SMTL ID : 8b3d.1

Structure of the Pol II-TCR-ELOF1 complex.

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

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: G.63, C.71, T.73, C.74, C.81, P.82, 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.2: 5 residues within 4Å: Chain A: C.111, F.113, C.114, C.154, C.184 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.111, A:C.114, A:C.154, A:C.184 ZN.4: 5 residues within 4Å: Chain B: C.1112, L.1114, C.1115, C.1130, C.1133 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1112, B:C.1115, B:C.1130, B:C.1133 ZN.5: 5 residues within 4Å: Chain C: C.88, C.90, C.94, E.96, 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: 8 residues within 4Å: Chain I: C.17, E.19, C.20, N.22, C.39, N.41, C.42, Y.44 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.17, I:C.20, I:C.39, I:C.42 ZN.7: 7 residues within 4Å: Chain I: C.86, K.88, C.89, C.114, A.116, C.119, H.121 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.86, I:C.89, I:C.114, I:C.119 ZN.8: 7 residues within 4Å: Chain J: C.7, T.9, C.10, K.12, R.42, 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.9: 8 residues within 4Å: Chain L: C.19, E.21, C.22, T.24, C.36, E.38, C.39, Y.41 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.19, L:C.22, L:C.36, L:C.39 ZN.10: 7 residues within 4Å: Chain M: C.26, F.28, C.29, C.50, V.52, C.53, E.55 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.26, M:C.29, M:C.50, M:C.53 ZN.14: 7 residues within 4Å: Chain S: C.567, A.569, C.577, R.579, C.585, F.587, H.588 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.567, S:C.577, S:C.585, S:H.588

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: R.460, D.495, D.497, D.499 Chain O: A.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.495, A:D.497, A:D.499, A:D.499 MG.13: 5 residues within 4Å: Chain R: T.539, D.646, G.920 Ligands: ADP.11, BEF.12 No protein-ligand interaction detected (PLIP)

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.11: 19 residues within 4Å: Chain R: K.506, L.507, F.508, Q.511, M.534, G.535, L.536, G.537, K.538, T.539, I.540, Q.580, E.584, W.588, N.922, R.950, I.951 Ligands: BEF.12, MG.13 16 PLIP interactions: 16 interactions with chain R Hydrogen bonds: R:K.506, R:Q.511, R:E.533, R:G.535, R:G.537, R:K.538, R:T.539, R:T.539, R:I.540, R:Q.580, R:E.584, R:N.922 Salt bridges: R:K.538, R:R.950, R:R.950 pi-Stacking: R:W.588

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.12: 10 residues within 4Å: Chain R: M.534, G.535, K.538, E.647, G.675, G.920, R.947, R.950 Ligands: ADP.11, MG.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kokic, G. et al., Structure of the Pol II-TCR-ELOF1 complex. To Be Published

Release Date

2023-09-27

Peptides

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: B
DNA-directed RNA polymerase II subunit RPB3: C
RNA polymerase II subunit D: D
DNA-directed RNA polymerase II subunit E: E
DNA-directed RNA polymerase II subunit F: F
RPB7: G
DNA-directed RNA polymerases I, II, and III subunit RPABC3: H
DNA-directed RNA polymerase II subunit RPB9: I
DNA-directed RNA polymerases I, II, and III subunit RPABC5: J
RNA_pol_L_2 domain-containing protein: K
RNA polymerase II subunit K: L
Transcription elongation factor 1 homolog: M
DNA excision repair protein ERCC-8: Q
DNA excision repair protein ERCC-6: R
UV-stimulated scaffold protein A: S
DNA damage-binding protein 1: T

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

M
M

Q
a

R
b

S
c

T
d

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase II subunit RPB3

RNA polymerase II subunit D

DNA-directed RNA polymerase II subunit E

DNA-directed RNA polymerase II subunit F

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_pol_L_2 domain-containing protein

RNA polymerase II subunit K

Transcription elongation factor 1 homolog

DNA excision repair protein ERCC-8

DNA excision repair protein ERCC-6

UV-stimulated scaffold protein A

DNA damage-binding protein 1

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