Crystal structure of spin-labeled BtuB V10R1 with bound calcium and cyanocobalamin. Determined by X-ray diffraction at 2.44 Å resolution. Released 15 Sept 2010.
Explore 3M8D in 3D Show helices and sheets RCSB PDB PDBe
3M8D contains 15 α-helices and 38 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.
| 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 | 96-98 | 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 | 164-175 | 12 | 4 |
| β-strand | 181 | 1 | 5 |
| β-strand | 187 | 1 | 6 |
| β-strand | 197-209 | 13 | 4 |
| β-strand | 214-228 | 15 | 4 |
| β-strand | 233 | 1 | 6 |
| β-strand | 242-257 | 16 | 4 |
| β-strand | 261-277 | 17 | 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 | |
| α-helix | 410-412 | 3 | |
| β-strand | 413-426 | 14 | 4 |
| β-strand | 429-447 | 19 | 4 |
| α-helix | 448-450 | 3 | |
| β-strand | 452-471 | 20 | 4 |
| β-strand | 475-488 | 14 | 4 |
| α-helix | 493 | 1 | |
| β-strand | 494 | 1 | 4 |
| α-helix | 495 | 1 | |
| β-strand | 501-511 | 11 | 4 |
| β-strand | 514-523 | 10 | 4 |
| β-strand | 526-530 | 5 | 7 |
| α-helix | 536 | 1 | |
| β-strand | 537-541 | 5 | 7 |
| β-strand | 544-554 | 11 | 4 |
| β-strand | 559-566 | 8 | 4 |
| β-strand | 579 | 1 | 5 |
| α-helix | 580-581 | 2 | |
| β-strand | 585-593 | 9 | 4 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Vitamin B12 transporter btuB | A | protein | 594 | Escherichia coli | P06129 (AlphaFold model) |
>3M8D_1 Vitamin B12 transporter btuB (chains A) QDTSPDTLVCTANRFEQPRSTVLAPTTVVTRQDIDRWQSTSVNDVLRRLPGVDITQNGGS GQLSSIFIRGTNASHVLVLIDGVRLNLAGVSGSADLSQFPIALVQRVEYIRGPRSAVYGS DAIGGVVNIITTRDEPGTEISAGWGSNSYQNYDVSTQQQLGDKTRVTLLGDYAHTHGYDV VAYGNTGTQAQTDNDGFLSKTLYGALEHNFTDAWSGFVRGYGYDNRTNYDAYYSPGSPLL DTRKLYSQSWDAGLRYNGELIKSQLITSYSHSKDYNYDPHYGRYDSSATLDEMKQYTVQW ANNVIVGHGSIGAGVDWQKQTTTPGTGYVEDGYDQRNTGIYLTGLQQVGDFTFEGAARSD DNSQFGRHGTWQTSAGWEFIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEG AFEGLTAGVNWRISGYRNDVSDLIDYDDHTLKYYNEGKARIKGVEATANFDTGPLTHTVS YDYVDARNAITDTPLLRRAKQQVKYQLDWQLYDFDWGITYQYLGTRYDKDYSSYPYQTVK MGGVSLWDLAVAYPVTSHLTVRGKIANLFDKDYETVYGYQTAGREYTLSGSYTF
| ID | Name | Formula | Copies |
|---|---|---|---|
| CA | Calcium ion | Ca | 3 |
| 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 | 6 |
| CNC | Cyanocobalamin | C63 H89 Co N14 O14 P | 1 |
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:
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