: Chain O: C.86, K.88, C.89, C.114, A.116, C.119, H.121 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.86, O:C.89, O:C.114, O:C.119 ZN.9: 5 residues within 4Å: Chain P: C.7, C.10, C.44, C.45, M.48 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.7, P:C.44, P:C.44, P:C.45 ZN.10: 7 residues within 4Å: Chain R: C.19, E.21, C.22, T.24, C.36, C.39, Y.41 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:C.19, R:C.22, R:C.36

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain E: C.17 Chain G: D.495, D.497, D.499 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.495, G:D.497, G:D.497

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, B.G. et al., Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing. Mol.Cell (2024)

Release Date

2024-03-20

Peptides

Negative elongation factor E: A
Transcription elongation factor SPT4: B
Transcription elongation factor SPT5: C
Negative elongation factor C/D: D
Negative elongation factor B: F
DNA-directed RNA polymerase subunit: G
DNA-directed RNA polymerase subunit beta: H
DNA-directed RNA polymerase II subunit RPB3: I
RNA polymerase Rpb4/RPC9 core domain-containing protein: J
DNA-directed RNA polymerase II subunit E: K
DNA-directed RNA polymerases I, II, and III subunit RPABC2: L
DNA-directed RNA polymerase II subunit RPB7: M
DNA-directed RNA polymerases I, II, and III subunit RPABC3: N
DNA-directed RNA polymerase II subunit RPB9: O
DNA-directed RNA polymerases I, II, and III subunit RPABC5: P
RNA polymerase II subunit J: Q
RNA polymerase II subunit K: R
Negative elongation factor A: U

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
Y

C
Z

D
W

F
V

G
A

H
B

I
C

J
D

K
E

L
F

M
G

N
H

O
I

P
J

Q
K

R
L

U
U

Negative elongation factor E

Transcription elongation factor SPT4

Transcription elongation factor SPT5

Negative elongation factor C/D

Negative elongation factor B

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase II subunit RPB3

RNA polymerase Rpb4/RPC9 core domain-containing protein

DNA-directed RNA polymerase II subunit E

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

RNA polymerase II subunit J

RNA polymerase II subunit K

Negative elongation factor A

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