SMTL ID : 7eh0.1

Thermus thermophilus RNA polymerase transcription initiation complex containing a template-strand purine at position TSS-2, UpA RNA primer and CMPcPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

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

Ligands

1 x U- A: RNA (5'-R(*UP*A)-3')(Non-covalent)

U-A.1: 14 residues within 4Å: Chain C: Q.567, K.838, K.846, H.999 Chain D: R.704, A.705, D.739, D.741, D.743 Chain H: T.15, A.16, A.17 Ligands: MG.5, 2TM.8 Protein-ligand interaction information (PLIP) not available

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: 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.5: 5 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: U-A.1, 2TM.8 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.739, D:D.741, D:D.741, D:D.743 MG.6: 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.7: 3 residues within 4Å: Chain D: W.897, E.898, I.900 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:W.897, D:I.900 MG.9: 3 residues within 4Å: Chain F: A.312, 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: 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 ZN.4: 4 residues within 4Å: Chain D: C.58, C.60, 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.8: 13 residues within 4Å: Chain C: G.446, R.557, S.878, R.879 Chain D: R.704, P.706, N.737, D.739, D.741, R.1029 Chain H: G.14 Ligands: U-A.1, MG.5 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:R.557, C:S.878, C:R.879, D:R.704, D:R.704, D:N.737 Salt bridges: C:R.879, D:R.1029

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skalenko, K.S. et al., Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli . Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-07-14

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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