+Open data
-Basic information
Entry | Database: PDB / ID: 7qbd | ||||||
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Title | TC:CD320 in complex with nanobody TC-Nb26 | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Transcobalamin / TC2 / CD320 / TCblR / B12 / nanobody | ||||||
Function / homology | Function and homology information regulation of vitamin metabolic process / Defective TCN2 causes TCN2 deficiency / Defective CD320 causes MMATC / Transport of RCbl within the body / cargo receptor ligand activity / B cell costimulation / ventral spinal cord development / cobalt ion transport / cobalamin transport / cobalamin binding ...regulation of vitamin metabolic process / Defective TCN2 causes TCN2 deficiency / Defective CD320 causes MMATC / Transport of RCbl within the body / cargo receptor ligand activity / B cell costimulation / ventral spinal cord development / cobalt ion transport / cobalamin transport / cobalamin binding / cargo receptor activity / positive regulation of B cell proliferation / lysosomal lumen / caveola / growth factor activity / external side of plasma membrane / calcium ion binding / endoplasmic reticulum / extracellular space / extracellular region / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Vicugna pacos (alpaca) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.18 Å | ||||||
Authors | Bloch, J.S. / Locher, K.P. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Faseb J. / Year: 2022 Title: Generation of nanobodies targeting the human, transcobalamin-mediated vitamin B 12 uptake route. Authors: Bloch, J.S. / Sequeira, J.M. / Ramirez, A.S. / Quadros, E.V. / Locher, K.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qbd.cif.gz | 228.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qbd.ent.gz | 177.4 KB | Display | PDB format |
PDBx/mmJSON format | 7qbd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/7qbd ftp://data.pdbj.org/pub/pdb/validation_reports/qb/7qbd | HTTPS FTP |
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-Related structure data
Related structure data | 7qbeC 7qbfC 7qbgC 4zrpS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45650.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TCN2, TC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P20062 #2: Protein | Mass: 15613.506 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD320, 8D6A, UNQ198/PRO224 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NPF0 #3: Antibody | | Mass: 14768.259 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: QVQLVESGGGLVQAGESLRLSCAASGRT FAMAWFRQAPGKEREFVAVRGWLGVTTYYADSVKGRFTISRDNAKNTLDL QMNSLKPEDTAVYYCAAGQYSSSLYDRETEYNYWGQGTRVTVSSHHHHHH EPEA Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) #4: Chemical | #5: Chemical | ChemComp-CA / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.95 Å3/Da / Density % sol: 68.89 % |
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Crystal grow | Temperature: 297.15 K / Method: vapor diffusion, sitting drop Details: 150 mM Ammonium citrate tribasic pH 7.0, 21% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4.18→49.24 Å / Num. obs: 28382 / % possible obs: 94.99 % / Redundancy: 2 % / Biso Wilson estimate: 164.22 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.17 |
Reflection shell | Resolution: 4.18→4.33 Å / Num. unique obs: 1406 / CC1/2: 0.851 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZRP Resolution: 4.18→49.14 Å / SU ML: 0.6154 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.4595 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 192.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.18→49.14 Å
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Refine LS restraints |
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LS refinement shell |
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