4DBL: E159Q mutant of BtuCDF

Crystal structure of E159Q mutant of BtuCDF. Determined by X-ray diffraction at 3.49 Å resolution. Released 7 Mar 2012.

Method: X-ray diffraction
Resolution: 3.49 Å
Organism: Escherichia coli
Chains: 10
Atoms: 21,230
Mol. weight: 317 kDa
Ligands: PO4
Released: 7 Mar 2012

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

Secondary structure: helices and β-sheets

4DBL contains 148 α-helices and 78 β-strands across 10 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.

Chains A and F: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	3-30	28
α-helix	46-51	6
α-helix	52-56	5
α-helix	57-80	24
α-helix	88-91	4
α-helix	93-107	15
α-helix	114-135	22
α-helix	142-165	24
α-helix	169-178	10
α-helix	188-190	3
α-helix	191-204	14
α-helix	208-214	7
α-helix	218-223	6
α-helix	228-250	23
α-helix	256-267	12
α-helix	272-296	25
α-helix	305-321	17

Chains B and G: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	3-31	29
α-helix	40-42	3
α-helix	46-47	2
α-helix	48-56	9
α-helix	57-80	24
α-helix	93-108	16
α-helix	114-136	23
α-helix	143-164	22
α-helix	169-180	12
α-helix	188-190	3
α-helix	191-204	14
α-helix	208-214	7
α-helix	218-223	6
α-helix	228-250	23
α-helix	259-267	9
α-helix	272-295	24
α-helix	305-320	16

Chains C and H: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
β-strand	16-24	9	1
β-strand	28-32	5	2
α-helix	39-46	8
β-strand	53-58	6	1
β-strand	61-62	2	1
α-helix	63-65	3
α-helix	68-74	7
β-strand	75-78	4	2
α-helix	83-85	3
β-strand	89	1	3
α-helix	90-97	8
α-helix	104-113	10
α-helix	117-119	3
β-strand	123	1	3
α-helix	124-126	3
α-helix	129-144	16
β-strand	154-157	4	2
α-helix	166-181	16
β-strand	185-189	5	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	223-230	8
β-strand	234-239	6	4
β-strand	242-247	6	4

Chains D and I: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	5
β-strand	16-24	9	5
β-strand	28-32	5	6
α-helix	39-46	8
β-strand	53-58	6	5
β-strand	61-62	2	5
α-helix	63-65	3
α-helix	68-74	7
β-strand	75-78	4	6
α-helix	83-85	3
β-strand	89	1	7
α-helix	90-96	7
α-helix	104-113	10
α-helix	117-119	3
β-strand	123	1	7
α-helix	124-126	3
α-helix	129-144	16
β-strand	154-157	4	6
α-helix	166-181	16
β-strand	185-189	5	6
α-helix	193-199	7
β-strand	202-207	6	6
β-strand	210-216	7	6
α-helix	217-220	4
α-helix	223-230	8
β-strand	234-239	6	8
β-strand	242-247	6	8

Chains E and J: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	9
α-helix	31-40	10
β-strand	46	1	9
β-strand	47-48	2	10
α-helix	55-58	4
α-helix	61	1
β-strand	62-64	3	10
β-strand	69	1	10
α-helix	71-76	6
β-strand	81-84	4	9
α-helix	91-100	10
β-strand	103-106	4	9
α-helix	113-122	10
α-helix	123-125	3
α-helix	130-151	22
β-strand	156-161	6	11
α-helix	175-182	8
β-strand	185-187	3	11
α-helix	201-206	6
β-strand	211-215	5	11
α-helix	218-220	3
α-helix	222-227	6
β-strand	236-239	4	11
α-helix	241-245	5
α-helix	251-262	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitamin B12 import system permease protein BtuC	A, B, F, G	protein	349	Escherichia coli	P06609 (AlphaFold model)
Vitamin B12 import ATP-binding protein BtuD	C, D, H, I	protein	249	Escherichia coli	P06611 (AlphaFold model)
Vitamin B12-binding protein	E, J	protein	255	Escherichia coli	P37028 (AlphaFold model)

Sequence of entity 1 (A, B, F, G), FASTA

>4DBL_1 Vitamin B12 import system permease protein BtuC (chains A, B, F, G)
MGHHHHHHHHHHSSGENLYFQGHMLTLARQQQRQNIRWLLSLSVLMLLALLLSLSAGEQW
ISPGDWFTPRGELFVWQIRLPRTLAVLLVGAALAISGAVMQALFENPLAEPGLLGVSNGA
GVGLIAAVLLGQGQLPNWALGLSAIAGALIITLILLRFARRHLSTSRLLLAGVALGIISS
ALMTWAIYFSTSVDLRQLMYWMMGGFGGVDWRQSWLMLALIPVLLWISSQSRPMNMLALG
EISARQLGLPLWFWRNVLVAATGWMVGVSVALAGAIGFIGLVIPHILRLSGLTDHRVLLP
GCALAGASALLLADIVARLALAAAELPIGVVTATLGAPVFIWLLLKAGR

Sequence of entity 2 (C, D, H, I), FASTA

>4DBL_2 Vitamin B12 import ATP-binding protein BtuD (chains C, D, H, I)
MSIVMQLQDVAESTRLGPLSGEVRAGEILHLVGPNGAGKSTLLARMAGMTSGKGSIQFAG
QPLEAWSATKLALHRAYLSQQQTPPFATPVWHYLTLHQHDKTRTELLNDVAGALALDDKL
GRSTNQLSGGEWQRVRLAAVVLQITPQANPAGQLLLLDQPMNSLDVAQQSALDKILSALS
QQGLAIVMSSHDLNHTLRHAHRAWLLKGGKMLASGRREEVLTPPNLAQAYGMNFRRLDIE
GHRMLISTI

Sequence of entity 3 (E, J), FASTA

>4DBL_3 Vitamin B12-binding protein (chains E, J)
MAAPRVITLSPANTELAFAAGITPVGVSSYSDYPPQAQKIEQVSTWQGMNLERIVALKPD
LVIAWRGGNAERQVDQLASLGIKVMWVDATSIEQIANALRQLAPWSPQPDKAEQAAQSLL
DQYAQLKAQYADKPKKRVFLQFGINPPFTSGKESIQNQVLEVCGGENIFKDSRVPWPQVS
REQVLARSPQAIVITGGPDQIPKIKQYWGEQLKIPVIPLTSDWFERASPRIILAAQQLCN
ALSQVDSGSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	4

Water and common crystallization additives (SO4) are not listed.

Primary citation

Asymmetric states of vitamin B12 transporter BtuCD are not discriminated by its cognate substrate binding protein BtuF. Korkhov, V.M., Mireku, S.A., Hvorup, R.N. et al. FEBS Lett (2012) 586:972-976. DOI 10.1016/j.febslet.2012.02.042 · 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
4R9U 2.79 Å, Structure of vitamin B12 transporter BtuCD in a nucleotide-bound outward facing state
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

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