7EGS: Lobe domain of E. coli RNA polymerase

Name: PDB 7EGS: The crystal structure of lobe domain of E. coli RNA polymerase complexed with the C-terminal domain of UvrD
Published: 2022-04-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

The crystal structure of lobe domain of E. coli RNA polymerase complexed with the C-terminal domain of UvrD. Determined by X-ray diffraction at 1.7 Å resolution. Released 6 Apr 2022.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Escherichia coli (strain K12)
Chains: 2
Atoms: 2,889
Mol. weight: 41.75 kDa
Released: 6 Apr 2022

Explore 7EGS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7EGS contains 16 α-helices and 25 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: 14 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	154-159	6	1
β-strand	172-177	6	1
β-strand	180	1	2
β-strand	184-188	5	1
β-strand	194-198	5	1
β-strand	204-205	2	1
α-helix	207-212	6
α-helix	217-224	8
β-strand	227-233	7	3
β-strand	236-240	5	3
α-helix	243-246	4
β-strand	250	1	4
β-strand	255-257	3	5
β-strand	260-263	4	5
β-strand	268	1	4
α-helix	269-270	2
α-helix	271-279	9
β-strand	284-287	4	3
α-helix	289-292	4
β-strand	296	1	6
β-strand	297	1	3
β-strand	301-303	3	7
β-strand	308-311	4	7
α-helix	315	1
β-strand	316	1	6
α-helix	317	1
α-helix	319-327	9
β-strand	332-336	5	3
α-helix	346-353	8
α-helix	359-370	12
α-helix	378-389	12
β-strand	396	1	2
α-helix	398-408	11
α-helix	422-436	15

Chain B: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	675-678	4	7
β-strand	682-690	9	7
α-helix	693-695	3
β-strand	697-702	6	7
β-strand	706-711	6	7
α-helix	712-714	3
β-strand	717-719	3	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA-directed RNA polymerase subunit beta	A	protein	295	Escherichia coli (strain K12)	P0A8V2 (AlphaFold model)
DNA helicase II	B	protein	70	Escherichia coli (strain K12)	P03018 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7EGS_1 DNA-directed RNA polymerase subunit beta (chains A)
AMDSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATI
ILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETASFDIEANGKVYVEKGRR
ITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQS
GHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENL
FFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVD

Sequence of entity 2 (B), FASTA

>7EGS_2 DNA helicase II (chains B)
AMDVSHQRMGTPMVENDSGYKLGQRVRHAKFGEGTIVNMEGSGEHSRLQVAFQGQGIKWL
VAAYARLESV

Primary citation

Crucial role and mechanism of transcription-coupled DNA repair in bacteria. Bharati, B.K., Gowder, M., Zheng, F. et al. Nature (2022) 604:152-159. DOI 10.1038/s41586-022-04530-6 · PubMed

Other PDB entries of the same protein (UniProt P0A8V2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3LTI 1.6 Å, Crystal structure of the Escherichia coli RNA polymerase beta subunit beta2-betai4 domains
8FVW 2.1 Å, CryoEM structure of E.coli transcription elongation complex bound to ppGpp
8FVR 2.42 Å, CryoEM structure of E.coli transcription elongation complex
9ZP4 2.42 Å, E. coli RNA polymerase elongation complex containing the unnatural dZ:PTP base pair in a…
8HKC 2.49 Å, Cryo-EM structure of E. coli RNAP sigma32 complex
6XL5 2.5 Å, Cryo-EM structure of EcmrR-RNAP-promoter open complex (EcmrR-RPo)
6XL9 2.5 Å, Cryo-EM structure of EcmrR-RNAP-promoter initial transcribing complex with 3-nt RNA…
12EC 2.6 Å, Half-translocated RNA polymerase elemental paused elongation complex, swiveled (ePEC…
8F1J 2.6 Å, SigN RNA polymerase early-melted intermediate bound to mismatch DNA fragment dhsU36mm2…
8PIB 2.6 Å, autoinhibited RfaH bound to E. coli transcription complex paused at ops site (encounter…
9MSF 2.6 Å, de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic…
9YMV 2.6 Å, De novo initial transcribing RNA polymerase with pretranslocated 3-mer RNA / product…

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