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- PDB-1ntj: Model of rat Crry determined by solution scattering, curve fittin... -

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Basic information

Entry
Database: PDB / ID: 1ntj
TitleModel of rat Crry determined by solution scattering, curve fitting and homology modelling
Componentscomplement receptor related protein
KeywordsIMMUNE SYSTEM / IMMUNOLOGY / COMPLEMENT / GLYCOPROTEIN / SCR / CCP
Function / homology
Function and homology information


Regulation of Complement cascade / negative regulation of complement activation, classical pathway / negative regulation of complement activation / T cell mediated immunity / regulation of complement-dependent cytotoxicity / regulation of complement activation / complement activation / Neutrophil degranulation / complement activation, classical pathway / female pregnancy ...Regulation of Complement cascade / negative regulation of complement activation, classical pathway / negative regulation of complement activation / T cell mediated immunity / regulation of complement-dependent cytotoxicity / regulation of complement activation / 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
Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily
Similarity search - Domain/homology
: / Complement component receptor 1-like protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION SCATTERING / SYNCHROTRON / NUCLEAR REACTOR / CONSTRAINED MODEL FIT / Resolution: 30 Å
AuthorsAslam, M. / Guthridge, J.M. / Hack, B.K. / Quigg, R.J. / Holers, V.M. / Perkins, S.J.
CitationJournal: 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
DepositionJan 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jun 13, 2018Group: Data collection / Category: diffrn_radiation
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_radiation.pdbx_scattering_type
Revision 1.5Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 2RESOLUTION. NOT APPLICABLE.
Remark 3 REFINEMENT. PROGRAM : INSIGHT II 98.0 AUTHORS : MSI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: complement receptor related protein


Theoretical massNumber of molelcules
Total (without water)35,2751
Polymers35,2751
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein complement receptor related protein / Coordinate model: Cα atoms only


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

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Experiment

ExperimentMethod: SOLUTION SCATTERING

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Sample preparation

Crystal grow
*PLUS
Method: unknown

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12881
22881
32881
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSRS 2.111
NUCLEAR REACTORILL D11210
SPALLATION SOURCEISISLOQ32.0-10.0
Detector
TypeIDDetectorDate
500 CHANNEL1QUADRANT DETECTORApr 15, 1999
BF3 DETECTOR2WIRE DETECTORMay 15, 1999
3-He ORDELA3AREA DETECTORJun 15, 1998
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMneutron2ROTATING DRUM
3LAUELneutron2TIME-OF-FLIGHT
Radiation wavelength
IDWavelength (Å)Relative weight
111
2101
321
4101
Soln scatter

Data analysis software list: SCTPL5, GNOM / Sample pH: 7.5 / Temperature: 288 K

TypeIDBuffer nameConc. range (mg/ml)Data reduction software listDetector typeMean guiner radius (nm)Mean guiner radius esd (nm)Min mean cross sectional radii gyration (nm)Min mean cross sectional radii gyration esd (nm)Num. of time framesProtein lengthSource beamlineSource classSource typeSource beamline instrument
x-ray1TRIS2-15OTOKO500-CHANNEL QUADRANT50.41.50.11012.1YSRS BEAMLINE 2.1
neutron2PBS IN 99.9% D2O8.2DETEC, RNILS, SPOLLYAREA4.90.21.20.2NILLD11
neutron3PBS IN 99.9% D2O4.5-6.8COLLETTEAREA (TIME-OF-FLIGHT)4.90.21.20.21PULSED NEUTRONNISISLOQ

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Processing

Software
NameVersionClassification
DETECTORdata collection
OTOKOdata reduction
COLLETTEdata reduction
SPOLLYdata reduction
SCTPL5model building
GNOMmodel building
Insight IIIImodel building
DISCOVERrefinement
DETECTORSUPPLIED SOFTWAREdata reduction
OTOKOdata scaling
COLLETTEdata scaling
SPOLLYdata scaling
SCTPLV. 5phasing
GNOMphasing
RefinementMethod 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 stepCycle: LAST / Resolution: 30→1300 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms320 0 0 0 320
Soln scatter modelMethod: 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

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