3M8B: Spin-labeled BtuB V10R1 in the apo state

Name: PDB 3M8B: Crystal structure of spin-labeled BtuB V10R1 in the apo state
Published: 2010-09-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transport protein

Crystal structure of spin-labeled BtuB V10R1 in the apo state. Determined by X-ray diffraction at 2.44 Å resolution. Released 15 Sept 2010.

Method: X-ray diffraction
Resolution: 2.44 Å
Organism: Escherichia coli
Chains: 1
Atoms: 4,605
Mol. weight: 68.9 kDa
Ligands: MG, MTN, C8E
Released: 15 Sept 2010

Explore 3M8B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3M8B contains 13 α-helices and 34 β-strands across 1 chain. 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, 34 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	1
β-strand	17-18	2	1
α-helix	19-21	3
β-strand	26-30	5	2
α-helix	31-37	7
α-helix	42-46	5
β-strand	52-56	5	3
β-strand	64-68	5	3
α-helix	73-75	3
β-strand	76-80	5	2
β-strand	83-84	2	2
α-helix	86-89	4
α-helix	101-103	3
β-strand	106-111	6	2
α-helix	115-118	4
β-strand	125-130	6	2
β-strand	137-145	9	4
α-helix	146-148	3
β-strand	149-159	11	4
β-strand	164-175	12	4
β-strand	197-209	13	4
β-strand	214-227	14	4
β-strand	243-257	15	4
β-strand	261-276	16	4
β-strand	289-305	17	4
β-strand	309-322	14	4
β-strand	334-348	15	4
β-strand	351-362	12	4
β-strand	366-380	15	4
β-strand	383-394	12	4
α-helix	395-397	3
α-helix	398-402	5
β-strand	413-426	14	4
β-strand	429-447	19	4
β-strand	452-472	21	4
β-strand	475-488	14	4
α-helix	493	1
β-strand	494	1	4
α-helix	495	1
β-strand	501-510	10	4
β-strand	515-523	9	4
β-strand	526-529	4	5
β-strand	538-541	4	5
α-helix	542-543	2
β-strand	544-554	11	4
β-strand	559-566	8	4
β-strand	585-593	9	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitamin B12 transporter btuB	A	protein	594	Escherichia coli	P06129 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3M8B_1 Vitamin B12 transporter btuB (chains A)
QDTSPDTLVCTANRFEQPRSTVLAPTTVVTRQDIDRWQSTSVNDVLRRLPGVDITQNGGS
GQLSSIFIRGTNASHVLVLIDGVRLNLAGVSGSADLSQFPIALVQRVEYIRGPRSAVYGS
DAIGGVVNIITTRDEPGTEISAGWGSNSYQNYDVSTQQQLGDKTRVTLLGDYAHTHGYDV
VAYGNTGTQAQTDNDGFLSKTLYGALEHNFTDAWSGFVRGYGYDNRTNYDAYYSPGSPLL
DTRKLYSQSWDAGLRYNGELIKSQLITSYSHSKDYNYDPHYGRYDSSATLDEMKQYTVQW
ANNVIVGHGSIGAGVDWQKQTTTPGTGYVEDGYDQRNTGIYLTGLQQVGDFTFEGAARSD
DNSQFGRHGTWQTSAGWEFIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEG
AFEGLTAGVNWRISGYRNDVSDLIDYDDHTLKYYNEGKARIKGVEATANFDTGPLTHTVS
YDYVDARNAITDTPLLRRAKQQVKYQLDWQLYDFDWGITYQYLGTRYDKDYSSYPYQTVK
MGGVSLWDLAVAYPVTSHLTVRGKIANLFDKDYETVYGYQTAGREYTLSGSYTF

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
MTN	S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl]…	C10 H18 N O3 S2	1
C8E	(hydroxyethyloxy)tri(ethyloxy)octane	C16 H34 O5	7

Primary citation

Conformational exchange in a membrane transport protein is altered in protein crystals. Freed, D.M., Horanyi, P.S., Wiener, M.C. et al. Biophys J (2010) 99:1604-1610. DOI 10.1016/j.bpj.2010.06.026 · PubMed

Other PDB entries of the same protein (UniProt P06129 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2GUF 1.95 Å, In meso crystal structure of the cobalamin transporter, BtuB
1NQE 2.0 Å, Outer membrane cobalamin transporter (BTUB) from E. Coli
2GSK 2.1 Å, Structure of the BtuB:TonB Complex
3RGN 2.3 Å, Crystal structure of spin-labeled BtuB W371R1
3M8D 2.44 Å, Crystal structure of spin-labeled BtuB V10R1 with bound calcium and cyanocobalamin
3RGM 2.6 Å, Crystal structure of spin-labeled BtuB T156R1
1NQF 2.7 Å, Outer membrane cobalamin transporter (BTUB) from E. Coli, methionine substiution…
1UJW 2.75 Å, Structure of the complex between BtuB and Colicin E3 Receptor binding domain
1NQH 3.1 Å, Outer membrane cobalamin transporter (BTUB) from E. Coli, with bound calcium and…
1NQG 3.31 Å, Outer membrane cobalamin transporter (BTUB) from E. Coli, with bound calcium
2YSU 3.5 Å, Structure of the complex between BtuB and Colicin E2 receptor binding domain
7NSU 4.7 Å, ColicinE9 intact translocation complex

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