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- PDB-4zrq: E88 deletion mutant of CD320 in complex with TC2 -

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Basic information

Entry
Database: PDB / ID: 4zrq
TitleE88 deletion mutant of CD320 in complex with TC2
Components
  • CD320 antigen
  • Transcobalamin-2
KeywordsTRANSPORT PROTEIN / LDLR-R / vitamin transporter
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
Ferric Hydroxamate Uptake Protein; Chain A, domain 1 - #30 / Domain of unknown function DUF4430 / Domain of unknown function (DUF4430) / Cobalamin (vitamin B12)-binding protein / Eukaryotic cobalamin-binding protein / Eukaryotic cobalamin-binding proteins signature. / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Glycosyltransferase - #20 / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site ...Ferric Hydroxamate Uptake Protein; Chain A, domain 1 - #30 / Domain of unknown function DUF4430 / Domain of unknown function (DUF4430) / Cobalamin (vitamin B12)-binding protein / Eukaryotic cobalamin-binding protein / Eukaryotic cobalamin-binding proteins signature. / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Glycosyltransferase - #20 / 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 / Glycosyltransferase / Alpha/alpha barrel / Beta Complex / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CYANOCOBALAMIN / Transcobalamin-2 / CD320 antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAlam, A. / Locher, K.P.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis of transcobalamin recognition by human CD320 receptor.
Authors: Alam, A. / Woo, J.S. / Schmitz, J. / Prinz, B. / Root, K. / Chen, F. / Bloch, J.S. / Zenobi, R. / Locher, K.P.
History
DepositionMay 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Oct 10, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen
Item: _entity.formula_weight / _entity_src_gen.pdbx_host_org_cell_line ..._entity.formula_weight / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector
Revision 2.0Aug 25, 2021Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcobalamin-2
B: Transcobalamin-2
C: CD320 antigen
D: CD320 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,88714
Polymers116,6454
Non-polymers3,24110
Water79344
1
A: Transcobalamin-2
C: CD320 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0358
Polymers58,3232
Non-polymers1,7136
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-18 kcal/mol
Surface area22470 Å2
MethodPISA
2
B: Transcobalamin-2
D: CD320 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8516
Polymers58,3232
Non-polymers1,5294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-15 kcal/mol
Surface area22490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.404, 98.404, 356.341
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA0 - 409
211chain BB0 - 409
112chain CC53 - 171
212chain DD53 - 170

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

#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 / Cell line (production host): Sf21 / 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: 12672.251 Da / Num. of mol.: 2 / Fragment: residues 53-171 / Mutation: DelE88
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD320, 8D6A, UNQ198/PRO224 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NPF0

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Non-polymers , 4 types, 54 molecules

#3: Chemical ChemComp-CNC / CYANOCOBALAMIN / Cyanocobalamin


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#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 / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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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: 3.62 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG3350, L-Proline, Hepes

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→29.434 Å / Num. obs: 54979 / % possible obs: 99.91 % / Redundancy: 10.8 % / Net I/σ(I): 16.8
Reflection shellHighest resolution: 2.6 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1.62 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.434 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2305 2731 4.97 %
Rwork0.1985 52248 -
obs0.2001 54979 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.04 Å2 / Biso mean: 74.4665 Å2 / Biso min: 32.53 Å2
Refinement stepCycle: final / Resolution: 2.6→29.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7488 0 28 44 7560
Biso mean--100.41 62.36 -
Num. residues----952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077702
X-RAY DIFFRACTIONf_angle_d1.88610490
X-RAY DIFFRACTIONf_chiral_restr0.1221178
X-RAY DIFFRACTIONf_plane_restr0.0081332
X-RAY DIFFRACTIONf_dihedral_angle_d13.6992808
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3651X-RAY DIFFRACTION11.005TORSIONAL
12B3651X-RAY DIFFRACTION11.005TORSIONAL
21C594X-RAY DIFFRACTION11.005TORSIONAL
22D594X-RAY DIFFRACTION11.005TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.64480.38981350.308125502685100
2.6448-2.69290.30731190.293925552674100
2.6929-2.74460.34171470.285125562703100
2.7446-2.80060.2961220.275625832705100
2.8006-2.86150.33941300.278825592689100
2.8615-2.9280.30931610.280825512712100
2.928-3.00110.30161080.262425932701100
3.0011-3.08220.30191330.258726072740100
3.0822-3.17280.29671420.260725842726100
3.1728-3.27510.27681450.244225572702100
3.2751-3.3920.27971440.243925952739100
3.392-3.52760.27781270.22925822709100
3.5276-3.68780.23761270.207626152742100
3.6878-3.88180.21921370.195825992736100
3.8818-4.12440.19921490.16726172766100
4.1244-4.44190.1811130.163826492762100
4.4419-4.88710.18951290.149926632792100
4.8871-5.59010.21481670.17726452812100
5.5901-7.0270.24051350.193627322867100
7.027-29.43590.15551610.14562856301799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.08411.37721.59161.71060.79572.940.1932-0.2816-0.08730.2175-0.13650.04550.13090.0117-0.05380.55980.05040.00450.31960.02660.286-19.1962-47.2355-39.7263
22.36611.58271.42073.03531.71174.5354-0.15390.09870.1789-0.37730.09140.0356-0.0690.22120.06730.39850.0163-0.01130.46520.0730.29525.764-28.8161-0.91
37.14656.06981.59438.1804-1.67355.70630.1239-1.407-2.86281.9065-0.3786-2.39621.33460.78140.2551.38680.1842-0.10721.15030.35921.70862.6599-68.1179-27.0565
46.8087-3.992-5.24057.80484.12392.00910.47240.2942-0.0213-0.66620.0643-1.8256-0.9971.386-0.51790.8006-0.0070.0531.01880.00840.78913.7629-40.8478-38.4217
54.5834.3647-3.82329.98250.58976.2584-0.32641.8625-1.5796-1.02580.7125-2.31990.96190.7462-0.38871.01470.14160.13721.4243-0.38211.225221.1109-53.1267-16.308
64.3452-3.65151.33216.7478-2.20093.84540.3482-0.5253-1.4076-0.11830.44720.40272.0794-0.4207-0.79221.1167-0.1511-0.12870.75210.10580.6902-6.4167-59.8983-3.2384
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 409 )A0
2X-RAY DIFFRACTION2chain 'B' and (resid 0 through 409 )B0
3X-RAY DIFFRACTION3chain 'C' and (resid 53 through 85 )C0
4X-RAY DIFFRACTION4chain 'C' and (resid 129 through 171 )C0
5X-RAY DIFFRACTION5chain 'D' and (resid 53 through 85 )D0
6X-RAY DIFFRACTION6chain 'D' and (resid 129 through 170 )D0

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