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Yorodumi- PDB-1ntj: Model of rat Crry determined by solution scattering, curve fittin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ntj | ||||||
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Title | Model of rat Crry determined by solution scattering, curve fitting and homology modelling | ||||||
Components | complement receptor related protein | ||||||
Keywords | IMMUNE SYSTEM / IMMUNOLOGY / COMPLEMENT / GLYCOPROTEIN / SCR / CCP | ||||||
Function / homology | Function and homology information Regulation of Complement cascade / negative regulation of complement activation / negative regulation of complement activation, classical pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / T cell mediated immunity / complement activation / Neutrophil degranulation / complement activation, classical pathway / female pregnancy ...Regulation of Complement cascade / negative regulation of complement activation / negative regulation of complement activation, classical pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / T cell mediated immunity / complement activation / Neutrophil degranulation / complement activation, classical pathway / female pregnancy / cellular response to hypoxia / basolateral plasma membrane / in utero embryonic development / receptor complex / external side of plasma membrane / innate immune response / cell surface / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | SOLUTION SCATTERING / SYNCHROTRON / NUCLEAR REACTOR / CONSTRAINED MODEL FIT / Resolution: 30 Å | ||||||
Authors | Aslam, M. / Guthridge, J.M. / Hack, B.K. / Quigg, R.J. / Holers, V.M. / Perkins, S.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: The Extended Multidomain Solution Structures of the Complement Protein Crry and its Chimeric Conjugate Crry-Ig by Scattering, Analytical Ultracentrifugation and Constrained Modelling: ...Title: The Extended Multidomain Solution Structures of the Complement Protein Crry and its Chimeric Conjugate Crry-Ig by Scattering, Analytical Ultracentrifugation and Constrained Modelling: Implications for Function and Therapy Authors: Aslam, M. / Guthridge, J.M. / Hack, B.K. / Quigg, R.J. / Holers, V.M. / Perkins, S.J. | ||||||
History |
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Remark 2 | RESOLUTION. NOT APPLICABLE. | ||||||
Remark 3 | REFINEMENT. PROGRAM : INSIGHT II 98.0 AUTHORS : MSI |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ntj.cif.gz | 22.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ntj.ent.gz | 9.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ntj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ntj_validation.pdf.gz | 286.5 KB | Display | wwPDB validaton report |
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Full document | 1ntj_full_validation.pdf.gz | 286.5 KB | Display | |
Data in XML | 1ntj_validation.xml.gz | 995 B | Display | |
Data in CIF | 1ntj_validation.cif.gz | 3.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/1ntj ftp://data.pdbj.org/pub/pdb/validation_reports/nt/1ntj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 35274.980 Da / Num. of mol.: 1 / Fragment: SCR-1 TO SCR-5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Pichia pastoris (fungus) / References: GenBank: 9506513, UniProt: Q63135*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION SCATTERING |
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-Sample preparation
Crystal grow | *PLUS Method: unknown |
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Soln scatter | Data analysis software list: SCTPL5, GNOM / Sample pH: 7.5 / Temperature: 288 K
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-Processing
Software |
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Refinement | Method to determine structure: CONSTRAINED MODEL FIT / Resolution: 30→1300 Å / Rfactor all: 0.073 / Stereochemistry target values: Engh & Huber Details: The structure was determined by x-ray scattering, analytical ultracentrifugation and constrained modelling | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 30→1300 Å
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Soln scatter model | Method: CONSTRAINED SCATTERING FITTING OF HOMOLOGY MODELS Conformer selection criteria: THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG AND RSX-1 VALUES IN THE SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE THEN ...Conformer selection criteria: THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG AND RSX-1 VALUES IN THE SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE THEN RANKED USING A GOODNESS-OF-FIT R-FACTOR DEFINED BY ANALOGY WITH PROTEIN CRYSTALLOGRAPHY AND BASED ON THE EXPERIMENTAL CURVES IN THE Q RANGE EXTENDING TO 2.2 NM-1 (X-RAYS) AND 1.12 NM-1 (ILL NEUTRONS). Details: HOMOLOGY MODELS WERE BUILT FOR THE 5 SCR DOMAINS AND ENERGY MINIMISATIONS WERE PERFORMED TO IMPROVE THE CONNECTIVITY IN THE FH MODEL. BIANTENNARY COMPLEX-TYPE CARBOHYDRATE STRUCTURES ...Details: HOMOLOGY MODELS WERE BUILT FOR THE 5 SCR DOMAINS AND ENERGY MINIMISATIONS WERE PERFORMED TO IMPROVE THE CONNECTIVITY IN THE FH MODEL. BIANTENNARY COMPLEX-TYPE CARBOHYDRATE STRUCTURES (MAN3GLCNAC4GAL2FUC0NEUNAC2) WERE ADDED TO EACH OF THE N-LINKED GLYCOSYLATION SITES. A LIBRARY OF LINKER PEPTIDE CONFORMATIONS WAS USED IN DOMAIN MODELLING CONSTRAINED BY THE SOLUTION SCATTERING FITS. MODELLING WITH THE SCATTERING DATA WAS ALSO CARRIED OUT BY ROTATIONAL SEARCH METHODS. THE X-RAY AND NEUTRON SCATTERING CURVE I(Q) WAS CALCULATED ASSUMING A UNIFORM SCATTERING DENSITY FOR THE SPHERES USING THE DEBYE EQUATION AS ADAPTED TO SPHERES. X-RAY CURVES WERE CALCULATED FROM THE HYDRATED SPHERE MODELS WITHOUT CORRECTIONS FOR WAVELENGTH SPREAD OR BEAM DIVERGENCE, WHILE THESE CORRECTIONS WERE APPLIED FOR THE NEUTRON CURVES BUT NOW USING UNHYDRATED MODELS. Num. of conformers calculated: 2000 / Num. of conformers submitted: 1 / Representative conformer: 1 / Software author list: MSI Software list: INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI |