4R9U: Vitamin B12 import system permease protein BtuC

Structure of vitamin B12 transporter BtuCD in a nucleotide-bound outward facing state. Determined by X-ray diffraction at 2.79 Å resolution. Released 19 Nov 2014.

Method: X-ray diffraction
Resolution: 2.79 Å
Organism: Escherichia coli
Chains: 4
Atoms: 8,792
Mol. weight: 127.12 kDa
Ligands: LDA, ANP, MG
Released: 19 Nov 2014

Explore 4R9U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4R9U contains 56 α-helices and 32 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: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	4-32	29
α-helix	40-42	3
α-helix	46-49	4
α-helix	56-80	25
α-helix	93-107	15
α-helix	115-136	22
α-helix	142-163	22
α-helix	172-178	7
α-helix	188-190	3
α-helix	191-206	16
α-helix	209-214	6
α-helix	218-224	7
α-helix	228-250	23
α-helix	256-266	11
α-helix	272-295	24
α-helix	305-322	18

Chain B: 18 helices, 0 β-strands

Element	Residues	Length
α-helix	3-32	30
α-helix	40-42	3
α-helix	46-51	6
α-helix	56-80	25
α-helix	93-107	15
α-helix	115-137	23
α-helix	142-163	22
α-helix	164-166	3
α-helix	172-178	7
α-helix	188-190	3
α-helix	191-206	16
α-helix	209-214	6
α-helix	218-224	7
α-helix	228-250	23
α-helix	256-266	11
α-helix	272-292	21
α-helix	302-304	3
α-helix	305-322	18

Chain C: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	1
β-strand	14	1	1
β-strand	16-23	8	1
β-strand	28-32	5	2
α-helix	39-46	8
β-strand	55-58	4	1
β-strand	61-62	2	1
α-helix	68-74	7
β-strand	77-78	2	2
α-helix	83-85	3
β-strand	89	1	3
α-helix	90-95	6
α-helix	105-113	9
β-strand	123	1	3
α-helix	129-144	16
β-strand	156-157	2	2
α-helix	166-181	16
β-strand	186-189	4	2
α-helix	193-199	7
β-strand	202-207	6	2
β-strand	210-216	7	2
α-helix	217-220	4
α-helix	223-229	7
β-strand	234-237	4	4
β-strand	244-247	4	4

Chain D: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	5
β-strand	10-12	3	6
β-strand	14	1	6
β-strand	16-19	4	6
β-strand	22-24	3	5
β-strand	28-32	5	7
α-helix	39-47	9
β-strand	55-58	4	5
β-strand	61-62	2	5
α-helix	63-65	3
α-helix	68-74	7
β-strand	75-78	4	7
α-helix	83-85	3
β-strand	89	1	8
α-helix	90-95	6
α-helix	105-113	9
β-strand	123	1	8
α-helix	124-126	3
α-helix	129-144	16
β-strand	154-157	4	7
α-helix	166-181	16
β-strand	186-189	4	7
α-helix	193-199	7
β-strand	202-207	6	7
β-strand	210-216	7	7
α-helix	217-220	4
α-helix	223-230	8
β-strand	234-237	4	9
β-strand	244-247	4	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitamin B12 import system permease protein BtuC	A, B	protein	333	Escherichia coli	P06609 (AlphaFold model)
Vitamin B12 import ATP-binding protein BtuD	C, D	protein	249	Escherichia coli	P06611 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4R9U_1 Vitamin B12 import system permease protein BtuC (chains A, B)
GPSGTSHMLTLARQQQRQNIRWLLSLSVLMLLALLLSLSAGEQWISPGDWFTPRGELFVW
QIRLPRTLAVLLVGAALAISGAVMQALFENPLAEPGLLGVSNGAGVGLIAAVLLGQGQLP
NWALGLSAIAGALIITLILLRFARRHLSTSRLLLAGVALGIISSALMTWAIYFSTSVDLR
QLMYWMMGGFGGVDWRQSWLMLALIPVLLWISSQSRPMNMLALGEISARQLGLPLWFWRN
VLVAATGWMVGVSVALAGAIGFIGLVIPHILRLSGLTDHRVLLPGCALAGASALLLADIV
ARLALAAAELPIGVVTATLGAPVFIWLLLKAGR

Sequence of entity 2 (C, D), FASTA

>4R9U_2 Vitamin B12 import ATP-binding protein BtuD (chains C, D)
MSIVMQLQDVAESTRLGPLSGEVRAGEILHLVGPNGAGKSTLLARMAGMTSGKGSIQFAG
QPLEAWSATKLALHRAYLSQQQTPPFATPVWHYLTLHQHDKTRTELLNDVAGALALDDKL
GRSTNQLSGGEWQRVRLAAVVLQITPQANPAGQLLLLDQPMCSLDVAQQSALDKILSALS
QQGLAIVMSSHDLNHTLRHAHRAWLLKGGKMLASGRREEVLTPPNLAQAYGMNFRRLDIE
GHRMLISTI

Ligands and cofactors

ID	Name	Formula	Copies
LDA	Lauryl dimethylamine-N-oxide	C14 H31 N O	4
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2
MG	Magnesium ion	Mg	2

Primary citation

Structure of AMP-PNP-bound BtuCD and mechanism of ATP-powered vitamin B12 transport by BtuCD-F. Korkhov, V.M., Mireku, S.A., Veprintsev, D.B. et al. Nat Struct Mol Biol (2014) 21:1097-1099. DOI 10.1038/nsmb.2918 · PubMed

Other PDB entries of the same protein (UniProt P06609 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2QI9 2.6 Å, ABC-transporter BtuCD in complex with its periplasmic binding protein BtuF
1L7V 3.2 Å, Bacterial ABC Transporter Involved in B12 Uptake
4FI3 3.47 Å, Structure of vitamin B12 transporter BtuCD-F in a nucleotide-bound state
4DBL 3.49 Å, Crystal structure of E159Q mutant of BtuCDF

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