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SMTL ID : 9q92.1

CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

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

5 x AF3: ALUMINUM FLUORIDE(Non-functional Binders)(Non-covalent)(Covalent)

AF3.2:	2 residues within 4Å: Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP)
AF3.5:	7 residues within 4Å: Chain D: G.36, E.37, R.38, G.39, N.149 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP)
AF3.8:	6 residues within 4Å: Chain E: G.36, R.38, N.149 Chain F: D.164 Ligands: ADP.7, MG.9 No protein-ligand interaction detected (PLIP)
AF3.11:	5 residues within 4Å: Chain F: E.37, G.39 Chain G: D.164 Ligands: ADP.10, MG.12 No protein-ligand interaction detected (PLIP)
AF3.14:	6 residues within 4Å: Chain G: G.36, E.37, R.38, G.39 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.12:	2 residues within 4Å: 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 specialization in AAA+ proteins and substrate unfolding during transcription complex remodeling. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-07-16

Peptides

Psp operon transcriptional activator: BCDEFG
RNA polymerase sigma-54 factor: H
DNA-directed RNA polymerase subunit alpha: IJ
DNA-directed RNA polymerase subunit beta: K
DNA-directed RNA polymerase subunit beta': L
DNA-directed RNA polymerase subunit omega: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
6

C
1

D
2

E
3

F
4

G
5

H
M

I
A

J
B

K
C

L
D

M
E

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 (DE)

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

Related Entries With Identical Sequence

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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