SMTL ID : 9ujl.1

CryoEM structure of the T.thermophilus transcription initiation complex in the presence of Ap4A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.61 Å

Oligo State

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

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain B: C.1112, R.1189, C.1194, Q.1195, C.1201, C.1204 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1112, B:C.1194, B:C.1201, B:C.1204 ZN.2: 4 residues within 4Å: Chain B: C.58, C.60, C.73, C.76 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.58, B:C.60, B:C.73, B:C.76

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain B: D.739, D.741, D.743 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.739, B:D.741, B:D.743, H2O.1 MG.4: 1 residues within 4Å: Chain B: K.840 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:K.840 MG.5: 1 residues within 4Å: Chain G: V.170 No protein-ligand interaction detected (PLIP)

1 x 1N7: CHAPSO(Non-covalent)

1N7.6: 9 residues within 4Å: Chain B: E.888, A.933, Y.936, Y.937 Chain H: Q.16, Y.20, Q.180, R.198, W.200 6 PLIP interactions: 3 interactions with chain H, 3 interactions with chain B Hydrophobic interactions: H:Y.20, H:W.200, B:Y.936, B:Y.936, B:Y.937 Hydrogen bonds: H:Q.16

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 beta': B
RNA polymerase sigma factor SigA: D
DNA-directed RNA polymerase subunit omega: E
DNA-directed RNA polymerase subunit beta: F
DNA-directed RNA polymerase subunit alpha: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
D

D
F

E
E

F
C

G
A

H
B

DNA-directed RNA polymerase subunit beta'

RNA polymerase sigma factor SigA

DNA-directed RNA polymerase subunit omega

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit alpha

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