SMTL ID : 6kqd.2 (1 other biounit)

Thermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 3 nt

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

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

Ligands

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

G-G-A.1: 13 residues within 4Å: Chain C: Q.567, K.838, K.846, H.999 Chain D: R.704, D.741, G.742, D.743 Chain G: T.15, C.16, C.17, A.18 Ligands: MG.5 Protein-ligand interaction information (PLIP) not available

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.51, V.170, F.171, S.172, D.202 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.170, H2O.1 MG.5: 4 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: G-G-A.1 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.739, D:D.741, D:D.743, D:D.743 MG.6: 4 residues within 4Å: Chain B: E.64, D.168 Chain D: L.839, K.840 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:K.840, H2O.1

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain D: C.1112, C.1194, 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: 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

1 x DGP: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

DGP.7: 4 residues within 4Å: Chain C: F.394 Chain F: I.341, G.342 Chain G: G.19 No protein-ligand interaction detected (PLIP)

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
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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