SMTL ID : 8w8o.1

Thermus thermophilus initiation complex in the half-translocated state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 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: 20 residues within 4Å: Chain C: P.444, E.445, G.446, A.447, N.448, 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, MG.9, MG.10 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:E.445, C:G.446, C:N.448, C:N.448, C:Q.567, C:H.999 Water bridges: C:R.405, C:A.447, C:A.447

7 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 4 residues within 4Å: Chain B: D.183, D.191, L.192, D.193 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.183, B:D.191, B:D.193 MG.5: 4 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: GTP-G-A.1 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.739, D:D.741, D:D.743, H2O.14, H2O.17 MG.6: 1 residues within 4Å: Chain D: K.840 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:K.840, H2O.3, H2O.3, H2O.18, H2O.18 MG.7: 3 residues within 4Å: Chain D: W.897, E.898, I.900 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:W.897, D:I.900, H2O.23 MG.8: 4 residues within 4Å: Chain F: A.312, E.313, G.316, W.319 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:A.312, F:G.316, F:W.319 MG.9: 2 residues within 4Å: Ligands: GTP-G-A.1, GTP-G-A.1 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: GTP-G-A.1 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain D: C.1112, R.1189, 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: 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

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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