SMTL ID : 8uhd.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain E: C.111, C.114, C.154, G.183, C.184, G.185, Q.188 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.111, E:C.114, E:C.154, E:C.184 ZN.2: 5 residues within 4Å: Chain E: C.71, T.73, C.74, C.81, H.84 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.71, E:C.74, E:C.81, E:H.84 ZN.4: 5 residues within 4Å: Chain F: C.1119, L.1121, C.1122, C.1137, C.1140 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.1119, F:C.1122, F:C.1140 ZN.5: 5 residues within 4Å: Chain G: C.88, C.90, F.93, C.94, C.97 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.88, G:C.90, G:C.94, G:C.97 ZN.6: 6 residues within 4Å: Chain M: C.17, E.19, C.20, C.39, C.42, Y.44 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.17, M:C.20, M:C.39, M:C.42 ZN.7: 7 residues within 4Å: Chain M: C.86, K.88, C.89, H.91, C.114, C.119, H.121 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.86, M:C.89, M:C.114, M:C.119 ZN.8: 7 residues within 4Å: Chain N: C.7, T.9, C.10, K.12, R.42, C.44, C.45 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.7, N:C.10, N:C.44, N:C.45 ZN.9: 6 residues within 4Å: Chain P: C.19, E.21, C.22, C.36, C.39, Y.41 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.19, P:C.22, P:C.36, P:C.39 ZN.10: 6 residues within 4Å: Chain U: C.16, L.18, C.19, C.33, L.40, M.42 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:C.16

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain E: D.495, D.497, D.499 Chain R: C.17 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.495, E:D.497, E:D.497, E:D.499, E: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
Transcription elongation factor SPT5: B
Negative elongation factor C/D: C
Negative elongation factor B: D
DNA-directed RNA polymerase subunit: E
DNA-directed RNA polymerase subunit beta: F
DNA-directed RNA polymerase II subunit RPB3: G
RNA polymerase Rpb4/RPC9 core domain-containing protein: H
DNA-directed RNA polymerase II subunit E: I
DNA-directed RNA polymerases I, II, and III subunit RPABC2: J
DNA-directed RNA polymerase II subunit RPB7: K
DNA-directed RNA polymerases I, II, and III subunit RPABC3: L
DNA-directed RNA polymerase II subunit RPB9: M
DNA-directed RNA polymerases I, II, and III subunit RPABC5: N
RNA polymerase II subunit J: O
RNA polymerase II subunit K: P
Negative elongation factor A: T
Transcription elongation factor SPT4: U

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
Z

C
W

D
V

E
A

F
B

G
C

H
D

I
E

J
F

K
G

L
H

M
I

N
J

O
K

P
L

T
U

U
Y

Negative elongation factor E

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

Transcription elongation factor SPT4

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