5OND: RfaH from Escherichia coli

Name: PDB 5OND: RfaH from Escherichia coli in complex with ops DNA
Published: 2018-06-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

RfaH from Escherichia coli in complex with ops DNA. Determined by X-ray diffraction at 2.1 Å resolution. Released 6 Jun 2018.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Escherichia coli
Chains: 4
Atoms: 2,615
Mol. weight: 42.19 kDa
Released: 6 Jun 2018

Explore 5OND in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5OND contains 14 α-helices and 18 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10	1
α-helix	14-23	10
β-strand	27-29	3	1
β-strand	32-39	8	2
β-strand	42-49	8	2
β-strand	54-59	6	1
α-helix	66-70	5
β-strand	75-78	4	1
β-strand	80-81	2	3
β-strand	84-85	2	3
β-strand	88	1	1
α-helix	90-96	7
α-helix	120-131	12
α-helix	135-152	18

Chain B: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	4
α-helix	10	1
α-helix	14-23	10
β-strand	27-29	3	4
β-strand	32-39	8	5
β-strand	42-49	8	5
β-strand	54-59	6	4
α-helix	66-70	5
β-strand	75-78	4	4
β-strand	80-81	2	6
β-strand	84-85	2	6
α-helix	86	1
β-strand	87-88	2	4
α-helix	89	1
α-helix	90-97	8
α-helix	120-129	10
α-helix	135-151	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription antitermination protein RfaH	A, B	protein	162	Escherichia coli	P0AFW0 (AlphaFold model)
DNA (5'-d(gpcpgpgptpapgptp*c)-3')	C, D	DNA	9	Escherichia coli

Sequence of entity 1 (A, B), FASTA

>5OND_1 Transcription antitermination protein RfaH (chains A, B)
MQSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFD
PEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLSVYKPKDIVDPATPYPGDKVIITE
GAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKNTEFRKA

Sequence of entity 2 (C, D), FASTA

>5OND_2 DNA (5'-D(*GP*CP*GP*GP*TP*AP*GP*TP*C)-3') (chains C, D)
GCGGTAGTC

Primary citation

The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand. Zuber, P.K., Artsimovitch, I., NandyMazumdar, M. et al. Elife (2018) 7. DOI 10.7554/eLife.36349 · PubMed

Other PDB entries of the same protein (UniProt P0AFW0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2OUG 2.1 Å, Crystal structure of the RfaH transcription factor at 2.1A resolution
8PIB 2.6 Å, autoinhibited RfaH bound to E. coli transcription complex paused at ops site (encounter…
8PID 3.0 Å, backtracked E. coli transcription complex paused at ops site and bound to RfaH
8PEN 3.1 Å, fully recruited RfaH bound to E. coli transcription complex paused at ops site…
8PFG 3.1 Å, autoinhibited RfaH bound to E. coli transcription complex paused at ops site (encounter…
8PHK 3.1 Å, fully recruited RfaH bound to E. coli transcription complex paused at ops site
8URY 3.1 Å, Escherichia coli transcription-translation coupled complex class B (TTC-B) containing…
8PIL 3.2 Å, E. coli transcription complex paused at ops site and bound to RfaH and NusA
8UQL 3.2 Å, Escherichia coli transcription-translation coupled complex class B (TTC-B) containing…
8PFJ 3.4 Å, fully recruited RfaH bound to E. coli transcription complex paused at ops site (not…
8PIM 3.4 Å, fully recruited RfaH bound to E. coli transcription complex paused at ops site (not…
8UR0 3.4 Å, Escherichia coli transcription-translation coupled complex class B (TTC-B) containing…

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