SMTL ID : 8w8p.1

Thermus thermophilus initiation transcription complex containing CMPcPP in the post-translocated state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.16 Å

Oligo State

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

Ligands

1 x GTP- G- A: RNA (5'-(GTP)GA-3')(Non-covalent)

GTP-G-A.1: 17 residues within 4Å: Chain C: P.444, N.448, Q.567, K.838, K.846, H.999 Chain D: R.704, A.705, D.741, G.742, D.743 Chain G: T.15, C.16, C.17, A.18 Ligands: MG.6, 2TM.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.448, C:Q.567, C:H.999

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain B: R.30, D.183, D.191, L.192, D.193 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.183, B:D.191, B:D.191, B:D.193 MG.3: 3 residues within 4Å: Chain B: E.154, D.168 Chain D: K.840 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:K.840 MG.6: 5 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: GTP-G-A.1, 2TM.9 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.741, D:D.741, D:D.743, D:D.743, H2O.2 MG.7: 2 residues within 4Å: Chain D: D.739 Ligands: 2TM.9 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: W.897, E.898, I.900 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:W.897 MG.10: 4 residues within 4Å: Chain F: A.312, G.316, P.317, 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.4: 5 residues within 4Å: Chain D: C.1112, 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.5: 5 residues within 4Å: Chain D: C.58, C.60, G.61, 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

1 x 2TM: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine(Non-covalent)

2TM.9: 14 residues within 4Å: Chain C: R.557, R.879 Chain D: R.704, P.706, N.737, D.739, D.741, Q.1235, M.1238, T.1240 Chain G: G.14 Ligands: GTP-G-A.1, MG.6, MG.7 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:R.704, D:R.704, D:N.737, D:Q.1235 Water bridges: D:M.1238, C:R.557, C:R.557 Salt bridges: C:R.557, C:R.879

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nova, I.C. et al., Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-07-24

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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