SMTL ID : 9uls.1

CryoEM structure of the T.thermophilus transcription initiation complex bound to Up4A-C and Up4A, -1 dA in the template DNA strand

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.50 Å

Oligo State

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

Ligands

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

MG.1: 1 residues within 4Å: Chain A: K.83 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: 01.3 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: C5P.10 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.739, D:D.741, D:D.743, H2O.1, H2O.1 MG.8: 2 residues within 4Å: Chain D: D.739 Ligands: 01.11 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.739, H2O.1 MG.9: 2 residues within 4Å: Chain B: E.154 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: Q.16, Y.20, Q.180, R.198 Chain D: E.888, A.933, Y.936, Y.937 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:Q.16 Hydrophobic interactions: D:Y.936, D:Y.936, D:Y.937

2 x 01: P1-(5'-Adenosyl) P4-(5'-uridyl) tetraphosphate

01.3: 13 residues within 4Å: Chain C: R.420, P.444, A.447, N.448, Q.567, K.838, H.999 Chain F: E.345 Chain G: T.12, A.13, G.14 Ligands: MG.4, C5P.10 6 PLIP interactions: 4 interactions with chain C, 1 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: C:A.447 Hydrogen bonds: C:R.420, C:N.448, C:Q.567, F:E.345, D:G.742 01.11: 17 residues within 4Å: Chain C: E.685 Chain D: R.704, P.706, C.733, E.734, N.737, D.739, S.782, R.783, R.1029, Q.1235, M.1238, R.1239 Chain G: A.10, G.11 Ligands: MG.8, C5P.10 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.704, D:R.704, D:N.737, D:S.782, D:R.783, D:Q.1235, D:R.1239, D:R.1239 Salt bridges: D:R.783, D:R.1029, D:R.1029, D:R.1239, D:R.1239 pi-Cation interactions: D:R.783, D:R.783 Water bridges: C:R.879

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 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.6: 5 residues within 4Å: Chain D: C.58, C.60, 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 C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.10: 10 residues within 4Å: Chain C: K.838, K.846 Chain D: R.704, D.739, D.741, D.743 Chain G: G.11 Ligands: 01.3, MG.7, 01.11 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.704, D:D.743 Salt bridges: C:K.838, C:K.846

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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