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- PDB-7qbf: TC:CD320 in complex with nanobody TC-Nb34 -

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Basic information

Entry
Database: PDB / ID: 7qbf
TitleTC:CD320 in complex with nanobody TC-Nb34
Components
  • Anti-transcobalamin-2 nanobody TC-Nb34
  • 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 / Transport of RCbl within the body / cargo receptor ligand activity / ventral spinal cord development / B cell costimulation / 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 / ventral spinal cord development / B cell costimulation / 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
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 ...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 / IODIDE ION / Transcobalamin-2 / CD320 antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcobalamin-2
C: CD320 antigen
B: Anti-transcobalamin-2 nanobody TC-Nb34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,33449
Polymers76,1913
Non-polymers5,14346
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14480 Å2
ΔGint53 kcal/mol
Surface area26990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.822, 104.822, 167.460
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
Components on special symmetry positions
IDModelComponents
11A-675-

HOH

21A-868-

HOH

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Components

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Protein , 2 types, 2 molecules AC

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


Mass: 45679.492 Da / Num. of mol.: 1
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.: 1
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, 1 molecules B

#3: Antibody Anti-transcobalamin-2 nanobody TC-Nb34


Mass: 14898.274 Da / Num. of mol.: 1
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 , 5 types, 453 molecules

#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: I
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CNC / CYANOCOBALAMIN


Mass: 1356.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C63H89CoN14O14P
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 200 mM Ammonium Iodide, 16% w/v PEG 3350 and 1.4 x 105-fold diluted seed stocks from crystals of the same protein, grown in similar conditions

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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: 1.85→49.27 Å / Num. obs: 158598 / % possible obs: 98.15 % / Redundancy: 2 % / Biso Wilson estimate: 31.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0272 / Net I/σ(I): 1.89
Reflection shellResolution: 1.85→1.92 Å / Num. unique obs: 15319 / CC1/2: 0.4422

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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: 1.85→49.27 Å / SU ML: 0.2011 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 20.657
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2048 7523 4.99 %
Rwork0.1744 143256 -
obs0.1759 150779 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.38 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4736 0 219 407 5362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01195226
X-RAY DIFFRACTIONf_angle_d2.57717099
X-RAY DIFFRACTIONf_chiral_restr0.2129759
X-RAY DIFFRACTIONf_plane_restr0.0085900
X-RAY DIFFRACTIONf_dihedral_angle_d21.11131914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.33122350.31294504X-RAY DIFFRACTION93.42
1.87-1.90.29012540.29424774X-RAY DIFFRACTION100
1.9-1.920.30812510.27254781X-RAY DIFFRACTION99.96
1.92-1.940.27462560.25434801X-RAY DIFFRACTION99.98
1.94-1.970.27722550.25294766X-RAY DIFFRACTION100
1.97-20.25512560.24374813X-RAY DIFFRACTION99.98
2-2.030.26192530.23254736X-RAY DIFFRACTION100
2.03-2.060.28372520.22934841X-RAY DIFFRACTION99.9
2.06-2.090.25122530.22534780X-RAY DIFFRACTION100
2.09-2.120.26572560.2224762X-RAY DIFFRACTION99.9
2.12-2.160.252460.20384757X-RAY DIFFRACTION99.92
2.16-2.20.2192560.1894826X-RAY DIFFRACTION99.92
2.2-2.240.23022460.18384780X-RAY DIFFRACTION99.84
2.24-2.290.2192530.18084779X-RAY DIFFRACTION99.72
2.29-2.340.20522540.17394764X-RAY DIFFRACTION99.92
2.34-2.390.21072530.16634804X-RAY DIFFRACTION99.98
2.39-2.450.20542440.16644754X-RAY DIFFRACTION99.98
2.45-2.520.22292510.16914786X-RAY DIFFRACTION99.98
2.52-2.590.19242600.164786X-RAY DIFFRACTION100
2.59-2.670.20322500.16624798X-RAY DIFFRACTION99.98
2.67-2.770.19732490.1634809X-RAY DIFFRACTION99.96
2.77-2.880.17052520.16054797X-RAY DIFFRACTION100
2.88-3.010.22312490.17394767X-RAY DIFFRACTION99.98
3.01-3.170.23492460.18494802X-RAY DIFFRACTION99.96
3.17-3.370.21912470.17624777X-RAY DIFFRACTION99.9
3.37-3.630.19112470.15774788X-RAY DIFFRACTION99.9
3.63-3.990.17882500.14714802X-RAY DIFFRACTION99.59
3.99-4.570.15312530.12894734X-RAY DIFFRACTION99.42
4.57-5.760.1712490.14794796X-RAY DIFFRACTION100
5.76-49.270.20112470.20134792X-RAY DIFFRACTION99.82

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