HEADER IMMUNE SYSTEM 30-JAN-03 1NTJ TITLE MODEL OF RAT CRRY DETERMINED BY SOLUTION SCATTERING, CURVE FITTING AND TITLE 2 HOMOLOGY MODELLING COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPLEMENT RECEPTOR RELATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SCR-1 TO SCR-5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS IMMUNOLOGY, COMPLEMENT, GLYCOPROTEIN, SCR, CCP, IMMUNE SYSTEM EXPDTA SOLUTION SCATTERING MDLTYP CA ATOMS ONLY, CHAIN A AUTHOR M.ASLAM,J.M.GUTHRIDGE,B.K.HACK,R.J.QUIGG,V.M.HOLERS,S.J.PERKINS REVDAT 7 14-FEB-24 1NTJ 1 REMARK REVDAT 6 17-JUL-19 1NTJ 1 REMARK REVDAT 5 13-JUN-18 1NTJ 1 REMARK REVDAT 4 11-OCT-17 1NTJ 1 REMARK REVDAT 3 07-APR-10 1NTJ 1 REMARK REVDAT 2 06-JAN-09 1NTJ 1 REMARK VERSN REVDAT 1 03-FEB-04 1NTJ 0 JRNL AUTH M.ASLAM,J.M.GUTHRIDGE,B.K.HACK,R.J.QUIGG,V.M.HOLERS, JRNL AUTH 2 S.J.PERKINS JRNL TITL THE EXTENDED MULTIDOMAIN SOLUTION STRUCTURES OF THE JRNL TITL 2 COMPLEMENT PROTEIN CRRY AND ITS CHIMERIC CONJUGATE CRRY-IG JRNL TITL 3 BY SCATTERING, ANALYTICAL ULTRACENTRIFUGATION AND JRNL TITL 4 CONSTRAINED MODELLING: IMPLICATIONS FOR FUNCTION AND THERAPY JRNL REF J.MOL.BIOL. V. 329 525 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12767833 JRNL DOI 10.1016/S0022-2836(03)00492-3 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : INSIGHT II 98.0 REMARK 3 AUTHORS : MSI REMARK 4 REMARK 4 1NTJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018189. REMARK 265 REMARK 265 EXPERIMENTAL DETAILS REMARK 265 REMARK 265 EXPERIMENT TYPE : SMALL ANGLE X-RAY SCATTERING REMARK 265 DATA ACQUISITION REMARK 265 RADIATION/NEUTRON SOURCE : SRS BEAMLINE 2.1 REMARK 265 SYNCHROTRON (Y/N) : Y REMARK 265 BEAMLINE TYPE : 2.1 REMARK 265 BEAMLINE INSTRUMENT : NULL REMARK 265 DETECTOR TYPE : 500-CHANNEL QUADRANT REMARK 265 DETECTOR MANUFACTURER DETAILS : NULL REMARK 265 TEMPERATURE (KELVIN) : 288 REMARK 265 PH : 7.5 REMARK 265 NUMBER OF TIME FRAMES USED : 10 REMARK 265 PROTEIN CONCENTRATION RANGE (MG/ML) : 2-15 REMARK 265 SAMPLE BUFFER : TRIS REMARK 265 DATA REDUCTION SOFTWARE : OTOKO REMARK 265 GUINIER MEAN RADIUS OF GYRATION (NM) : 5.0 REMARK 265 SIGMA MEAN RADIUS OF GYRATION : 0.4 REMARK 265 R(XS-1) MEAN CROSS SECTIONAL RADII (NM) : 1.5 REMARK 265 R(XS-1) SIGMA MEAN CROSS SECTIONAL RADII : 0.1 REMARK 265 R(XS-2) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-2) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 P(R) PROTEIN LENGTH (NM) : 1 REMARK 265 REMARK 265 EXPERIMENT TYPE : SMALL ANGLE NEUTRON SCATTERING REMARK 265 DATA ACQUISITION REMARK 265 RADIATION/NEUTRON SOURCE : ILL REMARK 265 SYNCHROTRON (Y/N) : N REMARK 265 BEAMLINE TYPE : NULL REMARK 265 BEAMLINE INSTRUMENT : D11 REMARK 265 DETECTOR TYPE : AREA REMARK 265 DETECTOR MANUFACTURER DETAILS : NULL REMARK 265 TEMPERATURE (KELVIN) : 288 REMARK 265 PH : 7.5 REMARK 265 NUMBER OF TIME FRAMES USED : NULL REMARK 265 