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Yorodumi- PDB-7df1: Crystal structure of human CD98 heavy chain extracellular domain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7df1 | ||||||
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Title | Crystal structure of human CD98 heavy chain extracellular domain in complex with S1-F4 scFv | ||||||
Components |
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Keywords | ANTITUMOR PROTEIN / Complex / tumor growth / antibody | ||||||
Function / homology | Function and homology information neutral L-amino acid secondary active transmembrane transporter activity / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / tyrosine transport / L-histidine transport / apical pole of neuron / aromatic amino acid transmembrane transporter activity / amino acid transport complex / methionine transport / : / L-leucine import across plasma membrane ...neutral L-amino acid secondary active transmembrane transporter activity / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / tyrosine transport / L-histidine transport / apical pole of neuron / aromatic amino acid transmembrane transporter activity / amino acid transport complex / methionine transport / : / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / isoleucine transport / L-alanine import across plasma membrane / phenylalanine transport / valine transport / L-leucine transmembrane transporter activity / proline transport / calcium:sodium antiporter activity / L-leucine transport / thyroid hormone transport / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / Tryptophan catabolism / exogenous protein binding / amino acid transport / anchoring junction / Basigin interactions / response to exogenous dsRNA / tryptophan transport / basal plasma membrane / calcium ion transport / melanosome / double-stranded RNA binding / virus receptor activity / basolateral plasma membrane / carbohydrate metabolic process / cadherin binding / symbiont entry into host cell / apical plasma membrane / protein heterodimerization activity / lysosomal membrane / synapse / cell surface / protein homodimerization activity / RNA binding / extracellular exosome / nucleoplasm / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.806 Å | ||||||
Authors | Liu, X. / Ding, J. / Sui, J. / Tian, X. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Biomed Eng / Year: 2022 Title: An anti-CD98 antibody displaying pH-dependent Fc-mediated tumour-specific activity against multiple cancers in CD98-humanized mice. Authors: Tian, X. / Liu, X. / Ding, J. / Wang, F. / Wang, K. / Liu, J. / Wei, Z. / Hao, X. / Li, Y. / Wei, X. / Zhang, H. / Sui, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7df1.cif.gz | 483.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7df1.ent.gz | 396.7 KB | Display | PDB format |
PDBx/mmJSON format | 7df1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/7df1 ftp://data.pdbj.org/pub/pdb/validation_reports/df/7df1 | HTTPS FTP |
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-Related structure data
Related structure data | 2dh2S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 46243.961 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC3A2, MDU1 / Production host: Escherichia coli (E. coli) / References: UniProt: P08195 #2: Antibody | Mass: 14741.354 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293-F / Production host: Homo sapiens (human) #3: Antibody | Mass: 13581.007 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293-F / Production host: Homo sapiens (human) / References: UniProt: A0A5C2G3X0 |
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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: 3.27 Å3/Da / Density % sol: 62.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium citrate tribasic dihydrate pH 5.0, 9% PEG20000, 5% PEG400, 9% glycerol |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.806→50.05 Å / Num. obs: 90217 / % possible obs: 99.8 % / Redundancy: 6.97 % / CC1/2: 0.998 / Rmerge(I) obs: 0.118 / Net I/σ(I): 12.69 |
Reflection shell | Resolution: 2.81→2.88 Å / Num. unique obs: 6299 / CC1/2: 0.896 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DH2 Resolution: 2.806→50.044 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.36 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.806→50.044 Å
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Refine LS restraints |
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LS refinement shell |
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