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- PDB-7qbg: TC:CD320 in complex with nanobody TC-Nb4 -

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Basic information

Entry
Database: PDB / ID: 7qbg
TitleTC:CD320 in complex with nanobody TC-Nb4
Components
  • Anti-TC:CD320 nanobody TC-Nb4
  • 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: 2.69 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-TC:CD320 nanobody TC-Nb4
G: Anti-TC:CD320 nanobody TC-Nb4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,31817
Polymers152,0896
Non-polymers3,22911
Water84747
1
A: Transcobalamin-2
D: CD320 antigen
G: Anti-TC:CD320 nanobody TC-Nb4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7059
Polymers76,0443
Non-polymers1,6616
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-29 kcal/mol
Surface area27200 Å2
MethodPISA
2
B: CD320 antigen
C: Transcobalamin-2
E: Anti-TC:CD320 nanobody TC-Nb4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6138
Polymers76,0443
Non-polymers1,5695
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-25 kcal/mol
Surface area27690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.339, 116.418, 125.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 4 molecules ACBD

#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

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Antibody , 1 types, 2 molecules EG

#3: Antibody Anti-TC:CD320 nanobody TC-Nb4


Mass: 14780.359 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 , 4 types, 58 molecules

#4: Chemical ChemComp-CNC / CYANOCOBALAMIN


Mass: 1356.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H89CoN14O14P
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis-Tris pH 5.5, 25% w/v PEG 3350, supplemented with 10% (0.2% w/v Betaine anhydrous, 0.2% w/v L-Glutamic acid, 0.2% w/v L-Proline, 0.2% w/v Taurine, 0.2% w/v Trimethylamine N-oxide ...Details: 100 mM Bis-Tris pH 5.5, 25% w/v PEG 3350, supplemented with 10% (0.2% w/v Betaine anhydrous, 0.2% w/v L-Glutamic acid, 0.2% w/v L-Proline, 0.2% w/v Taurine, 0.2% w/v Trimethylamine N-oxide dihydrate, 0.02 M HEPES sodium pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979502 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: 0.979502 Å / Relative weight: 1
ReflectionResolution: 2.69→48.92 Å / Num. obs: 84243 / % possible obs: 97.98 % / Redundancy: 2 % / Biso Wilson estimate: 56.39 Å2 / CC1/2: 0.993 / Net I/σ(I): 7.97
Reflection shellResolution: 2.69→2.79 Å / Num. unique obs: 7177 / CC1/2: 0.459

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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: 2.69→48.92 Å / SU ML: 0.4359 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 32.9931
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2854 4022 5 %
Rwork0.227 76397 -
obs0.2299 80419 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.61 Å2
Refinement stepCycle: LAST / Resolution: 2.69→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9092 0 210 47 9349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01069496
X-RAY DIFFRACTIONf_angle_d2.02512926
X-RAY DIFFRACTIONf_chiral_restr0.11931442
X-RAY DIFFRACTIONf_plane_restr0.01231643
X-RAY DIFFRACTIONf_dihedral_angle_d24.16633483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.720.4739810.41711533X-RAY DIFFRACTION56.3
2.72-2.760.3471370.36052688X-RAY DIFFRACTION99.65
2.76-2.790.37191460.3532696X-RAY DIFFRACTION99.23
2.79-2.830.43611440.34082685X-RAY DIFFRACTION99.65
2.83-2.870.35161440.33112679X-RAY DIFFRACTION99.47
2.87-2.910.35461410.32622717X-RAY DIFFRACTION99.65
2.91-2.950.39631400.32162655X-RAY DIFFRACTION99.36
2.95-30.33131430.31822711X-RAY DIFFRACTION99.58
3-3.050.39511400.32672669X-RAY DIFFRACTION99.22
3.05-3.10.34491420.30912675X-RAY DIFFRACTION99.12
3.1-3.160.36731420.2982713X-RAY DIFFRACTION99.76
3.16-3.220.38551410.29442704X-RAY DIFFRACTION99.37
3.22-3.280.31421400.26712699X-RAY DIFFRACTION99.89
3.28-3.350.32951440.25172717X-RAY DIFFRACTION99.79
3.35-3.430.32611420.24142671X-RAY DIFFRACTION99.82
3.43-3.520.30911440.24172696X-RAY DIFFRACTION99.75
3.52-3.610.33941370.22982696X-RAY DIFFRACTION99.86
3.61-3.720.34911420.20892732X-RAY DIFFRACTION99.76
3.72-3.840.30411370.21172659X-RAY DIFFRACTION99.64
3.84-3.980.24741390.19992695X-RAY DIFFRACTION99.58
3.98-4.140.27081450.19392703X-RAY DIFFRACTION99.55
4.14-4.320.28871270.18312389X-RAY DIFFRACTION88.75
4.32-4.550.22471330.1852439X-RAY DIFFRACTION90.12
4.55-4.840.24911440.17762709X-RAY DIFFRACTION99.83
4.84-5.210.20371430.18442704X-RAY DIFFRACTION99.96
5.21-5.730.28731460.20812692X-RAY DIFFRACTION99.93
5.73-6.560.2511430.20962708X-RAY DIFFRACTION99.76
6.56-8.260.22561430.1982695X-RAY DIFFRACTION99.65
8.26-48.920.19351320.17582668X-RAY DIFFRACTION98.63

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