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SMTL ID : 9q93.1

CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 6.60 Å

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 B: L.8, L.9, E.37, R.38, G.39, T.40, G.41, K.42, I.226 Ligands: AF3.2, MG.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.37, B:T.40, B:G.41, B:K.42
ADP.4:	10 residues within 4Å: Chain C: N.7, L.8, L.9, R.38, G.39, T.40, G.41, E.43 Ligands: AF3.5, MG.6 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.9, C:G.39, C:E.43
ADP.7:	12 residues within 4Å: Chain D: L.8, L.9, G.10, G.39, T.40, G.41, K.42, E.43, L.44, I.226 Ligands: AF3.8, MG.9 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:L.9, D:G.39, D:G.41, D:K.42, D:E.43, D:L.44
ADP.10:	13 residues within 4Å: Chain E: L.9, R.38, G.39, T.40, G.41, E.43, L.44, M.189, F.193, I.226, K.230 Ligands: AF3.11, MG.12 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:L.9, E:T.40, E:G.41, E:E.43, E:L.44
ADP.13:	12 residues within 4Å: Chain F: N.7, L.8, L.9, 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 F Hydrogen bonds: F:L.8, F:L.9, F:E.43, F:L.44

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

AF3.2:	5 residues within 4Å: Chain B: G.36, E.37, R.38 Ligands: ADP.1, MG.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.37
AF3.5:	3 residues within 4Å: Chain C: D.107 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP)
AF3.8:	5 residues within 4Å: Chain D: R.38, G.39, E.43 Ligands: ADP.7, MG.9 No protein-ligand interaction detected (PLIP)
AF3.11:	6 residues within 4Å: Chain E: R.38, G.39, T.40 Chain F: D.164 Ligands: ADP.10, MG.12 No protein-ligand interaction detected (PLIP)
AF3.14:	6 residues within 4Å: Chain F: E.37, K.42, E.43, D.107 Ligands: ADP.13, MG.15 No protein-ligand interaction detected (PLIP)

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

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:	3 residues within 4Å: Chain D: E.43 Ligands: ADP.7, AF3.8 No protein-ligand interaction detected (PLIP)
MG.12:	3 residues within 4Å: Chain E: E.43 Ligands: ADP.10, AF3.11 No protein-ligand interaction detected (PLIP)
MG.15:	4 residues within 4Å: Chain F: E.43, D.107 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

2025-04-02

Peptides

Psp operon transcriptional activator: ABCDEF
RNA polymerase sigma-54 factor: G
DNA-directed RNA polymerase subunit alpha: JK
DNA-directed RNA polymerase subunit beta: L
DNA-directed RNA polymerase subunit beta': M
DNA-directed RNA polymerase subunit omega: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
6

B
1

C
2

D
3

E
4

F
5

G
M

J
A

K
B

L
C

M
D

N
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 (CD)

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...

