SMTL ID : 8gzh.1

Cryo-EM structure of Synechocystis sp. PCC 6803 CTP-bound RPitc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x C- C- G- A: RNA (5'-R(*CP*CP*GP*A)-3')(Non-covalent)

C-C-G-A.1: 18 residues within 4Å: Chain C: Q.369, P.420, N.424, I.428, Q.546, K.823, K.831, H.956 Chain D: R.432, G.470, D.471 Chain F: D.334 Chain I: T.30, C.31, G.32, G.33, A.34 Ligands: CTP.6 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain D: D.467, D.469, D.471 Ligands: MG.4, CTP.6 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.467, D:D.469 MG.4: 5 residues within 4Å: Chain C: D.672 Chain D: D.467, D.469 Ligands: MG.2, CTP.6 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.467, D:D.469

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain D: C.71, C.73, G.74, K.75, C.86, C.89 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.71, D:C.73, D:C.86 ZN.5: 4 residues within 4Å: Chain G: C.220, C.292, C.299, C.302 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.220, G:C.292, G:C.299, G:C.302

1 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.6: 17 residues within 4Å: Chain C: R.536, D.672, K.831, R.864 Chain D: R.432, P.434, N.465, D.467, D.469 Chain G: Q.333, M.336, F.339, H.340 Chain I: G.29 Ligands: C-C-G-A.1, MG.2, MG.4 9 PLIP interactions: 5 interactions with chain C, 2 interactions with chain G, 2 interactions with chain D Hydrogen bonds: C:D.672, G:Q.333, D:R.432, D:N.465 Salt bridges: C:R.536, C:K.831, C:K.831, C:R.864, G:H.340

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, L. et al., An SI3-sigma arch stabilizes cyanobacteria transcription initiation complex. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-04-19

Peptides

DNA-directed RNA polymerase subunit alpha: AB
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase subunit gamma: D
DNA-directed RNA polymerase subunit omega: E
RNA polymerase sigma factor SigA: F
DNA-directed RNA polymerase subunit beta': G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
Z

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit gamma

DNA-directed RNA polymerase subunit omega

RNA polymerase sigma factor SigA

DNA-directed RNA polymerase subunit beta'

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