PROTEIN CONCENTRATION RANGE (MG/ML) : 8.2 REMARK 265 SAMPLE BUFFER : PBS IN 99.9% D2O REMARK 265 DATA REDUCTION SOFTWARE : DETEC, RNILS, SPOLLY REMARK 265 GUINIER MEAN RADIUS OF GYRATION (NM) : 4.9 REMARK 265 SIGMA MEAN RADIUS OF GYRATION : 0.2 REMARK 265 R(XS-1) MEAN CROSS SECTIONAL RADII (NM) : 1.2 REMARK 265 R(XS-1) SIGMA MEAN CROSS SECTIONAL RADII : 0.2 REMARK 265 R(XS-2) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-2) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 P(R) PROTEIN LENGTH (NM) : NULL REMARK 265 REMARK 265 EXPERIMENT TYPE : SMALL ANGLE NEUTRON SCATTERING REMARK 265 DATA ACQUISITION REMARK 265 RADIATION/NEUTRON SOURCE : ISIS REMARK 265 SYNCHROTRON (Y/N) : N REMARK 265 BEAMLINE TYPE : PULSED NEUTRON REMARK 265 BEAMLINE INSTRUMENT : LOQ REMARK 265 DETECTOR TYPE : AREA (TIME-OF-FLIGHT) REMARK 265 DETECTOR MANUFACTURER DETAILS : NULL REMARK 265 TEMPERATURE (KELVIN) : 288 REMARK 265 PH : 7.5 REMARK 265 NUMBER OF TIME FRAMES USED : NULL REMARK 265 PROTEIN CONCENTRATION RANGE (MG/ML) : 4.5-6.8 REMARK 265 SAMPLE BUFFER : PBS IN 99.9% D2O REMARK 265 DATA REDUCTION SOFTWARE : COLLETTE REMARK 265 GUINIER MEAN RADIUS OF GYRATION (NM) : 4.9 REMARK 265 SIGMA MEAN RADIUS OF GYRATION : 0.2 REMARK 265 R(XS-1) MEAN CROSS SECTIONAL RADII (NM) : 1.2 REMARK 265 R(XS-1) SIGMA MEAN CROSS SECTIONAL RADII : 0.2 REMARK 265 R(XS-2) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-2) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 P(R) PROTEIN LENGTH (NM) : 1 REMARK 265 REMARK 265 DATA ANALYSIS AND MODEL FITTING: REMARK 265 METHOD USED TO DETERMINE THE STRUCTURE: CONSTRAINED SCATTERING REMARK 265 FITTING OF HOMOLOGY MODELS REMARK 265 SOFTWARE USED : INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, REMARK 265 DELPHI REMARK 265 SOFTWARE AUTHORS : MSI REMARK 265 STARTING MODEL : NULL REMARK 265 REMARK 265 CONFORMERS, NUMBER CALCULATED : 2000 REMARK 265 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 265 CONFORMERS, SELECTION CRITERIA : THE MODELLED SCATTERING CURVES REMARK 265 WERE ASSESSED BY CALCULATION OF THE RG AND RSX-1 VALUES IN THE REMARK 265 SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE REMARK 265 THEN RANKED USING A GOODNESS-OF-FIT R-FACTOR DEFINED BY ANALOGY REMARK 265 WITH PROTEIN CRYSTALLOGRAPHY AND BASED ON THE EXPERIMENTAL REMARK 265 CURVES IN THE Q RANGE EXTENDING TO 2.2 NM-1 (X-RAYS) AND 1.12 NM- REMARK 265 1 (ILL NEUTRONS). REMARK 265 REMARK 265 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 265 REMARK 265 OTHER DETAILS: HOMOLOGY MODELS WERE BUILT FOR THE 5 SCR DOMAINS REMARK 265 AND ENERGY MINIMISATIONS WERE PERFORMED TO IMPROVE THE REMARK 265 CONNECTIVITY IN THE FH MODEL. BIANTENNARY COMPLEX-TYPE REMARK 265 CARBOHYDRATE STRUCTURES (MAN3GLCNAC4GAL2FUC0NEUNAC2) WERE ADDED REMARK 265 TO EACH OF THE N-LINKED GLYCOSYLATION SITES. A LIBRARY OF LINKER REMARK 