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- PDB-6wjl: Crystal structure of Glypican-2 core protein in complex with D3 Fab -

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Basic information

Entry
Database: PDB / ID: 6wjl
TitleCrystal structure of Glypican-2 core protein in complex with D3 Fab
Components
  • D3 Fab Heavy chain
  • D3 Fab Light Chain
  • Glypican-2
  • VHH domain
KeywordsOncoprotein/Immune System / Neuroblastoma / Oncoprotein / Proteoglycan / Therapeutic antibody / Oncoprotein-Immune System complex
Function / homology
Function and homology information


regulation of protein localization to membrane / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / Glycosaminoglycan-protein linkage region biosynthesis / HS-GAG biosynthesis / HS-GAG degradation / smoothened signaling pathway ...regulation of protein localization to membrane / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / Glycosaminoglycan-protein linkage region biosynthesis / HS-GAG biosynthesis / HS-GAG degradation / smoothened signaling pathway / RSV-host interactions / Respiratory syncytial virus (RSV) attachment and entry / regulation of signal transduction / Retinoid metabolism and transport / side of membrane / lysosomal lumen / positive regulation of neuron projection development / Golgi lumen / neuron differentiation / cell migration / Attachment and Entry / synapse / cell surface / endoplasmic reticulum / extracellular region / plasma membrane
Similarity search - Function
Glypican, conserved site / Glypicans signature. / Glypican / Glypican / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsRaman, S. / Maris, J.M. / Bosse, K.R. / Julien, J.P.
Funding support2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)ACB-12002
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AGM-12006
CitationJournal: Cell Rep Med / Year: 2021
Title: A GPC2 antibody-drug conjugate is efficacious against neuroblastoma and small-cell lung cancer via binding a conformational epitope.
Authors: Raman, S. / Buongervino, S.N. / Lane, M.V. / Zhelev, D.V. / Zhu, Z. / Cui, H. / Martinez, B. / Martinez, D. / Wang, Y. / Upton, K. / Patel, K. / Rathi, K.S. / Navia, C.T. / Harmon, D.B. / ...Authors: Raman, S. / Buongervino, S.N. / Lane, M.V. / Zhelev, D.V. / Zhu, Z. / Cui, H. / Martinez, B. / Martinez, D. / Wang, Y. / Upton, K. / Patel, K. / Rathi, K.S. / Navia, C.T. / Harmon, D.B. / Li, Y. / Pawel, B. / Dimitrov, D.S. / Maris, J.M. / Julien, J.P. / Bosse, K.R.
History
DepositionApr 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Nov 17, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Glypican-2
H: D3 Fab Heavy chain
K: VHH domain
L: D3 Fab Light Chain
E: Glypican-2
F: D3 Fab Heavy chain
I: VHH domain
J: D3 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)223,4338
Polymers223,4338
Non-polymers00
Water00
1
G: Glypican-2
H: D3 Fab Heavy chain
K: VHH domain
L: D3 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)111,7164
Polymers111,7164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Glypican-2
F: D3 Fab Heavy chain
I: VHH domain
J: D3 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)111,7164
Polymers111,7164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.942, 225.646, 107.250
Angle α, β, γ (deg.)90.000, 104.750, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Glypican-2


Mass: 53427.738 Da / Num. of mol.: 2 / Mutation: S55T, S92T, S155T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPC2 / Production host: Homo sapiens (human) / References: UniProt: Q8N158
#2: Antibody D3 Fab Heavy chain


Mass: 23499.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody VHH domain


Mass: 11326.253 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
#4: Antibody D3 Fab Light Chain


Mass: 23463.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NaCl, 10% (w/v) PEG 3350 and 0.1 M disodium hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 3.3→29.476 Å / Num. obs: 37835 / % possible obs: 99.76 % / Redundancy: 5.8 % / Biso Wilson estimate: 79.2 Å2 / CC1/2: 0.991 / Net I/σ(I): 7.3
Reflection shellResolution: 3.3→3.418 Å / Num. unique obs: 3807 / CC1/2: 0.826

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XPREPdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ACR

4acr


Resolution: 3.3→29.476 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 34.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.317 1831 4.84 %
Rwork0.2775 35990 -
obs0.2794 37821 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.22 Å2 / Biso mean: 72.9611 Å2 / Biso min: 23.99 Å2
Refinement stepCycle: final / Resolution: 3.3→29.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14241 0 0 0 14241
Num. residues----1916
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.3-3.38910.37431380.31542789
3.3891-3.48870.32631400.30372752
3.4887-3.60110.35521340.30572751
3.6011-3.72960.36081380.29692777
3.7296-3.87860.34281380.29382771
3.8786-4.05470.38031400.28652734
4.0547-4.26790.31631400.27542789
4.2679-4.53440.29241400.26452764
4.5344-4.8830.29371440.25762767
4.883-5.37170.28451370.26422772
5.3717-6.14290.32841480.29922772
6.1429-7.71640.37171460.30152770
7.7164-29.4760.25731480.24342782

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