SMTL ID : 6kqm.1

Thermus thermophilus initial transcription complex comprising sigma A and 5'-triphosphate RNA of 5 nt

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

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

Ligands

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

CTP-U-C-G-A.1: 24 residues within 4Å: Chain C: Q.390, R.409, L.413, R.420, P.444, N.448, I.452, Q.567, K.838, K.846, H.999 Chain D: R.704, D.739, D.741, D.743 Chain F: D.343, D.346 Chain G: T.15, C.16, G.17, A.18, G.19, G.20 Ligands: MG.5 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:Q.390, F:D.346, F:D.346 Water bridges: C:R.420, C:R.420 Salt bridges: C:R.420

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain B: D.183, D.191, D.193 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.183 MG.5: 4 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: CTP-U-C-G-A.1 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.739, D:D.741, D:D.741, D:D.743, D:D.743 MG.6: 3 residues within 4Å: Chain B: E.154, D.168 Chain D: K.840 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:K.840, H2O.4 MG.7: 4 residues within 4Å: Chain F: A.312, E.313, G.316, W.319 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:A.312, F:G.316, F:W.319

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain D: C.1112, R.1189, C.1194, T.1196, C.1201, C.1204 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.1112, D:C.1194, D:C.1201, D:C.1204 ZN.4: 4 residues within 4Å: Chain D: C.58, C.60, C.73, C.76 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.60, D:C.73, D:C.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, L. et al., RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-03-11

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 sigma factor SigA: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

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 sigma factor SigA

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