1IGA

MODEL OF HUMAN IGA1 DETERMINED BY SOLUTION SCATTERING CURVE-FITTING AND HOMOLOGY MODELLING


SOLUTION SCATTERING
Solution Scattering Data Acquistion12
Scattering Typex-rayneutron
Radiation/Neutron SourceSRS DARESBURYISIS RUTHERFORD
SynchrotronYY
Beamline Type2.1LOQ
Detector TypeQUADRANT DETECTORHE-3 ORDELA DETECTOR
Detector Manufacturer Details
Temperature (K)
pH
Numer of Time Frames Used11
Protein Concentration Range (mg/mL)
Sample Buffer
Data Reduction SoftwareOTOKOCOLETTE
Guiner Mean Radius Of Gyration (nm)
Sigma Mean Radius Of Gyration
R(XS-1) Mean Cross Sectional Radii (nm)
R(XS-1) Sigma Mean Cross Sectional Radii
R(XS-2) Mean Cross Sectional Radii (nm)
R(XS-2) Sigma Mean Cross Sectional Radii
P(R) Protein Length (nm)
Solution Scattering Data Analysis and Model Fitting
MethodSoftwareSoftware AuthorsStarting ModelConformers, Number CalculatedConformers, Number SubmittedConformers, Selection CriteriaBest Representative ConformerOther Details
SCATTERING FITTING, ENERGY MINIMIZATIONINSIGHT II, DISCOVERY 2.9.7, BIOSYM11THE MODEL OF HUMAN IGA1 WAS BASED ON SEVERAL IMMUNOGLOBULIN CRYSTAL STRUCTURES FROM THE PDB. AN IGA1 MONOMER CONTAINS TWEL ...THE MODEL OF HUMAN IGA1 WAS BASED ON SEVERAL IMMUNOGLOBULIN CRYSTAL STRUCTURES FROM THE PDB. AN IGA1 MONOMER CONTAINS TWELVE DOMAINS ON TWO FOUR-DOMAIN HEAVY CHAINS AND TWO TWO-DOMAIN LIGHT CHAINS. THE CHAINS ASSOCIATE TO FORM TWO FOUR-DOMAIN FAB FRAGMENTS AND ONE FOUR-DOMAIN FC FRAGMENT. EACH FAB FRAGMENT IS JOINED TO THE FC FRAGMENT BY A 23-RESIDUE PEPTIDE LINKER. THERE ARE SIX DOMAIN TYPES IN IGA1 (VH, CH1, CH2, CH3, VL AND CL), AND A MONOMER CONTAINS TWO COPIES OF EACH DOMAIN-TYPE. THE SEQUENCES OF THE CH1, CH2 AND CH3 DOMAINS ARE SPECIFIC TO IGA1. REFINEMENT WAS CARRIED OUT USING DISCOVER 2.9.7, BIOSYM. ALSO USED ENERGY MINIMISATION. THE IGA1 CH1 DOMAIN WAS MODELLED USING THE CORRESPONDING DOMAIN FROM THE THE MOUSE IGA J539 FAB STRUCTURE (CODE: 2FBJ) AND THE HUMAN IGG1 TR1.9 FAB STRUCTURE (CODE: 1VGE) AS TEMPLATES. THE IGA1 CH2 AND CH3 DOMAINS WERE MODELLED USING THE CORRESPONDING DOMAINS FROM THE HUMAN IGG1 FC STRUCTURE (CODE: 1FC1) AS TEMPLATES. THE REMAINING DOMAINS IN THE IGA1 MODEL (VL, CL AND VH) USED THE APPROPRIATE DOMAINS FROM THE TR1.9 FAB STRUCTURE DIRECTLY. EACH FAB FRAGMENT CONTAINS A SINGLE COPY OF THE VH, CH1, VL AND CL DOMAINS, AND THEIR ARRANGEMENT WAS BASED DIRECTLY ON THE TR1.9 FAB STRUCTURE. IN THE FC STRUCTURE, TWO COPIES OF THE CH2 AND CH3 DOMAINS WERE USED. THEIR ARRANGEMENT WAS BASED ON THAT IN THE HUMAN IGG1 FC STRUCTURE (CODE 1FC1) EXCEPT THAT THE TWO CH2 DOMAINS WERE REORIENTATED AND REMODELLED SLIGHTLY TO ACCOMMODATE A PROPOSED DISULPHIDE BRIDGING PATTERN. THE POSITIONS OF THE FAB FRAGMENTS RELATIVE TO THE FC FRAGMENT WERE DETERMINED BY AN APPROACH THAT COMBINED RANDOM HINGE PEPTIDE STRUCTURES PRODUCED BY MOLECULAR DYNAMICS SIMULATIONS WITH CURVE-FITTING TO EXPERIMENTAL SOLUTION SCATTERING DATA. A SINGLE ARRANGEMENT OF THE FAB FRAGMENTS IS PRESENTED, WHICH IS REPRESENTATIVE OF A FAMILY OF STRUCTURES THAT FIT THE SCATTERING DATA. IN ADDITION, IGA1 CONTAINS AN 18-RESIDUE TAILPIECE PEPTIDE AT THE C-TERMINAL OF EACH CH3 DOMAIN. THE TAILPIECE STRUCTURE PRODUCED BY MOLECULAR DYNAMICS SIMULATIONS THAT BEST-FITTED THE EXPERIMENTAL DATA IS SHOWN ON EACH MODEL. MORE DETAILS ON THE MODELLING STRATEGY ARE CONTAINED IN THE PRIMARY REFERENCE.