5M3B: Vitamin B12-binding protein

Structure of cobinamide-bound BtuF mutant W66L, the periplasmic vitamin B12 binding protein in E.coli. Determined by X-ray diffraction at 1.5 Å resolution. Released 1 Mar 2017.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Escherichia coli
Chains: 2
Atoms: 4,266
Mol. weight: 65.21 kDa
Ligands: CBY, CYN
Released: 1 Mar 2017

Explore 5M3B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M3B contains 26 α-helices and 27 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: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	1
α-helix	31-39	9
β-strand	46	1	1
β-strand	47-48	2	2
α-helix	55-59	5
α-helix	61	1
β-strand	62-65	4	2
β-strand	68-69	2	2
α-helix	71-76	6
β-strand	81-84	4	1
α-helix	91-99	9
β-strand	104-106	3	1
α-helix	112-122	11
α-helix	123-125	3
α-helix	129-150	22
α-helix	153-155	3
β-strand	156-162	7	3
β-strand	168	1	3
α-helix	175-182	8
β-strand	185-187	3	3
β-strand	198	1	3
α-helix	201-206	6
β-strand	211-215	5	3
β-strand	236-238	3	3
α-helix	241-244	4
α-helix	251-263	13

Chain B: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	4
α-helix	31-39	9
β-strand	46	1	4
β-strand	47-48	2	5
α-helix	55-59	5
α-helix	61	1
β-strand	62-65	4	5
β-strand	68-69	2	5
α-helix	71-76	6
β-strand	81-84	4	4
α-helix	91-99	9
β-strand	104-106	3	4
α-helix	112-122	11
α-helix	123-125	3
α-helix	129-150	22
α-helix	153-155	3
β-strand	156-160	5	6
β-strand	162	1	7
β-strand	168	1	7
α-helix	175-182	8
β-strand	185-187	3	6
β-strand	198	1	7
α-helix	201-206	6
β-strand	211-215	5	6
β-strand	236-239	4	6
α-helix	241-245	5
α-helix	251-262	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitamin B12-binding protein	A, B	protein	289	Escherichia coli	P37028 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5M3B_1 Vitamin B12-binding protein (chains A, B)
MKKTAIAIAVALAGFATVAQAASMAAPRVITLSPANTELAFAAGITPVGVSSYSDYPPQA
QKIEQVSTLQGMNLERIVALKPDLVIAWRGGNAERQVDQLASLGIKVMWVDATSIEQIAN
ALRQLAPWSPQPDKAEQAAQSLLDQYAQLKAQYADKPKKRVFLQFGINPPFTSGKESIQN
QVLEVCGGENIFKDSRVPWPQVSREQVLARSPQAIVITGGPDQIPKIKQYWGEQLKIPVI
PLTSDWFERASPRIILAAQQLCNALSQVDSGSLEVLFQGPGGSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CBY	Cob(ii)inamide	C48 H72 Co N11 O8	2
CYN	Cyanide ion	C N	3

Water and common crystallization additives (GOL) are not listed.

Primary citation

Conformational Change of a Tryptophan Residue in BtuF Facilitates Binding and Transport of Cobinamide by the Vitamin B12 Transporter BtuCD-F. Mireku, S.A., Ruetz, M., Zhou, T. et al. Sci Rep (2017) 7:41575-41575. DOI 10.1038/srep41575 · PubMed

Other PDB entries of the same protein (UniProt P37028 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5M29 1.5 Å, Structure of cobinamide-bound BtuF, the periplasmic vitamin B12 binding protein in E.coli
5M34 1.6 Å, Structure of cobinamide-bound BtuF mutant W66Y, the periplasmic vitamin B12 binding…
5M2Q 1.7 Å, Structure of cobinamide-bound BtuF mutant W66F, the periplasmic vitamin B12 binding…
1N2Z 2.0 Å, 2.0 Angstrom structure of BtuF, the vitamin B12 binding protein of E. coli
1N4A 2.0 Å, The Ligand Bound Structure of E.coli BtuF, the Periplasmic Binding Protein for Vitamin B12
2QI9 2.6 Å, ABC-transporter BtuCD in complex with its periplasmic binding protein BtuF
5OVW 2.65 Å, Nanobody-bound BtuF, the vitamin B12 binding protein in Escherichia coli
1N4D 3.0 Å, The Ligand-Free Structure of E coli BtuF, the Periplasmic Binding Protein for Vitamin B12
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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