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SMTL ID : 6ldi.1

The cryo-EM structure of E. coli CueR transcription activation complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x C- U- C- G- A: RNA (5'-R(*CP*UP*CP*GP*A)-3')(Non-covalent)

C-U-C-G-A.1:

24 residues within 4Å:

Chain C: Q.510, L.533, R.540, P.564, E.565, N.568, I.572, R.687, Q.688, K.1065, K.1073, H.1237
Chain D: R.425, D.460, D.462, D.464
Chain F: D.533, D.534
Chain H: T.12, C.13, G.14, A.15, G.16
Ligands: MG.4

Protein-ligand interaction information (PLIP) not available

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	4 residues within 4Å: Chain D: C.70, C.72, C.85, C.88 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.70, D:C.72, D:C.85, D:C.88
ZN.3:	4 residues within 4Å: Chain D: C.814, C.888, C.895, C.898 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.814, D:C.888, D:C.895, D:C.898

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4:

4 residues within 4Å:

Chain D: D.460, D.462, D.464
Ligands: C-U-C-G-A.1

3 PLIP interactions:

3 interactions with chain D

Metal complexes: D:D.460, D:D.462, D:D.464

1 x AG: SILVER ION(Non-covalent)

AG.5:

4 residues within 4Å:

Chain J: C.116, C.124, I.126, I.127

1 PLIP interactions:

1 interactions with chain J

Metal complexes: J:C.116

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Fang, C. et al., CueR activates transcription through a DNA distortion mechanism. Nat.Chem.Biol. (2020)

Release Date

2020-09-30

Peptides

DNA-directed RNA polymerase subunit alpha: AB
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase subunit beta': D
DNA-directed RNA polymerase subunit omega: E
RNA polymerase sigma factor RpoD: F
HTH-type transcriptional regulator CueR: IJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

I
G

J
H

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

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 factor RpoD

HTH-type transcriptional regulator CueR

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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 | 4xsx.2 more...less...

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 | 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 | 6n57.1 | 6n58.1 | 6n60.1 | 6n61.1 | 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 | 6vu3.7 | 6vyq.9 | 6vyq.10 | 6vyr.7 | 6vyr.9 | 6vyr.10 | 6vys.7 | 6vys.9 | 6vys.10 | 6vyt.6 | 6vyt.8 | 6vyt.9 | 6vyu.6 | 6vyu.8 | 6vyu.9 | 6vyu.11 | 6vyw.6 | 6vyw.8 | 6vyw.9 | 6vyw.11 | 6vyx.6 | 6vyx.8 | 6vyx.9 | 6vyx.11 | 6vyy.6 | 6vyy.8 | 6vyy.9 | 6vyy.11 | 6vyz.6 | 6vyz.8 | 6vyz.9 | 6vyz.11 | 6vz2.6 | 6vz2.8 | 6vz2.9 | 6vz2.11 | 6vz3.6 | 6vz5.6 | 6vz5.8 | 6vz5.9 | 6vz5.11 | 6vzj.7 | 6vzj.8 | 6vzj.9 | 6wmu.1 | 6x26.1 | 6x2f.1 | 6x2n.1 | 6x43.1 | 6x4w.1 | 6x4y.1 | 6x50.1 | 6x6t.7 | 6x6t.9 | 6x6t.10 | 6x6t.12 | 6x7f.7 | 6x7f.9 | 6x7f.10 | 6x7f.12 | 6x7k.7 | 6x7k.9 | 6x7k.10 | 6x7k.12 | 6x9q.7 | 6x9q.9 | 6x9q.10 | 6x9q.12 | 6xas.1 | 6xav.1 | 6xdq.7 | 6xdq.9 | 6xdq.10 | 6xdq.12 | 6xdr.7 | 6xdr.9 | 6xdr.10 | 6xdr.12 | 6xgf.7 | 6xgf.9 | 6xgf.10 | 6xgf.12 | 6xh7.1 | 6xh8.1 | 6xii.7 | 6xii.9 | 6xii.10 | 6xii.12 | 6xij.7 | 6xij.9 | 6xij.10 | 6xl5.1 | 6xl9.1 | 6xlj.1 | 6xll.1 | 6xlm.1 | 6xln.1 | 6z9p.1 | 6z9q.1 | 6z9r.1 | 6z9s.1 | 6z9t.1 | 6ztj.53 | 6ztj.54 | 6ztj.55 | 6ztj.57 | 6ztl.1 | 6ztm.1 | 6ztn.49 | 6ztn.50 | 6ztn.51 | 6ztn.53 | 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 | 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 | 8fvr.1 | 8fvw.1 | 8igr.1 | 8igs.1

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