Model of human carcinoembryonic antigen by homology modelling and curve-fitting to experimental solution scattering data
SOLUTION SCATTERING
Solution Scattering Data Acquistion
1
2
3
Scattering Type
x-ray
neutron
modelling
Radiation/Neutron Source
ESRF BEAMLINE ID02
ISIS RUTHERFORD LOQ
Synchrotron
Y
N
Beamline Type
Detector Type
QUADRANT DETECTOR
HE-3 ORDELA DETECTOR
Detector Manufacturer Details
Temperature (K)
288
288
pH
Numer of Time Frames Used
10
1
Protein Concentration Range (mg/mL)
1.2-7.0
3.6-7.3
Sample Buffer
12 MM NA, K PHOSPHATE, 140 MM NACL
12 MM NA, K PHOSPHATE, 140 MM NACL 99.9% D2O
Data Reduction Software
OTOKO
COLETTE
Guiner Mean Radius Of Gyration (nm)
8
8.8
Sigma Mean Radius Of Gyration
0.6
0.5
R(XS-1) Mean Cross Sectional Radii (nm)
2.1
2.3
R(XS-1) Sigma Mean Cross Sectional Radii
0.2
0.3
R(XS-2) Mean Cross Sectional Radii (nm)
R(XS-2) Sigma Mean Cross Sectional Radii
P(R) Protein Length (nm)
33
29
Solution Scattering Data Analysis and Model Fitting
Method
Software
Software Authors
Starting Model
Conformers, Number Calculated
Conformers, Number Submitted
Conformers, Selection Criteria
Best Representative Conformer
Other Details
CONSTRAINED SCATTERING FITTING OF HOMOLOGY MODELS
INSIGHT II, HOMOLOGY, SCTPL4, GNOM
BIOSYM/MSI
PDB CODE 3CD4, 1CD8
1
HUMAN CARCINOEMBRYONIC ANTIGEN (CEA) CONTAINS SEVEN EXTRACELLULAR IMMUNOGLOBULIN (IG) FOLD DOMAINS. THE N- TERMINAL DOMAIN IS PREDICTED TO HAVE A V-TY ...
HUMAN CARCINOEMBRYONIC ANTIGEN (CEA) CONTAINS SEVEN EXTRACELLULAR IMMUNOGLOBULIN (IG) FOLD DOMAINS. THE N- TERMINAL DOMAIN IS PREDICTED TO HAVE A V-TYPE IG FOLD, AND WAS MODELLED USING THE V-TYPE DOMAIN STRUCTURES FROM HUMAN CD2 (CODE: 1HNF), HUMAN CD4 (CODE: 3CD4) AND HUMAN CD8 (CODE: 1CD8) . THE SECOND, FOURTH AND SIXTH DOMAINS (COMMONLY REFERRED TO AS IA, IIA AND IIIA) ARE PREDICTED TO HAVE I-TYPE IG FOLDS, AND WERE MODELLED USING THE I-TYPE DOMAIN STRUCTURE FROM HUMAN VCAM-1 (CODE: 1VCA). THE THIRD, FIFTH AND SEVENTH DOMAINS (COMMONLY REFERRED TO AS IB, IIB AND IIIB) ARE PREDICTED TO HAVE C2-TYPE IG FOLDS, AND WERE MODELLED USING THE C2-TYPE DOMAIN STRUCTURE FROM HUMAN CD2 (CODE: 1HNF). FURTHER DETAILS OF THE HOMOLOGY MODELLING ARE GIVEN IN THE PRIMARY REFERENCE. IN THE COMPLETE CEA MODEL, ALL INTER-DOMAIN ORIENTATIONS BETWEEN NEIGHBOURING DOMAINS ARE BASED ON THAT BETWEEN THE TWO DOMAINS IN HUMAN CD2. SUCH AN ARRANGEMENT OF THE DOMAINS WAS SHOWN TO BE COMPATIBLE WITH THE SOLUTION STRUCTURE OF CEA BY X- RAY AND NEUTRON SCATTERING (SEE REFERENCE TWO).