4xsx.2 | 4xsy.1 | 4xsy.2 | 4xsz.1 | 4xsz.2 | 4yfk.1 | 4yfk.2 | 4yfn.1 | 4yfn.2 | 4yfx.1 | 4yfx.2 | 4yg2.1 | 4yg2.2 | 4yln.1 | 4yln.2 | 4yln.3 | 4ylo.1 | 4ylo.2 | 4ylo.3 | 4ylp.1 | 4ylp.2 | 4ylp.3 | 4zh2.1 | 4zh2.2 | 4zh3.1 | 4zh3.2 | 4zh4.1 | 4zh4.2 | 5ezk.1 | 5ipl.1 | 5ipm.1 | 5ipn.1 | 5ms0.1 | 5my1.1 | 5nsr.1 | 5nss.1 | 5nwt.1 | 5tbz.1 | 5tbz.2 | 5uac.1 | 5uac.2 | 5uag.1 | 5uag.2 | 5uah.1 | 5uah.2 | 5uaj.1 | 5uaj.2 | 5ual.1 | 5ual.2 | 5uaq.1 | 5uaq.2 | 5ui8.1 | 5vsw.1 | 5vsw.2 | 5vt0.1 | 5w1s.1 | 5w1s.2 | 5w1t.1 | 5w1t.2 | 6alf.1 | 6alg.1 | 6alh.1 | 6asx.1 | 6b6h.1 | 6bjs.1 | 6byu.1 | 6byu.2 | 6c6s.1 | 6c6t.1 | 6c6u.1 | 6c9y.1 | 6ca0.1 | 6cux.1 | 6cux.2 | 6flp.1 | 6flq.1 | 6gfw.1 | 6gh5.1 | 6gh6.1 | 6gov.1 | 6jbq.1 | 6jnx.1 | 6k4y.1 | 6kj6.1 | 6ldi.1 | 6n57.1 | 6n58.1 | 6n60.1 | 6n62.1 | 6omf.1 | 6oul.1 | 6p18.1 | 6p19.1 | 6p1k.1 | 6pb4.1 | 6pb5.1 | 6pb6.1 | 6pmi.1 | 6pmj.1 | 6psq.1 | 6psr.1 | 6pss.1 | 6pst.1 | 6psu.1 | 6psv.1 | 6psw.1 | 6r9b.1 | 6r9g.1 | 6rh3.1 | 6ri7.1 | 6ri9.1 | 6rin.1 | 6rip.1 | 6tqn.1 | 6tqo.1 | 6utv.1 | 6utw.1 | 6utx.1 | 6uty.1 | 6utz.1 | 6uu0.1 | 6uu1.1 | 6uu2.1 | 6uu3.1 | 6uu4.1 | 6uu5.1 | 6uu6.1 | 6uu7.1 | 6uu8.1 | 6uu9.1 | 6uua.1 | 6uub.1 | 6uuc.1 | 6vjs.1 | 6vjs.2 | 6vyx.8 | 6vyx.9 | 6vyx.11 | 6wmu.1 | 6x26.1 | 6x2f.1 | 6x2n.1 | 6x43.1 | 6x4w.1 | 6x4y.1 | 6x50.1 | 6xas.1 | 6xav.1 | 6xh7.1 | 6xh8.1 | 6xl5.1 | 6xl9.1 | 6xlj.1 | 6xll.1 | 6xlm.1 | 6xln.1 | 6z9p.1 | 6z9q.1 | 6z9r.1 | 6z9s.1 | 6z9t.1 | 6ztl.1 | 6ztm.1 | 6zto.1 | 6ztp.1 | 6zu1.1 | 7adb.1 | 7adc.1 | 7add.1 | 7ade.1 | 7bef.1 | 7beg.1 | 7c17.1 | 7c97.1 | 7chw.1 | 7d7c.1 | 7d7d.1 | 7dy6.1 | 7khb.1 | 7khc.1 | 7khe.1 | 7khi.1 | 7m8e.1 | 7mkd.1 | 7mke.1 | 7mki.1 | 7mkj.1 | 7mkn.1 | 7mko.1 | 7mkp.1 | 7mkq.1 | 7n4e.1 | 7py0.1 | 7py1.1 | 7py3.1 | 7py5.1 | 7py6.1 | 7py7.1 | 7py8.1 | 7pyj.1 | 7pyk.1 | 7q0j.1 | 7q0k.1 | 7qv9.1 | 7qwp.1 | 7qxi.1 | 7szj.1 | 7szk.1 | 7ubm.1 | 7ubn.1 | 7uwe.1 | 7uwh.1 | 7vwy.1 | 7vwz.1 | 7w5w.1 | 7w5x.1 | 7w5y.1 | 7xue.1 | 7xug.1 | 7xui.1 | 7yp9.1 | 7ypa.1 | 7ypb.1 | 8aby.1 | 8abz.1 | 8ac0.1 | 8ac1.1 | 8ac2.1 | 8acp.1 | 8ad1.1 | 8e3f.1 | 8e5k.1 | 8e5o.1 | 8e6x.1 | 8e6z.1 | 8eg7.1 | 8eg8.1 | 8egb.1 | 8eh8.1 | 8eh9.1 | 8eha.1 | 8ehf.1 | 8ehi.1 | 8f1i.1 | 8f1j.1 | 8f1k.1 | 8fix.1 | 8fiy.1 | 8ftd.1 | 8fvr.1 | 8fvw.1 | 8g00.1 | 8g7e.1 | 8igr.1 | 8igs.1 | 8jo2.1 | 8pbl.1 | 8pdy.1 | 8pen.1 | 8pfg.1 | 8pfj.1 | 8ph9.1 | 8phk.1 | 8pib.1 | 8pid.1 | 8pil.1 | 8pim.1 | 8re4.1 | 8rea.1 | 8reb.1 | 8rec.1 | 8red.1 | 8ree.1 | 8sy5.1 | 8sy6.1 | 8sy7.1 | 8szw.1 | 8t02.1 | 8to1.1 | 8to6.1 | 8to8.1 | 8toe.1 | 8tom.1 | 8txo.1 | 8u3b.1 | 8y6u.1 | 9guw.1 | 9gux.1 | 9q90.1 | 9q91.1 | 9q94.1 | 9q95.1 | 9q96.1 | 9q97.1 | 9q98.1

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