+Open data
-Basic information
Entry | Database: PDB / ID: 6i9q | ||||||
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Title | Structure of the mouse CD98 heavy chain ectodomain | ||||||
Components | 4F2 cell-surface antigen heavy chain | ||||||
Keywords | MEMBRANE PROTEIN / CD98hc / 4F2hc / amino acid transport / CD98 light chain / LAT-1 / LAT-2 / integrin beta subunit binding / single-pass type II membrane protein | ||||||
Function / homology | Function and homology information Amino acid transport across the plasma membrane / Tryptophan catabolism / apical pole of neuron / aromatic amino acid transmembrane transporter activity / amino acid transport complex / : / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / L-alanine import across plasma membrane / phenylalanine transport ...Amino acid transport across the plasma membrane / Tryptophan catabolism / apical pole of neuron / aromatic amino acid transmembrane transporter activity / amino acid transport complex / : / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / L-alanine import across plasma membrane / phenylalanine transport / L-leucine transmembrane transporter activity / L-leucine transport / neutral amino acid transport / neutral L-amino acid transmembrane transporter activity / anchoring junction / response to exogenous dsRNA / tryptophan transport / basal plasma membrane / melanosome / double-stranded RNA binding / basolateral plasma membrane / carbohydrate metabolic process / symbiont entry into host cell / apical plasma membrane / lysosomal membrane / neuronal cell body / synapse / cell surface / nucleoplasm / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Schiefner, A. / Deuschle, F.-C. / Skerra, A. | ||||||
Citation | Journal: Proteins / Year: 2019 Title: Structural differences between the ectodomains of murine and human CD98hc. Authors: Deuschle, F.C. / Schiefner, A. / Skerra, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i9q.cif.gz | 102.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i9q.ent.gz | 76.3 KB | Display | PDB format |
PDBx/mmJSON format | 6i9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/6i9q ftp://data.pdbj.org/pub/pdb/validation_reports/i9/6i9q | 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 |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 48366.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slc3a2, Mdu1 / Plasmid: pASK-IBA5+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P10852 | ||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.17 % / Description: thin plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 24 % (w/v) PEG 3350, 0.1 M Bis-tris propane/HCl, 0.2 M sodium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 22, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→34.45 Å / Num. obs: 31196 / % possible obs: 99.9 % / Redundancy: 26.556 % / Biso Wilson estimate: 42.827 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.133 / Χ2: 1.008 / Net I/σ(I): 21.43 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DH2 Resolution: 2.1→34.45 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.404 / SU ML: 0.115 / SU R Cruickshank DPI: 0.1786 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.161 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 145.23 Å2 / Biso mean: 39.43 Å2 / Biso min: 19.44 Å2
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Refinement step | Cycle: final / Resolution: 2.1→34.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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