SMTL ID : 7x74.1

Cryo-EM structure of Streptomyces coelicolor transcription initial complex with two Zur dimers.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-1-4-mer

Ligands

1 x G- U- A- G- G: RNA(Non-covalent)

G-U-A-G-G.1: 26 residues within 4Å: Chain C: R.440, L.444, R.451, P.475, E.476, N.479, N.596, M.597, R.599, Q.600, K.870, K.878, H.1020 Chain D: R.500, D.535, G.538, D.539 Chain F: G.431, E.432, D.433 Chain L: C.16, C.17, T.18, A.19, C.20 Ligands: MG.2 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain D: R.500, D.535, D.539 Ligands: G-U-A-G-G.1 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.535, D:D.535, D:D.539

14 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain D: C.60, Y.61, C.62, G.63, C.75, C.78 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.60, D:C.62, D:C.75, D:C.78 ZN.4: 4 residues within 4Å: Chain D: C.886, C.962, C.969, C.972 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.886, D:C.962, D:C.969, D:C.972 ZN.5: 4 residues within 4Å: Chain G: C.110, C.113, C.150, C.153 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.110, G:C.113, G:C.150, G:C.153 ZN.6: 3 residues within 4Å: Chain G: C.99, H.105, H.107 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.99, G:H.105, G:H.107 ZN.7: 4 residues within 4Å: Chain G: H.104, H.106, E.125, H.142 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:H.104, G:H.106, G:E.125, G:E.125, G:H.142 ZN.8: 6 residues within 4Å: Chain H: C.110, C.113, K.115, C.150, D.152, C.153 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.110, H:C.113, H:C.150, H:C.153 ZN.9: 4 residues within 4Å: Chain H: D.85, C.99, H.105, H.107 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:C.99, H:H.105, H:H.107 ZN.10: 5 residues within 4Å: Chain H: H.104, H.106, E.120, E.125, H.142 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:H.104, H:H.106, H:E.125, H:E.125, H:H.142 ZN.11: 4 residues within 4Å: Chain I: C.110, C.113, C.150, C.153 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.110, I:C.113, I:C.150, I:C.153 ZN.12: 6 residues within 4Å: Chain I: D.85, C.99, T.101, H.105, H.107, E.118 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.99, I:H.105, I:H.107 ZN.13: 4 residues within 4Å: Chain I: H.104, H.106, E.125, H.142 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:H.104, I:H.106, I:E.125, I:E.125, I:H.142 ZN.14: 5 residues within 4Å: Chain J: C.110, C.113, C.150, D.152, C.153 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.110, J:C.113, J:C.150, J:C.153 ZN.15: 5 residues within 4Å: Chain J: D.85, C.99, H.105, H.107, E.118 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:D.85, J:C.99, J:H.105, J:H.107 ZN.16: 5 residues within 4Å: Chain J: H.104, H.106, V.124, E.125, H.142 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:H.104, J:H.106, J:E.125, J:E.125, J:H.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, X. et al., Structural basis of Streptomyces transcription activation by zinc uptake regulator. Nucleic Acids Res. (2022)

Release Date

2022-08-03

Peptides

DNA-directed RNA polymerase subunit alpha: AB
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase subunit beta': D
DNA-directed RNA polymerase subunit omega: E
RNA polymerase principal sigma factor HrdB: F
Putative metal uptake regulation protein: GHIJ

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
M

J
N

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

RNA polymerase principal sigma factor HrdB

Putative metal uptake regulation protein

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