SMTL ID : 7eh2.2 (1 other biounit)

Thermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.34 Å

Oligo State

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

Ligands

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

G-G.1: 16 residues within 4Å: Chain C: E.445, Q.567, K.838, K.846, H.999 Chain D: R.704, A.705, P.706, D.739, D.741, G.742, D.743 Chain H: C.15, C.16, T.17 Ligands: MG.5 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

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

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain D: C.1112, T.1114, R.1189, 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 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.58, D:C.60, D:C.73, D:C.76, H2O.1

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
K

B
L

C
M

D
N

E
O

F
P

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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