5OVW: Vitamin B12-binding protein

Nanobody-bound BtuF, the vitamin B12 binding protein in Escherichia coli. Determined by X-ray diffraction at 2.65 Å resolution. Released 8 Nov 2017.

Method: X-ray diffraction
Resolution: 2.65 Å
Organisms: Escherichia coli, Lama glama
Chains: 12
Atoms: 17,352
Mol. weight: 291.32 kDa
Released: 8 Nov 2017

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

Secondary structure: helices and β-sheets

5OVW contains 129 α-helices and 150 β-strands across 12 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: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	23-25	3
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	91-98	8
β-strand	104-106	3	1
α-helix	112-122	11
α-helix	123-125	3
α-helix	129-149	21
β-strand	156-161	6	3
β-strand	168	1	4
α-helix	175-182	8
β-strand	185-187	3	3
β-strand	198	1	4
α-helix	201-206	6
β-strand	211-214	4	3
α-helix	220-226	7
α-helix	235	1
β-strand	236-238	3	3
α-helix	241-244	4
α-helix	251-262	12

Chains B and E: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	5
α-helix	31-39	9
β-strand	46	1	5
β-strand	47-48	2	6
α-helix	55-59	5
α-helix	61	1
β-strand	62-65	4	6
β-strand	68-69	2	6
α-helix	71-76	6
β-strand	81-84	4	5
α-helix	91-99	9
β-strand	104-106	3	5
α-helix	112-122	11
α-helix	123-125	3
α-helix	129-149	21
β-strand	156-161	6	7
β-strand	168	1	8
α-helix	175-182	8
β-strand	185-187	3	7
β-strand	198	1	8
α-helix	201-206	6
β-strand	211-214	4	7
α-helix	220-226	7
α-helix	229-231	3
β-strand	236-238	3	7
α-helix	241-244	4
α-helix	251-262	12

Chain C: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	9
α-helix	31-39	9
β-strand	46	1	9
β-strand	47-48	2	10
α-helix	55-58	4
α-helix	61	1
β-strand	62-65	4	10
β-strand	68-69	2	10
α-helix	71-76	6
β-strand	81-84	4	9
α-helix	91-99	9
β-strand	104-106	3	9
α-helix	112-122	11
α-helix	123-125	3
α-helix	129-149	21
β-strand	156-161	6	11
β-strand	168	1	12
α-helix	175-182	8
β-strand	185-187	3	11
β-strand	198	1	12
α-helix	201-206	6
β-strand	211-214	4	11
α-helix	220-226	7
α-helix	229-231	3
β-strand	236-238	3	11
α-helix	241-244	4
α-helix	251-262	12

Chain D: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	23-25	3
β-strand	26-28	3	13
α-helix	31-39	9
β-strand	46	1	13
β-strand	47-48	2	14
α-helix	55-59	5
α-helix	61	1
β-strand	62-65	4	14
β-strand	68-69	2	14
α-helix	71-76	6
β-strand	81-84	4	13
α-helix	91-99	9
β-strand	104-106	3	13
α-helix	112-122	11
α-helix	123-125	3
α-helix	129-149	21
β-strand	156-161	6	15
β-strand	168	1	16
α-helix	175-182	8
β-strand	185-187	3	15
β-strand	198	1	16
α-helix	201-206	6
β-strand	211-214	4	15
α-helix	220-226	7
α-helix	229-231	3
β-strand	236-238	3	15
α-helix	241-244	4
α-helix	251-262	12

Chain F: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	21
α-helix	31-39	9
β-strand	46	1	21
β-strand	47-48	2	22
α-helix	55-59	5
α-helix	61	1
β-strand	62-65	4	22
β-strand	68-69	2	22
α-helix	71-76	6
β-strand	81-84	4	21
α-helix	86-88	3
α-helix	91-99	9
β-strand	104-106	3	21
α-helix	112-122	11
α-helix	123-125	3
α-helix	129-149	21
β-strand	156-161	6	23
β-strand	168	1	24
α-helix	175-182	8
β-strand	185-187	3	23
β-strand	198	1	24
α-helix	201-206	6
β-strand	211-214	4	23
α-helix	220-226	7
α-helix	229-231	3
β-strand	236-238	3	23
α-helix	241-244	4
α-helix	251-262	12

Chains G, I and J: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	25
α-helix	34-35	2
β-strand	40-45	6	25
β-strand	54-61	8	26
α-helix	66-67	2
β-strand	68-73	6	26
β-strand	80-82	3	26
β-strand	90-95	6	25
β-strand	100-105	6	25
α-helix	110-112	3
β-strand	114-122	9	26
α-helix	123-125	3
α-helix	127-130	4
β-strand	138-139	2	26
α-helix	140	1
β-strand	141	1	25
α-helix	142	1
β-strand	143-145	3	26

Chains H, K and L: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	27
β-strand	34	1	28
α-helix	35	1
β-strand	40-45	6	27
β-strand	54-61	8	29
α-helix	66-67	2
β-strand	68-73	6	29
β-strand	80-82	3	29
β-strand	90-95	6	27
β-strand	100-105	6	27
α-helix	110-112	3
β-strand	114-122	9	29
α-helix	123-125	3
α-helix	127-130	4
β-strand	138-139	2	29
α-helix	140	1
β-strand	141	1	27
α-helix	142	1
β-strand	143-145	3	29
β-strand	147	1	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitamin B12-binding protein	A, B, C, D, E, F	protein	289	Escherichia coli	P37028 (AlphaFold model)
Nanobody	G, H, I, J, K, L	protein	159	Lama glama

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

>5OVW_1 Vitamin B12-binding protein (chains A, B, C, D, E, F)
MKKTAIAIAVALAGFATVAQAASMAAPRVITLSPANTELAFAAGITPVGVSSYSDYPPQA
QKIEQVSTWQGMNLERIVALKPDLVIAWRGGNAERQVDQLASLGIKVMWVDATSIEQIAN
ALRQLAPWSPQPDKAEQAAQSLLDQYAQLKAQYADKPKKRVFLQFGINPPFTSGKESIQN
QVLEVCGGENIFKDSRVPWPQVSREQVLARSPQAIVITGGPDQIPKIKQYWGEQLKIPVI
PLTSDWFERASPRIILAAQQLCNALSQVDSGSLEVLFQGPGGSHHHHHH

Sequence of entity 2 (G, H, I, J, K, L), FASTA

>5OVW_2 Nanobody (chains G, H, I, J, K, L)
MKYLLPTAAAGLLLLAAQPAMAQMQLVESGGGLVQPGGSLRLSCAAPESTLDDYAIGWFR
QAPGKEREGVSCIGSSGDSTNYADSVKGRFTVSRDNAKNTVYLQMNDLRPEDTAVYYCAA
AHRIFGGCLVIHSSGYVSWGQGTPVTVSSHHHHHHEPEA

Primary citation

Structural basis of nanobody-mediated blocking of BtuF, the cognate substrate-binding protein of the Escherichia coli vitamin B12 transporter BtuCD. Mireku, S.A., Sauer, M.M., Glockshuber, R. et al. Sci Rep (2017) 7:14296-14296. DOI 10.1038/s41598-017-14512-8 · 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
5M3B 1.5 Å, Structure of cobinamide-bound BtuF mutant W66L, the periplasmic vitamin B12 binding…
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
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

Browse structure collections

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