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Yorodumi- PDB-6wjl: Crystal structure of Glypican-2 core protein in complex with D3 Fab -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wjl | |||||||||
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Title | Crystal structure of Glypican-2 core protein in complex with D3 Fab | |||||||||
Components |
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Keywords | Oncoprotein/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 / A tetrasaccharide linker sequence is required for GAG synthesis / 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 / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / smoothened signaling pathway / regulation of signal transduction / Retinoid metabolism and transport / lysosomal lumen / neuron differentiation / positive regulation of neuron projection development / Golgi lumen / cell migration / collagen-containing extracellular matrix / Attachment and Entry / synapse / cell surface / endoplasmic reticulum / extracellular space / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Lama glama (llama) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||
Authors | Raman, S. / Maris, J.M. / Bosse, K.R. / Julien, J.P. | |||||||||
Funding support | 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wjl.cif.gz | 368.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wjl.ent.gz | 292.8 KB | Display | PDB format |
PDBx/mmJSON format | 6wjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wjl_validation.pdf.gz | 493.7 KB | Display | wwPDB validaton report |
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Full document | 6wjl_full_validation.pdf.gz | 525.2 KB | Display | |
Data in XML | 6wjl_validation.xml.gz | 62.9 KB | Display | |
Data in CIF | 6wjl_validation.cif.gz | 86 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/6wjl ftp://data.pdbj.org/pub/pdb/validation_reports/wj/6wjl | HTTPS FTP |
-Related structure data
Related structure data | 4acrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | 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 | 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 | 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 | 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) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M NaCl, 10% (w/v) PEG 3350 and 0.1 M disodium hydrogen phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03319 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 3.3→3.418 Å / Num. unique obs: 3807 / CC1/2: 0.826 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 159.22 Å2 / Biso mean: 72.9611 Å2 / Biso min: 23.99 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.3→29.476 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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