9q98.1 | SWISS-MODEL Template Library

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SMTL ID : 9q98.1

CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 8.30 Å

Oligo State

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

Ligands

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

ADP.1:	13 residues within 4Å: Chain A: N.7, L.8, E.37, R.38, G.39, T.40, G.41, K.42, T.148, I.226, R.227 Ligands: AF3.2, MG.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.8, A:T.40, A:G.41, A:K.42, A:R.227
ADP.4:	9 residues within 4Å: Chain B: N.7, L.8, R.38, G.39, T.40, G.41, I.226 Ligands: AF3.5, MG.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.39, B:T.40, B:G.41
ADP.7:	12 residues within 4Å: Chain C: N.7, L.8, G.39, T.40, G.41, K.42, E.43, L.44, I.226 Chain D: D.164 Ligands: AF3.8, MG.9 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.8, C:G.41, C:K.42, C:E.43
ADP.10:	15 residues within 4Å: Chain D: N.7, L.9, E.37, R.38, G.39, T.40, G.41, K.42, E.43, L.44, I.226, R.227, K.230 Ligands: AF3.11, MG.12 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.7, D:L.9, D:G.39, D:K.42, D:E.43, D:L.44
ADP.13:	12 residues within 4Å: Chain E: N.7, L.8, G.39, T.40, G.41, K.42, E.43, L.44, I.226, R.227 Ligands: AF3.14, MG.15 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.40, E:G.41, E:K.42, E:E.43

5 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.2:	4 residues within 4Å: Chain A: T.148 Chain B: D.164 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP)
AF3.5:	4 residues within 4Å: Chain C: E.125, D.164 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP)
AF3.8:	5 residues within 4Å: Chain C: R.38, G.39 Chain D: D.164 Ligands: ADP.7, MG.9 No protein-ligand interaction detected (PLIP)
AF3.11:	6 residues within 4Å: Chain D: E.37, R.38, G.39, K.42 Ligands: ADP.10, MG.12 No protein-ligand interaction detected (PLIP)
AF3.14:	8 residues within 4Å: Chain E: E.37, R.38, G.39, T.40, G.41, I.226 Ligands: ADP.13, MG.15 No protein-ligand interaction detected (PLIP)

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

MG.3:	3 residues within 4Å: Chain A: T.148 Ligands: ADP.1, AF3.2 No protein-ligand interaction detected (PLIP)
MG.6:	3 residues within 4Å: Chain C: E.125 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.12:	3 residues within 4Å: Chain D: E.43 Ligands: ADP.10, AF3.11 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

Psp operon transcriptional activator: ABCDEF
DNA-directed RNA polymerase subunit alpha: GH
DNA-directed RNA polymerase subunit beta: I
DNA-directed RNA polymerase subunit beta': J
DNA-directed RNA polymerase subunit omega: K
RNA polymerase sigma-54 factor: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
6

G
A

H
B

I
C

J
D

K
E

L
M

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Psp operon transcriptional activator

Toggle Identical (BD) Toggle Identical (EF)

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-54 factor

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2vii.1 | 3iyd.1 | 3lu0.1 | 4jk1.1 | 4jk1.2 | 4jk2.1 | 4jk2.2 | 4jkr.1 | 4jkr.2 | 4kmu.1 | 4kmu.2 | 4kn4.1 | 4kn4.2 | 4kn7.1 | 4kn7.2 | 4ljz.1 | 4ljz.2 | 4lk0.1 | 4lk0.2 | 4lk1.1 | 4lk1.2 | 4llg.1 | 4llg.2 | 4mex.1 | 4mex.2 | 4mey.1 | 4mey.2 | 4s20.1 | 4s20.2 | 4xsx.1 more...less...

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