Experimental Data Snapshot
Starting Model:experimental
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(2006) Proc Natl Acad Sci U S A 103: 4386-4391
Cobalamin (Cbl, vitamin B(12)) serves for two essential cofactors in mammals. The pathway for its intestinal absorption, plasma transport, and cellular uptake uses cell surface receptors and three Cbl-transporting proteins, haptocorrin, intrinsic factor, and transcobalamin (TC). We present the structure determination of a member of the mammalian Cbl-transporter family. The crystal structures of recombinant human and bovine holo-TCs reveal a two-domain architecture, with an N-terminal alpha(6)-alpha(6) barrel and a smaller C-terminal domain. One Cbl molecule in base-on conformation is buried inside the domain interface. Structural data combined with previous binding assays indicate a domain motion in the first step of Cbl binding. In a second step, the weakly coordinated ligand H(2)O at the upper axial side of added H(2)O-Cbl is displaced by a histidine residue of the alpha(6)-alpha(6) barrel. Analysis of amino acid conservation on TC's surface in orthologous proteins suggests the location of the TC-receptor-recognition site in an extended region on the alpha(6)-alpha(6) barrel. The TC structure allows for the mapping of sites of amino acid variation due to polymorphisms of the human TC gene. Structural information is used to predict the overall fold of haptocorrin and intrinsic factor and permits a rational approach to the design of new Cbl-based bioconjugates for diagnostic or therapeutic drug delivery.
Centre of Excellence in Biocrystallography, Department of Chemical Sciences, University of Trieste, Via L. Giorgieri 1, I-34127 Trieste, Italy.
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (B12)
Biological assembly 1 assigned by authors and generated by PISA (software)
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (B12)
Biological assembly 2 assigned by authors and generated by PISA (software)
Macromolecule Content
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Transcobalamin II | 409 | Homo sapiens | Mutation(s): 1 Gene Names: TCN2, TC2 | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P20062 (Homo sapiens) Explore P20062 Go to UniProtKB: P20062 | |||||
PHAROS: P20062 GTEx: ENSG00000185339 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P20062 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 1 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
B12 Query on B12 Download Ideal Coordinates CCD File | C [auth A], D [auth B] | COBALAMIN C62 H89 Co N13 O14 P LKVIQTCSMMVGFU-DWSMJLPVSA-N |
Length ( Å ) | Angle ( ˚ ) |
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a = 49.127 | α = 90 |
b = 145.497 | β = 90 |
c = 165.043 | γ = 90 |
Software Name | Purpose |
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SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
CCP4 | data scaling |
AMoRE | phasing |
RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.