- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-2-1-1-1-1-2-mer
- Ligands
- 1 x GTP- C- A- G: RNA (5'-D(*(GTP))-R(P*CP*AP*G)-3')(Non-covalent)
GTP-C-A-G.1: 25 residues within 4Å:- Chain C: Q.510, Q.513, L.533, R.540, P.564, N.568, Q.688, K.1065, K.1073, H.1237
- Chain D: R.425, A.426, P.427, D.460, D.462, D.464
- Chain F: G.512, D.513
- Chain J: C.13, T.14, G.15, C.16, A.17
- Ligands: MG.5, MG.13
6 PLIP interactions:4 interactions with chain C, 2 interactions with chain F- Hydrogen bonds: C:Q.510, C:N.568, F:D.513, F:D.513
- Salt bridges: C:R.540, C:R.540
- 5 x 1N7: CHAPSO(Non-covalent)
1N7.2: 9 residues within 4Å:- Chain A: E.72, D.135
- Chain C: Q.725, Y.726, R.731, E.962, Q.965, I.966, A.969
9 PLIP interactions:9 interactions with chain C- Hydrophobic interactions: C:Q.725, C:Y.726, C:Y.726, C:Y.726, C:Y.726, C:E.962, C:I.966, C:A.969
- Hydrogen bonds: C:Q.965
1N7.3: 13 residues within 4Å:- Chain C: Q.46, Y.47, Y.179, D.396, S.398, A.399, V.400, R.452, E.458, E.461, R.465, E.583, Y.584
15 PLIP interactions:15 interactions with chain C- Hydrophobic interactions: C:Q.46, C:Y.47, C:Y.179, C:A.399, C:V.400, C:E.583, C:Y.584, C:Y.584
- Hydrogen bonds: C:Q.46, C:D.396, C:S.398, C:A.399, C:V.400, C:R.465, C:R.465
1N7.8: 8 residues within 4Å:- Chain C: Q.1264
- Chain D: L.255, D.256
- Chain F: I.505, L.519, F.522
- Chain J: A.19, C.20
4 PLIP interactions:1 interactions with chain C, 1 interactions with chain D, 2 interactions with chain F- Hydrophobic interactions: C:Q.1264, F:I.505, F:F.522
- Hydrogen bonds: D:D.256
1N7.9: 12 residues within 4Å:- Chain G: Y.168, D.170, E.172, Y.173, K.174, E.175, M.178, L.218, R.219, Y.222, M.226, E.242
13 PLIP interactions:13 interactions with chain G- Hydrophobic interactions: G:Y.168, G:Y.168, G:D.170, G:Y.173, G:L.218, G:R.219, G:Y.222, G:Y.222, G:Y.222
- Hydrogen bonds: G:Y.173, G:K.174, G:K.174, G:E.175
1N7.11: 10 residues within 4Å:- Chain H: Y.168, K.171, E.172, Y.173, K.174, E.175, M.178, R.219, Y.222, M.226
10 PLIP interactions:10 interactions with chain H- Hydrophobic interactions: H:Y.168, H:Y.168, H:R.219, H:Y.222, H:Y.222, H:Y.222
- Hydrogen bonds: H:Y.173, H:K.174, H:K.174, H:E.175
- 3 x 118: TETRAPHENYLANTIMONIUM ION(Non-covalent)
118.4: 10 residues within 4Å:- Chain C: R.540, E.541, R.542, A.543, G.544
- Chain D: L.788, A.791, N.792
- Chain I: C.44
- Chain J: G.11
7 PLIP interactions:5 interactions with chain D, 2 interactions with chain C- Hydrophobic interactions: D:L.788, D:L.788, D:A.791, D:A.791, D:N.792, C:E.541, C:R.542
118.10: 8 residues within 4Å:- Chain G: Y.126, I.142, G.146, A.162, C.164, E.184, Y.244, W.249
7 PLIP interactions:7 interactions with chain G- Hydrophobic interactions: G:I.142, G:A.162, G:Y.244, G:W.249, G:W.249, G:W.249
- pi-Stacking: G:W.249
118.12: 8 residues within 4Å:- Chain H: Y.126, I.142, G.146, A.162, C.164, F.182, Y.244, W.249
7 PLIP interactions:7 interactions with chain H- Hydrophobic interactions: H:I.142, H:A.162, H:F.182, H:W.249, H:W.249, H:W.249
- pi-Stacking: H:W.249
- 2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.5: 4 residues within 4Å:- Chain D: D.460, D.462, D.464
- Ligands: GTP-C-A-G.1
5 PLIP interactions:5 interactions with chain D- Metal complexes: D:D.460, D:D.460, D:D.462, D:D.464, D:D.464
MG.13: 1 residues within 4Å:- Ligands: GTP-C-A-G.1
No protein-ligand interaction detected (PLIP)- 2 x ZN: ZINC ION(Non-covalent)
ZN.6: 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.7: 6 residues within 4Å:- Chain D: C.814, R.883, C.888, D.889, 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
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Yang, Y. et al., Structural visualization of transcription activated by a multidrug-sensing MerR family regulator. Nat Commun (2021)
- Release Date
- 2021-04-07
- 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
MerR family transcriptional regulator EcmrR: GH - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
H
SMTL ID : 6xlj.1
Cryo-EM structure of EcmrR-RNAP-promoter initial transcribing complex with 4-nt RNA transcript (EcmrR-RPitc-4nt)
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
MerR family transcriptional regulator EcmrR
Toggle Identical (GH)Related Entries With Identical Sequence
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 | 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 | 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 | 6vyx.6 | 6vyx.8 | 6vyx.9 | 6vyx.11 | 6vz3.6 | 6vzj.7 | 6vzj.8 | 6vzj.9 | 6wmu.1 | 6x26.1 | 6x2f.1 | 6x2n.1 | 6x43.1 | 6x4w.1 | 6x4y.1 | 6x50.1 | 6xas.1 | 6xav.1 | 6xdq.7 | 6xdq.9 | 6xdq.10 | 6xdq.11 | 6xdq.12 | 6xh7.1 | 6xh8.1 | 6xl5.1 | 6xl6.1 | 6xl9.1 | 6xla.1 | 6xlk.1 | 6xll.1 | 6xlm.1 | 6xln.1 | 6z9p.1 | 6z9q.1 | 6z9r.1 | 6z9s.1 | 6z9t.1 | 6ztj.53 | 6ztj.54 | 6ztj.55 | 6ztj.56 | 6ztj.57 | 6ztl.1 | 6ztm.1 | 6ztn.49 | 6ztn.50 | 6ztn.51 | 6ztn.52 | 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 | 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 | 8f3c.1 | 8fix.1 | 8fiy.1 | 8ftd.1 | 8fvr.1 | 8fvw.1 | 8g00.1 | 8g1s.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 | 8sy5.1 | 8sy6.1 | 8sy7.1 | 8to1.1 | 8to6.1 | 8to8.1 | 8toe.1 | 8tom.1 | 8txo.1 | 8u3b.1 | 8urx.7 | 8urx.9 | 8urx.10 | 8urx.11 | 8urx.12 | 8y6u.1