1BDF: RNA polymerase alpha subunit

Structure of escherichia coli RNA polymerase alpha subunit N-terminal domain. Determined by X-ray diffraction at 2.5 Å resolution. Released 11 May 1999.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Escherichia coli
Chains: 4
Atoms: 7,179
Mol. weight: 103.65 kDa
Released: 11 May 1999

Explore 1BDF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1BDF contains 23 α-helices and 62 β-strands across 4 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, 17 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	1
β-strand	23-32	10	1
α-helix	35-47	13
β-strand	54-61	8	2
β-strand	74	1	3
α-helix	78-86	9
β-strand	90-91	2	4
β-strand	97-105	9	2
β-strand	108-111	4	3
α-helix	112-114	3
β-strand	115	1	2
β-strand	122-123	2	4
β-strand	129-133	5	3
β-strand	139-148	10	2
β-strand	152-153	2	5
α-helix	155-157	3
β-strand	172	1	2
β-strand	175-176	2	5
β-strand	180-186	7	1
β-strand	189	1	1
β-strand	198-207	10	1
α-helix	213-227	15
α-helix	228-231	4

Chain B: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	13-18	6	6
β-strand	23-31	9	6
α-helix	35-47	13
β-strand	54-61	8	7
β-strand	74	1	7
α-helix	78-86	9
β-strand	90-92	3	8
β-strand	97-111	15	7
α-helix	112-114	3
β-strand	121-123	3	8
β-strand	129-148	20	7
β-strand	152-153	2	9
α-helix	156-158	3
β-strand	171-172	2	7
β-strand	175-176	2	9
β-strand	180-186	7	6
β-strand	189	1	6
β-strand	199-207	9	6
α-helix	213-227	15
α-helix	228-231	4

Chain C: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	10
β-strand	23-31	9	10
α-helix	35-47	13
β-strand	54-61	8	11
β-strand	74	1	12
α-helix	78-86	9
β-strand	90-92	3	13
β-strand	97-105	9	11
β-strand	108-111	4	12
α-helix	112-114	3
β-strand	115	1	11
β-strand	121-123	3	13
β-strand	129-133	5	12
β-strand	139-148	10	11
β-strand	171-172	2	11
β-strand	180-186	7	10
β-strand	189	1	10
β-strand	199-207	9	10
α-helix	213-227	15
α-helix	228-231	4

Chain D: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	14
β-strand	23-31	9	14
α-helix	35-47	13
β-strand	54-61	8	15
β-strand	74	1	16
α-helix	78-86	9
β-strand	90-92	3	17
β-strand	97-105	9	15
β-strand	108-111	4	16
α-helix	112-114	3
β-strand	121-123	3	17
β-strand	129-133	5	16
β-strand	139-148	10	15
β-strand	152-153	2	18
β-strand	171-172	2	15
β-strand	175-176	2	18
β-strand	180-186	7	14
β-strand	189	1	14
β-strand	199-207	9	14
α-helix	213-227	15
α-helix	228-231	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA polymerase alpha subunit	A, B, C, D	protein	235	Escherichia coli	P0A7Z4 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>1BDF_1 RNA POLYMERASE ALPHA SUBUNIT (chains A, B, C, D)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLR

Primary citation

Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain. Zhang, G., Darst, S.A. Science (1998) 281:262-266. DOI 10.1126/science.281.5374.262 · PubMed

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

3K4G 2.05 Å, Crystal structure of E. coli RNA polymerase alpha subunit C-terminal domain
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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