1UJW: Vitamin B12 receptor

Structure of the complex between BtuB and Colicin E3 Receptor binding domain. Determined by X-ray diffraction at 2.75 Å resolution. Released 25 Nov 2003.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Escherichia coli
Chains: 2
Atoms: 5,714
Mol. weight: 84.97 kDa
Ligands: AAE, LDA, LIM, GP1
Released: 25 Nov 2003

Explore 1UJW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1UJW contains 15 α-helices and 37 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: 11 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	1
β-strand	17-18	2	1
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	77-80	4	2
β-strand	83-84	2	2
α-helix	86-88	3
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
β-strand	149-159	11	4
β-strand	164-174	11	4
β-strand	198-209	12	4
β-strand	214-228	15	4
β-strand	242-257	16	4
β-strand	261-277	17	4
β-strand	289-305	17	4
β-strand	309-322	14	4
α-helix	326-328	3
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	398-402	5
α-helix	410-412	3
β-strand	413-426	14	4
β-strand	429-441	13	4
β-strand	445-447	3	5
β-strand	452-454	3	5
β-strand	459-472	14	4
β-strand	475-477	3	4
β-strand	480-488	9	4
β-strand	494	1	4
β-strand	501-511	11	4
β-strand	514-523	10	4
β-strand	526-527	2	6
α-helix	536	1
β-strand	540-541	2	6
α-helix	542-543	2
β-strand	544-554	11	4
β-strand	559-566	8	4
β-strand	585-593	9	4

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	328-331	4
α-helix	333-374	42
α-helix	375-378	4
α-helix	387-434	48

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitamin B12 receptor	A	protein	594	Escherichia coli	P06129 (AlphaFold model)
Colicin E3	B	protein	135	Escherichia coli	P00646 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1UJW_1 Vitamin B12 receptor (chains A)
QDTSPDTLVVTANRFEQPRSTVLAPTTVVTRQDIDRWQSTSVNDVLRRLPGVDITQNGGS
GQLSSIFIRGTNASHVLVLIDGVRLNLAGVSGSADLSQFPIALVQRVEYIRGPRSAVYGS
DAIGGVVNIITTRDEPGTEISAGWGSNSYQNYDVSTQQQLGDKTRVTLLGDYAHTHGYDV
VAYGNTGTQAQTDNDGFLSKTLYGALEHNFTDAWSGFVRGYGYDNRTNYDAYYSPGSPLL
DTRKLYSQSWDAGLRYNGELIKSQLITSYSHSKDYNYDPHYGRYDSSATLDEMKQYTVQW
ANNVIVGHGSIGAGVDWQKQTTTPGTGYVEDGYDQRNTGIYLTGLQQVGDFTFEGAARSD
DNSQFGRHGTWQTSAGWEFIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEG
AFEGLTAGVNWRISGYRNDVSDLIDYDDHTLKYYNEGKARIKGVEATANFDTGPLTHTVS
YDYVDARNAITDTPLLRRAKQQVKYQLDWQLYDFDWGITYQYLGTRYDKDYSSYPYQTVK
MGGVSLWDLAVAYPVTSHLTVRGKIANLFDKDYETVYGYQTAGREYTLSGSYTF

Sequence of entity 2 (B), FASTA

>1UJW_2 Colicin E3 (chains B)
HPVEAAERNYERARAELNQANEDVARNQERQAKAVQVYNSRKSELDAANKTLADAIAEIK
QFNRFAHDPMAGGHRMWQMAGLKAQRAQTDVNNKQAAFDAAAKEKSDADAALSSAMESRK
KKEDKKRSAENNLND

Ligands and cofactors

ID	Name	Formula	Copies
AAE	Acetoacetic acid	C4 H6 O3	1
LDA	Lauryl dimethylamine-N-oxide	C14 H31 N O	7
LIM	3-oxo-pentadecanoic acid	C15 H28 O3	2
GP1	2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose	C6 H14 N O8 P	2

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

Primary citation

The structure of BtuB with bound colicin E3 R-domain implies a translocon. Kurisu, G., Zakharov, S.D., Zhalnina, M.V. et al. Nat Struct Biol (2003) 10:948-954. DOI 10.1038/nsb997 · 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
3M8B 2.44 Å, Crystal structure of spin-labeled BtuB V10R1 in the apo state
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…
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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