SMTL ID : 8uhg.1

Structure of paused transcription complex Pol II-DSIF-NELF - poised post-translocated

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-mer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain D: C.71, T.73, C.74, C.81, H.84 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.71, D:C.74, D:H.84 ZN.2: 5 residues within 4Å: Chain D: C.111, C.114, C.154, C.184, Q.188 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.111, D:C.114, D:C.154, D:C.184 ZN.4: 5 residues within 4Å: Chain E: C.1119, C.1122, C.1137, C.1140, N.1142 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.1119, E:C.1122, E:C.1137, E:C.1140 ZN.5: 4 residues within 4Å: Chain F: C.88, C.90, C.94, C.97 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.88, F:C.90, F:C.94, F:C.97 ZN.6: 6 residues within 4Å: Chain L: C.17, E.19, C.20, C.39, C.42, Y.44 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.17, L:C.20, L:C.39, L:C.42 ZN.7: 7 residues within 4Å: Chain L: C.86, K.88, C.89, C.114, A.116, C.119, H.121 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.86, L:C.89, L:C.114, L:C.119 ZN.8: 6 residues within 4Å: Chain M: C.7, T.9, C.10, R.42, C.44, C.45 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.7, M:C.10, M:C.44, M:C.45 ZN.9: 7 residues within 4Å: Chain O: C.19, E.21, C.22, T.24, C.36, C.39, Y.41 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.19, O:C.22, O:C.36, O:C.39

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain D: D.495, D.497, D.499 Chain Q: C.15 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.495, D:D.497, D:D.497, D:D.499

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
Negative elongation factor B: B
Negative elongation factor C/D: C
DNA-directed RNA polymerase subunit: D
DNA-directed RNA polymerase subunit beta: E
DNA-directed RNA polymerase II subunit RPB3: F
RNA polymerase Rpb4/RPC9 core domain-containing protein: G
DNA-directed RNA polymerase II subunit E: H
DNA-directed RNA polymerases I, II, and III subunit RPABC2: I
DNA-directed RNA polymerase subunit: J
DNA-directed RNA polymerases I, II, and III subunit RPABC3: K
DNA-directed RNA polymerase II subunit RPB9: L
DNA-directed RNA polymerases I, II, and III subunit RPABC5: M
DNA-directed RNA polymerase II subunit RPB11-a: N
RNA polymerase II subunit K: O
Negative elongation factor A: S
Transcription elongation factor SPT5: T

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
V

C
W

D
A

E
B

F
C

G
D

H
E

I
F

J
G

K
H

L
I

M
J

N
K

O
L

S
U

T
Z

Negative elongation factor E

Negative elongation factor B

Negative elongation factor C/D

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 subunit

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-a

RNA polymerase II subunit K

Negative elongation factor A

Transcription elongation factor SPT5

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