3K4G: DNA-directed RNA polymerase subunit alpha

Crystal structure of E. coli RNA polymerase alpha subunit C-terminal domain. Determined by X-ray diffraction at 2.05 Å resolution. Released 7 Jul 2010.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Escherichia coli K-12
Chains: 8
Atoms: 5,585
Mol. weight: 78.39 kDa
Released: 7 Jul 2010

Explore 3K4G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3K4G contains 59 α-helices and 36 β-strands across 8 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: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	251-254	4
β-strand	256	1	1
α-helix	257-260	4
α-helix	264-272	9
β-strand	277	1	1
α-helix	278-283	6
α-helix	286-290	5
α-helix	297-308	12
β-strand	318-319	2	2
β-strand	321	1	3
α-helix	323-324	2
β-strand	325-326	2	4
α-helix	327-328	2

Chains B and G: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	251-254	4
β-strand	256	1	5
α-helix	257-260	4
α-helix	264-271	8
β-strand	277	1	5
α-helix	278-282	5
α-helix	286-290	5
α-helix	297-308	12
β-strand	318-319	2	4
α-helix	323-324	2
β-strand	325-326	2	2

Chain C: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	251-254	4
β-strand	256	1	6
α-helix	257-260	4
α-helix	264-271	8
β-strand	277	1	6
α-helix	278-283	6
α-helix	286-290	5
α-helix	297-308	12
β-strand	318-319	2	7
α-helix	323-324	2
β-strand	325-326	2	8
α-helix	327-328	2

Chain D: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	251-254	4
β-strand	256	1	9
α-helix	257-260	4
α-helix	264-272	9
β-strand	277	1	9
α-helix	278-283	6
α-helix	286-290	5
α-helix	297-308	12
β-strand	318-319	2	8
β-strand	321	1	3
α-helix	323-324	2
β-strand	325-326	2	7

Chain E: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	251-254	4
β-strand	256	1	10
α-helix	257-260	4
α-helix	264-272	9
β-strand	277	1	10
α-helix	278-283	6
α-helix	286-290	5
α-helix	297-308	12
β-strand	318-319	2	11
α-helix	323-324	2
β-strand	325-326	2	12

Chain F: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	251-254	4
β-strand	256	1	13
α-helix	257-260	4
α-helix	264-272	9
β-strand	277	1	13
α-helix	278-282	5
α-helix	286-290	5
α-helix	297-308	12
β-strand	318-319	2	12
β-strand	321	1	14
α-helix	323-324	2
β-strand	325-326	2	11
α-helix	327-328	2

Chain H: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	251-254	4
β-strand	256	1	18
α-helix	257-260	4
α-helix	264-272	9
β-strand	277	1	18
α-helix	278-282	5
α-helix	286-289	4
α-helix	297-308	12
β-strand	318-319	2	17
β-strand	321	1	14
α-helix	323-324	2
β-strand	325-326	2	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA-directed RNA polymerase subunit alpha	A, B, C, D, E, F, G, H	protein	86	Escherichia coli K-12	P0A7Z4 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>3K4G_1 DNA-directed RNA polymerase subunit alpha (chains A, B, C, D, E, F, G, H)
MEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEI
KDVLASRGLSLGMRLENWPPASIADE

Primary citation

Structure of the Escherichia coli RNA polymerase alpha subunit C-terminal domain. Lara-Gonzalez, S., Birktoft, J.J., Lawson, C.L. Acta Crystallogr D Biol Crystallogr (2010) 66:806-812. DOI 10.1107/S0907444910018470 · PubMed

Other PDB entries of the same protein (UniProt P0A7Z4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
1BDF 2.5 Å, Structure of escherichia coli RNA polymerase alpha subunit N-terminal domain
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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