SMTL ID : 5vo8.1

X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

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

Ligands

1 x GTP- G- G- G- G- G- G- G: RNA (5'-D(*(GTP))-R(P*GP*GP*GP*GP*GP*GP*G)-3')(Non-covalent)

GTP-G-G-G-G-G-G-G.1: 32 residues within 4Å: Chain C: K.188, Q.390, Q.393, F.394, D.396, H.406, R.409, L.413, T.419, R.420, P.444, N.448, I.452, Q.567, K.838, K.846, H.999 Chain D: K.610, R.704, A.705, P.706, D.741, D.743 Chain G: A.9, G.10, A.11, C.13, C.14, C.15, A.16 Chain H: C.18 Ligands: MG.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.188

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain B: E.154, D.168 Chain D: K.840 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain B Metal complexes: D:K.840, B:E.154, B:E.154, B:D.168, B:D.168 MG.4: 4 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: GTP-G-G-G-G-G-G-G.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

1 x POP: PYROPHOSPHATE 2-(Covalent)

POP.3: 5 residues within 4Å: Chain C: R.879 Chain D: N.737, D.739, R.783, R.1029 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.739 Salt bridges: D:R.1029, C:R.879

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain D: C.58, C.60, G.61, K.62, C.73, C.76 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.58, D:C.60, D:C.73, D:C.76 ZN.6: 5 residues within 4Å: Chain D: C.1112, C.1194, Q.1195, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murakami, K.S. et al., X-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-05-24

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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