265 PEPTIDE CONFORMATIONS WAS USED IN DOMAIN MODELLING CONSTRAINED REMARK 265 BY THE SOLUTION SCATTERING FITS. MODELLING WITH THE SCATTERING REMARK 265 DATA WAS ALSO CARRIED OUT BY ROTATIONAL SEARCH METHODS. THE X- REMARK 265 RAY AND NEUTRON SCATTERING CURVE I(Q) WAS CALCULATED ASSUMING A REMARK 265 UNIFORM SCATTERING DENSITY FOR THE SPHERES USING THE DEBYE REMARK 265 EQUATION AS ADAPTED TO SPHERES. X-RAY CURVES WERE CALCULATED REMARK 265 FROM THE HYDRATED SPHERE MODELS WITHOUT CORRECTIONS FOR REMARK 265 WAVELENGTH SPREAD OR BEAM DIVERGENCE, WHILE THESE CORRECTIONS REMARK 265 WERE APPLIED FOR THE NEUTRON CURVES BUT NOW USING UNHYDRATED REMARK 265 MODELS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QUB RELATED DB: PDB REMARK 900 B2 GLYCOPROTEIN I WAS USED AS A TEMPLATE FOR THREE SCR DOMAINS REMARK 900 RELATED ID: 1GKG RELATED DB: PDB REMARK 900 COMPLEMENT RECEPTOR TYPE 1 SCR-17 WAS USED AS A TEMPLATE FOR ONE REMARK 900 SCR DOMAIN REMARK 900 RELATED ID: 1VVC RELATED DB: PDB REMARK 900 VACCINIA COAT PROTEIN SCR-4 WAS USED AS A TEMPLATE FOR ONE SCR REMARK 900 DOMAIN DBREF 1NTJ A 1 320 GB 9506513 NP_062174 34 353 SEQRES 1 A 320 THR LEU GLY GLN CYS PRO ALA PRO PRO LEU PHE PRO TYR SEQRES 2 A 320 ALA LYS PRO ILE ASN PRO THR ASP GLU SER THR PHE PRO SEQRES 3 A 320 VAL GLY THR SER LEU LYS TYR GLU CYS ARG PRO GLY TYR SEQRES 4 A 320 ILE LYS ARG GLN PHE SER ILE THR CYS GLU VAL ASN SER SEQRES 5 A 320 VAL TRP THR SER PRO GLN ASP VAL CYS ILE ARG LYS GLN SEQRES 6 A 320 CYS GLU THR PRO LEU ASP PRO GLN ASN GLY ILE VAL HIS SEQRES 7 A 320 VAL ASN THR ASP ILE ARG PHE GLY SER SER ILE THR TYR SEQRES 8 A 320 THR CYS ASN GLU GLY TYR ARG LEU ILE GLY SER SER SER SEQRES 9 A 320 ALA MET CYS ILE ILE SER ASP GLN SER VAL ALA TRP ASP SEQRES 10 A 320 ALA GLU ALA PRO ILE CYS GLU SER ILE PRO CYS GLU ILE SEQRES 11 A 320 PRO PRO SER ILE PRO ASN GLY ASP PHE PHE SER PRO ASN SEQRES 12 A 320 ARG GLU ASP PHE HIS TYR GLY MET VAL VAL THR TYR GLN SEQRES 13 A 320 CYS ASN THR ASP ALA ARG GLY LYS LYS LEU PHE ASN LEU SEQRES 14 A 320 VAL GLY GLU PRO SER ILE HIS CYS THR SER ILE ASP GLY SEQRES 15 A 320 GLN VAL GLY VAL TRP SER GLY PRO PRO PRO GLN CYS ILE SEQRES 16 A 320 GLU LEU ASN LYS CYS THR PRO PRO HIS VAL GLU ASN ALA SEQRES 17 A 320 VAL ILE VAL SER LYS ASN LYS SER LEU PHE SER LEU ARG SEQRES 18 A 320 ASP MET VAL GLU PHE ARG CYS GLN ASP GLY PHE MET MET SEQRES 19 A 320 LYS GLY ASP SER SER VAL TYR CYS ARG SER LEU ASN ARG SEQRES 20 A 320 TRP GLU PRO GLN LEU PRO SER CYS PHE LYS VAL LYS SER SEQRES 21 A 320 CYS GLY ALA PHE LEU GLY GLU LEU PRO ASN GLY HIS VAL SEQRES 22 A 320 PHE VAL PRO GLN ASN LEU GLN LEU GLY ALA LYS VAL THR SEQRES 23 A 320 PHE VAL CYS ASN THR GLY TYR GLN LEU LYS GLY ASN SER SEQRES 24 A 320 SER SER HIS CYS VAL LEU ASP GLY VAL GLU SER ILE TRP SEQRES 25 A 320 ASN SER SER VAL PRO VAL CYS GLU CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000