+Open data
-Basic information
Entry | Database: PDB / ID: 8g0m | ||||||
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Title | Structure of complex between TV6.6 and CD98hc ECD | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Transport vehicle | ||||||
Function / homology | Function and homology information neutral L-amino acid secondary active transmembrane transporter activity / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / methionine transport / tyrosine transport / L-histidine transport / 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 ...neutral L-amino acid secondary active transmembrane transporter activity / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / methionine transport / tyrosine transport / L-histidine transport / 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 / isoleucine transport / L-alanine import across plasma membrane / phenylalanine transport / valine transport / L-leucine transmembrane transporter activity / calcium:sodium antiporter activity / L-leucine transport / thyroid hormone transport / proline transport / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / Tryptophan catabolism / exogenous protein binding / anchoring junction / Basigin interactions / amino acid transport / response to exogenous dsRNA / tryptophan transport / basal plasma membrane / calcium ion transport / double-stranded RNA binding / virus receptor activity / melanosome / basolateral plasma membrane / carbohydrate metabolic process / cadherin binding / apical plasma membrane / symbiont entry into host cell / 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Kariolis, M.S. / Lexa, K. / Liau, N.P.D. / Srivastava, D. / Tran, H. / Wells, R.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: CD98hc is a target for brain delivery of biotherapeutics. Authors: Chew, K.S. / Wells, R.C. / Moshkforoush, A. / Chan, D. / Lechtenberg, K.J. / Tran, H.L. / Chow, J. / Kim, D.J. / Robles-Colmenares, Y. / Srivastava, D.B. / Tong, R.K. / Tong, M. / Xa, K. / ...Authors: Chew, K.S. / Wells, R.C. / Moshkforoush, A. / Chan, D. / Lechtenberg, K.J. / Tran, H.L. / Chow, J. / Kim, D.J. / Robles-Colmenares, Y. / Srivastava, D.B. / Tong, R.K. / Tong, M. / Xa, K. / Yang, A. / Zhou, Y. / Akkapeddi, P. / Annamalai, L. / Bajc, K. / Blanchette, M. / Cherf, G.M. / Earr, T.K. / Gill, A. / Huynh, D. / Joy, D. / Knight, K.N. / Lac, D. / Leung, A.W. / Lexa, K.W. / Liau, N.P.D. / Becerra, I. / Malfavon, M. / McInnes, J. / Nguyen, H.N. / Lozano, E.I. / Pizzo, M.E. / Roche, E. / Sacayon, P. / Calvert, M.E.K. / Daneman, R. / Dennis, M.S. / Duque, J. / Gadkar, K. / Lewcock, J.W. / Mahon, C.S. / Meisner, R. / Solanoy, H. / Thorne, R.G. / Watts, R.J. / Zuchero, Y.J.Y. / Kariolis, M.S. #1: Journal: Nat Commun / Year: 2023 Title: CD98hc is a target for brain delivery of biotherapeutics. Authors: Chew, K.S. / Wells, R.C. / Moshkforoush, A. / Chan, D. / Lechtenberg, K.J. / Tran, H.L. / Chow, J. / Kim, D.J. / Robles-Colmenares, Y. / Srivastava, D.B. / Tong, R.K. / Tong, M. / Xa, K. / ...Authors: Chew, K.S. / Wells, R.C. / Moshkforoush, A. / Chan, D. / Lechtenberg, K.J. / Tran, H.L. / Chow, J. / Kim, D.J. / Robles-Colmenares, Y. / Srivastava, D.B. / Tong, R.K. / Tong, M. / Xa, K. / Yang, A. / Zhou, Y. / Akkapeddi, P. / Annamalai, L. / Bajc, K. / Blanchette, M. / Cherf, G.M. / Earr, T.K. / Gill, A. / Huynh, D. / Joy, D. / Knight, K.N. / Lac, D. / Leung, A.W. / Lexa, K.W. / Liau, N.P.D. / Becerra, I. / Malfavon, M. / McInnes, J. / Nguyen, H.N. / Lozano, E.I. / Pizzo, M.E. / Roche, E. / Sacayon, P. / Calvert, M.E.K. / Daneman, R. / Dennis, M.S. / Duque, J. / Gadkar, K. / Lewcock, J.W. / Mahon, C.S. / Meisner, R. / Solanoy, H. / Thorne, R.G. / Watts, R.J. / Zuchero, Y.J.Y. / Kariolis, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g0m.cif.gz | 257.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g0m.ent.gz | 207.6 KB | Display | PDB format |
PDBx/mmJSON format | 8g0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/8g0m ftp://data.pdbj.org/pub/pdb/validation_reports/g0/8g0m | HTTPS FTP |
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-Related structure data
Related structure data | 6irsS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Antibody / Sugars , 3 types, 3 molecules AB
#1: Protein | Mass: 46951.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC3A2, MDU1 / Production host: Homo sapiens (human) / References: UniProt: P08195 |
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#2: Antibody | Mass: 25757.346 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Homo sapiens (human) |
#3: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 1422.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 163 molecules
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PG4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.29 Å3/Da / Density % sol: 62.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 10% Glycerol, 0.1 M HEPES pH 7.5, 5% PEG 3000, 30% PEG 40 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.18071 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.18071 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→44.681 Å / Num. obs: 45610 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.058 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 2.25→2.32 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4148 / Rrim(I) all: 1.07 / Rsym value: 0.994 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IRS Resolution: 2.25→44.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.95 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.194 Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.39 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→44.68 Å
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Refine LS restraints |
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