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SMTL ID : 9q97.1

CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.60 Å

Oligo State

hetero-1-2-1-1-1-6-mer

Ligands

5 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)(Non-covalent)

ADP.1:	10 residues within 4Å: Chain G: L.8, L.9, G.10, R.38, G.39, T.40, G.41, I.226 Ligands: AF3.2, MG.3 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.10
ADP.4:	12 residues within 4Å: Chain H: L.8, L.9, G.10, E.37, G.39, T.40, G.41, K.42, E.43, K.230 Ligands: AF3.5, MG.6 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:L.9, H:G.10, H:G.39, H:T.40, H:G.41, H:K.42, H:E.43
ADP.7:	11 residues within 4Å: Chain I: L.8, L.9, G.36, G.39, T.40, G.41, K.42, E.43, R.227 Ligands: AF3.8, MG.9 5 PLIP interactions: 5 interactions with chain I Hydrogen bonds: I:L.9, I:G.39, I:G.41, I:G.41, I:E.43
ADP.10:	14 residues within 4Å: Chain J: N.7, L.8, L.9, E.37, G.39, T.40, G.41, K.42, E.43, I.226, R.227 Chain K: D.164 Ligands: MG.11, AF3.12 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:L.9, J:G.39, J:K.42, J:E.43, J:I.226
ADP.13:	11 residues within 4Å: Chain K: D.6, N.7, L.8, L.9, G.41, K.42, E.43, L.44, I.226 Ligands: AF3.14, MG.15 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:G.41, K:K.42, K:E.43, K:L.44

5 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.2:	3 residues within 4Å: Chain G: T.148 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP)
AF3.5:	8 residues within 4Å: Chain H: G.36, E.37, R.38, G.39, T.148, N.149 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP)
AF3.8:	7 residues within 4Å: Chain I: G.36, E.37, R.38, G.39, N.149 Ligands: ADP.7, MG.9 No protein-ligand interaction detected (PLIP)
AF3.12:	4 residues within 4Å: Chain K: R.162, D.164 Ligands: ADP.10, MG.11 No protein-ligand interaction detected (PLIP)
AF3.14:	5 residues within 4Å: Chain K: E.37, G.39, D.107 Ligands: ADP.13, MG.15 No protein-ligand interaction detected (PLIP)

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

MG.3:	2 residues within 4Å: Ligands: ADP.1, AF3.2 No protein-ligand interaction detected (PLIP)
MG.6:	2 residues within 4Å: Ligands: ADP.4, AF3.5 No protein-ligand interaction detected (PLIP)
MG.9:	2 residues within 4Å: Ligands: ADP.7, AF3.8 No protein-ligand interaction detected (PLIP)
MG.11:	2 residues within 4Å: Ligands: ADP.10, AF3.12 No protein-ligand interaction detected (PLIP)
MG.15:	2 residues within 4Å: Ligands: ADP.13, AF3.14 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Gao, F. et al., Subunit specialisation in AAA+ proteins and substrate unfolding during transcription complex remodelling. To Be Published

Release Date

2025-03-26

Peptides

RNA polymerase sigma-54 factor: A
DNA-directed RNA polymerase subunit alpha: BC
DNA-directed RNA polymerase subunit beta: D
DNA-directed RNA polymerase subunit beta': E
DNA-directed RNA polymerase subunit omega: F
Psp operon transcriptional activator: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
A

C
B

D
C

E
D

F
E

G
1

H
2

I
3

J
4

K
5

L
6

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

RNA polymerase sigma-54 factor

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

Psp operon transcriptional activator

Toggle Identical (HI)

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