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Yorodumi- PDB-6sua: Structure of the high affinity engineered lipocalin C1B12 in comp... -
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-Basic information
Entry | Database: PDB / ID: 6sua | ||||||
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Title | Structure of the high affinity engineered lipocalin C1B12 in complex with the mouse CD98 heavy chain ectodomain | ||||||
Components |
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Keywords | PROTEIN BINDING / Lipocalin / Lcn2 / Anticalin / lipocalin-based binding protein / CD98hc / 4F2hc / amino acid transport / presentation of CD98 light chain / interaction with integrin beta subunit / single-pass type II membrane protein | ||||||
Function / homology | Function and homology information Amino acid transport across the plasma membrane / Tryptophan catabolism / Basigin interactions / neutral L-amino acid secondary active transmembrane transporter activity / apical pole of neuron / aromatic amino acid transmembrane transporter activity / tyrosine transport / L-histidine transport / amino acid transport complex / L-leucine import across plasma membrane ...Amino acid transport across the plasma membrane / Tryptophan catabolism / Basigin interactions / neutral L-amino acid secondary active transmembrane transporter activity / apical pole of neuron / aromatic amino acid transmembrane transporter activity / tyrosine transport / L-histidine transport / amino acid transport complex / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / L-alanine import across plasma membrane / isoleucine transport / phenylalanine transport / methionine transport / valine transport / L-leucine transmembrane transporter activity / thyroid hormone transport / L-leucine transport / proline transport / siderophore transport / Metal sequestration by antimicrobial proteins / neutral amino acid transport / neutral L-amino acid transmembrane transporter activity / exogenous protein binding / iron ion sequestering activity / enterobactin binding / anchoring junction / response to exogenous dsRNA / tryptophan transport / basal plasma membrane / Iron uptake and transport / specific granule lumen / double-stranded RNA binding / melanosome / positive regulation of cold-induced thermogenesis / basolateral plasma membrane / Interleukin-4 and Interleukin-13 signaling / carbohydrate metabolic process / defense response to bacterium / iron ion binding / symbiont entry into host cell / protein heterodimerization activity / apical plasma membrane / lysosomal membrane / innate immune response / neuronal cell body / Neutrophil degranulation / synapse / apoptotic process / cell surface / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Schiefner, A. / Deuschle, F.-C. / Skerra, A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Protein Sci. / Year: 2020 Title: Design of a surrogate Anticalin protein directed against CD98hc for preclinical studies in mice. Authors: Deuschle, F.C. / Schiefner, A. / Brandt, C. / Skerra, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sua.cif.gz | 248.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sua.ent.gz | 198 KB | Display | PDB format |
PDBx/mmJSON format | 6sua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sua_validation.pdf.gz | 479.2 KB | Display | wwPDB validaton report |
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Full document | 6sua_full_validation.pdf.gz | 484.7 KB | Display | |
Data in XML | 6sua_validation.xml.gz | 41.3 KB | Display | |
Data in CIF | 6sua_validation.cif.gz | 57.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/su/6sua ftp://data.pdbj.org/pub/pdb/validation_reports/su/6sua | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 21462.252 Da / Num. of mol.: 2 Mutation: Q28H, A40G, I41N, Q49L, S68D, R72I, K73D, D77H, W79L, R81N, C87S, N96S, Y100T, P101L, L103S, Y106R, K125W, S127H, Y132W, K134Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Plasmid: pNGAL118 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P80188 #2: Protein | Mass: 48366.570 Da / Num. of mol.: 2 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 BL21 (bacteria) / References: UniProt: P10852 #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | Y | |
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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: 2.71 Å3/Da / Density % sol: 54.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 12 %(w/v) PEG8000, 0.2 M Li2SO4 |
-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 PILATUS3 2M / Detector: PIXEL / Date: Mar 22, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.75→34.71 Å / Num. obs: 39856 / % possible obs: 99.1 % / Redundancy: 13.198 % / Biso Wilson estimate: 42.73 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.197 / Rrim(I) all: 0.205 / Χ2: 0.944 / Net I/σ(I): 15.36 / Num. measured all: 526014 / Scaling rejects: 244 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6I9Q, 6S8V Resolution: 2.75→34.71 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.874 / WRfactor Rfree: 0.2251 / WRfactor Rwork: 0.1825 / FOM work R set: 0.7783 / SU B: 16.437 / SU ML: 0.314 / SU Rfree: 0.3831 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 145.8 Å2 / Biso mean: 43.758 Å2 / Biso min: 12.68 Å2
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Refinement step | Cycle: final / Resolution: 2.75→34.71 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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