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- PDB-7qbd: TC:CD320 in complex with nanobody TC-Nb26 -

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Basic information

Entry
Database: PDB / ID: 7qbd
TitleTC:CD320 in complex with nanobody TC-Nb26
Components
  • Antitranscobalamin-nanobody TC-Nb26
  • CD320 antigen
  • Transcobalamin-2
KeywordsTRANSPORT 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 / cargo receptor ligand activity / B cell costimulation / Transport of RCbl within the body / cobalamin transport / cobalt ion transport / cobalamin binding / cargo receptor activity ...regulation of vitamin metabolic process / Defective TCN2 causes TCN2 deficiency / Defective CD320 causes MMATC / cargo receptor ligand activity / B cell costimulation / Transport of RCbl within the body / cobalamin transport / cobalt ion transport / cobalamin binding / cargo receptor activity / positive regulation of B cell proliferation / lysosomal lumen / growth factor activity / external side of plasma membrane / calcium ion binding / endoplasmic reticulum / extracellular space / extracellular region / metal ion binding / membrane / plasma membrane
Similarity search - Function
: / Domain of unknown function DUF4430 / Domain of unknown function (DUF4430) / Cobalamin (vitamin B12)-binding protein / : / Eukaryotic cobalamin-binding protein / Eukaryotic cobalamin-binding proteins signature. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. ...: / Domain of unknown function DUF4430 / Domain of unknown function (DUF4430) / Cobalamin (vitamin B12)-binding protein / : / Eukaryotic cobalamin-binding protein / Eukaryotic cobalamin-binding proteins signature. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid
Similarity search - Domain/homology
CYANOCOBALAMIN / Transcobalamin-2 / CD320 antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.18 Å
AuthorsBloch, J.S. / Locher, K.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: 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
DepositionNov 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcobalamin-2
B: Transcobalamin-2
C: CD320 antigen
D: CD320 antigen
E: Antitranscobalamin-nanobody TC-Nb26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,24913
Polymers137,2965
Non-polymers2,9538
Water00
1
A: Transcobalamin-2
C: CD320 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7416
Polymers61,2642
Non-polymers1,4774
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcobalamin-2
D: CD320 antigen
E: Antitranscobalamin-nanobody TC-Nb26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5097
Polymers76,0323
Non-polymers1,4774
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.129, 102.129, 360.998
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Transcobalamin-2 / TC-2 / Transcobalamin II / TCII


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 CD320 antigen / 8D6 antigen / FDC-signaling molecule 8D6 / FDC-SM-8D6 / Transcobalamin receptor / TCblR


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 Antitranscobalamin-nanobody TC-Nb26


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 ChemComp-CNC / CYANOCOBALAMIN


Mass: 1356.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H89CoN14O14P
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.95 Å3/Da / Density % sol: 68.89 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, sitting drop
Details: 150 mM Ammonium citrate tribasic pH 7.0, 21% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 4.18→4.33 Å / Num. unique obs: 1406 / CC1/2: 0.851

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZRP

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
RfactorNum. reflection% reflection
Rfree0.2724 1272 4.99 %
Rwork0.2616 24220 -
obs0.2621 25492 94.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 192.11 Å2
Refinement stepCycle: LAST / Resolution: 4.18→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8201 0 192 0 8393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03838581
X-RAY DIFFRACTIONf_angle_d2.003711708
X-RAY DIFFRACTIONf_chiral_restr0.17391312
X-RAY DIFFRACTIONf_plane_restr0.00671489
X-RAY DIFFRACTIONf_dihedral_angle_d15.4333120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.18-4.350.3289680.37811448X-RAY DIFFRACTION50.4
4.35-4.540.32511500.31342837X-RAY DIFFRACTION99.24
4.54-4.780.26681490.28672854X-RAY DIFFRACTION99.73
4.78-5.080.38461550.30982855X-RAY DIFFRACTION99.67
5.08-5.470.32361510.28852810X-RAY DIFFRACTION99.7
5.47-6.020.33981500.31922888X-RAY DIFFRACTION99.8
6.02-6.890.30651470.30132844X-RAY DIFFRACTION99.8
6.89-8.680.24171460.23282838X-RAY DIFFRACTION100
8.68-49.140.21581560.20862846X-RAY DIFFRACTION99.77

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