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- PDB-7qbe: TC:CD320 in complex with nanobody TC-Nb11 -

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Basic information

Entry
Database: PDB / ID: 7qbe
TitleTC:CD320 in complex with nanobody TC-Nb11
Components
  • Anti-transcobalamin-2 nanobody TC-Nb11
  • 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
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: 3 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 1.2Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: Transcobalamin-2
B: CD320 antigen
C: Transcobalamin-2
D: CD320 antigen
E: Anti-transcobalamin-2 nanobody TC-Nb11
F: Anti-transcobalamin-2 nanobody TC-Nb11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,53512
Polymers151,6626
Non-polymers2,8736
Water1086
1
A: Transcobalamin-2
B: CD320 antigen
E: Anti-transcobalamin-2 nanobody TC-Nb11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2686
Polymers75,8313
Non-polymers1,4373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Transcobalamin-2
D: CD320 antigen
F: Anti-transcobalamin-2 nanobody TC-Nb11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2686
Polymers75,8313
Non-polymers1,4373
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.717, 195.831, 198.385
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 3 types, 6 molecules ACBDEF

#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: Protein Anti-transcobalamin-2 nanobody TC-Nb11


Mass: 14567.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 12 molecules

#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.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.78 Å3/Da / Density % sol: 67.48 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium malonate pH 6.0, 20% 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: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→48.97 Å / Num. obs: 81479 / % possible obs: 99.84 % / Redundancy: 2 % / Biso Wilson estimate: 70.42 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.45
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 8030 / CC1/2: 0.791

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Processing

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

4zrp


Resolution: 3→48.96 Å / SU ML: 0.5159 / Cross valid method: FREE R-VALUE / σ(F): 0.98 / Phase error: 31.2246
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2837 2037 5 %
Rwork0.2523 38689 -
obs0.2539 40726 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.43 Å2
Refinement stepCycle: LAST / Resolution: 3→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9243 0 190 6 9439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01299640
X-RAY DIFFRACTIONf_angle_d2.209113115
X-RAY DIFFRACTIONf_chiral_restr0.15291454
X-RAY DIFFRACTIONf_plane_restr0.00971666
X-RAY DIFFRACTIONf_dihedral_angle_d16.93553513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.53111370.47582570X-RAY DIFFRACTION99.74
3.07-3.150.4041340.3922523X-RAY DIFFRACTION99.74
3.15-3.230.32641330.35532528X-RAY DIFFRACTION99.96
3.23-3.330.33541330.2882550X-RAY DIFFRACTION99.89
3.33-3.430.31831350.27882557X-RAY DIFFRACTION99.93
3.43-3.560.32271360.28482568X-RAY DIFFRACTION99.96
3.56-3.70.33221350.2942569X-RAY DIFFRACTION99.93
3.7-3.870.33411360.28212550X-RAY DIFFRACTION99.96
3.87-4.070.28941350.23612569X-RAY DIFFRACTION99.67
4.07-4.330.24191330.22252562X-RAY DIFFRACTION99.63
4.33-4.660.24041360.21162589X-RAY DIFFRACTION100
4.66-5.130.25721360.21552589X-RAY DIFFRACTION100
5.13-5.870.26311370.23862618X-RAY DIFFRACTION100
5.87-7.390.25721390.24412635X-RAY DIFFRACTION100
7.39-48.960.22851420.19982712X-RAY DIFFRACTION99.3

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