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- PDB-1ntl: Model of mouse Crry-Ig determined by solution scattering, curve f... -

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Basic information

Entry
Database: PDB / ID: 1ntl
TitleModel of mouse Crry-Ig determined by solution scattering, curve fitting and homology modelling
ComponentsComplement component receptor 1-like protein,Ig gamma-1 chain C region secreted form
KeywordsIMMUNE SYSTEM / IMMUNOLOGY / COMPLEMENT / GLYCOPROTEIN / SCR / CCP
Function / homology
Function and homology information


negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / complement activation / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment ...negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / complement activation / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin mediated immune response / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / B cell differentiation / complement activation, classical pathway / female pregnancy / antigen binding / positive regulation of immune response / antibacterial humoral response / cellular response to hypoxia / basolateral plasma membrane / in utero embryonic development / membrane => GO:0016020 / receptor complex / blood microparticle / defense response to bacterium / external side of plasma membrane / innate immune response / cell surface / extracellular space / extracellular exosome / cytoplasm
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 / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain ...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 / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Ig gamma-1 chain C region secreted form / Complement component receptor 1-like protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
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 chimaeric conjugate Crry-Ig by scattering, analytical ultracentrifugation and constrained modelling: ...Title: The extended multidomain solution structures of the complement protein Crry and its chimaeric 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 1.3Aug 31, 2016Group: Other
Revision 1.4Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name / _struct.pdbx_descriptor / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.5Oct 11, 2017Group: Refinement description / Category: software
Revision 1.6Apr 25, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.7Jun 13, 2018Group: Data collection
Category: diffrn_radiation / diffrn_radiation_wavelength / diffrn_source
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ..._diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_radiation.pdbx_scattering_type / _diffrn_source.pdbx_wavelength_list
Revision 1.8Feb 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
Remark 999SEQUENCE INSERTED LINKER PEPTIDE (LADPE) CONFLICTING RESIDUES 1 AND 82 IN BOTH CHAINS REPRESENT ...SEQUENCE INSERTED LINKER PEPTIDE (LADPE) CONFLICTING RESIDUES 1 AND 82 IN BOTH CHAINS REPRESENT POSSIBLE POLYMORPHISMS

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement component receptor 1-like protein,Ig gamma-1 chain C region secreted form
B: Complement component receptor 1-like protein,Ig gamma-1 chain C region secreted form


Theoretical massNumber of molelcules
Total (without water)123,6382
Polymers123,6382
Non-polymers00
Water00
1


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

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Components

#1: Protein Complement component receptor 1-like protein,Ig gamma-1 chain C region secreted form / Complement regulatory protein Crry / Protein p65 / Coordinate model: Cα atoms only


Mass: 61818.758 Da / Num. of mol.: 2 / Fragment: Q64735 residues 83-401,P01868 residues 98-324
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cr1l, Crry, Cry, Ighg1, Igh-4 / Production host: Mus musculus (house mouse) / Strain (production host): NS/0 plasmacytoma cells / References: UniProt: Q64735, UniProt: P01868

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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
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSRS SRS BEAMLINE11
NUCLEAR REACTORILL D11210
NUCLEAR REACTORISIS INSTRUMENT LOQ32-10
Detector
TypeIDDetectorDate
500 CHANNEL1QUADRANT DETECTORApr 15, 1999
WIRE DETECTOR2BF3 DETECTORMay 15, 1999
WIRE DETECTOR33HE ORDELAJun 15, 1998
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE CRYSTALSINGLE WAVELENGTHMx-ray1
2ROTATING DRUMSINGLE WAVELENGTHMneutron1
3TIME-OF-FLIGHTLAUELneutron1
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: 0.096 / Stereochemistry target values: Engh & Huber
Refinement stepCycle: LAST / Resolution: 30→1300 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1102 0 0 0 1102
Soln scatter modelMethod: CONSTRAINED SCATTERING FITTING OF HOMOLOGY MODELS
Conformer selection criteria: THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG, RSX-1 AND 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, RSX-1 AND 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). TWO MODELS ARE SUBMITTED. PLEASE SEE LEGENDS TO FIGURE 15(B) AND FIGURE 15(C) IN ASLAM ET AL. FOR AN EXPLANATION OF MODELS 1 AND 2 RESPECTIVELY.
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: 2 / Software author list: MSI
Software list: INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI, SCTPL5, GNOM

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