SMTL ID : 9uko.1

CryoEM structure of the T.thermophilus transcription initiation complex bound to Ap4A-C, -1 dA in the template DNA strand

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.89 Å

Oligo State

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

Ligands

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

MG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain C: E.445 Ligands: B4P.9 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: C5P.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.739, D:D.741, D:D.743 MG.7: 1 residues within 4Å: Chain D: K.840 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:K.840

1 x 1N7: CHAPSO(Non-covalent)

1N7.2: 8 residues within 4Å: Chain B: Y.20, Q.180, R.198, W.200 Chain D: E.888, A.933, Y.936, Y.937 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:W.200, B:W.200, D:Y.936, D:Y.937 Hydrogen bonds: B:Q.16, B:Y.20

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 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.5: 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 C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.8: 9 residues within 4Å: Chain C: K.838, K.846 Chain D: R.704, D.739, D.741, D.743 Chain G: G.11 Ligands: MG.6, B4P.9 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Salt bridges: C:K.838, C:K.846 Hydrogen bonds: D:R.704

1 x B4P: BIS(ADENOSINE)-5'-TETRAPHOSPHATE(Non-covalent)

B4P.9: 15 residues within 4Å: Chain C: R.420, P.444, A.447, N.448, Q.567, K.838, H.999 Chain D: G.742 Chain F: E.345 Chain G: G.11, T.12, A.13, G.14 Ligands: MG.3, C5P.8 8 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D, 2 interactions with chain F Hydrogen bonds: C:R.409, C:N.448, C:Q.567, C:K.1004, D:G.742, F:E.345, F:E.345 pi-Cation interactions: C:R.420

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duan, W. et al., Molecular basis for noncanonical transcription initiation from Np4A alarmones. Nat.Chem.Biol. (2025)

Release Date

2025-10-22

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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