HEADER GLYCOPROTEIN 11-MAR-00 1E07 TITLE MODEL OF HUMAN CARCINOEMBRYONIC ANTIGEN BY HOMOLOGY MODELLING AND TITLE 2 CURVE-FITTING TO EXPERIMENTAL SOLUTION SCATTERING DATA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARCINOEMBRYONIC ANTIGEN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS GLYCOPROTEIN, CEA, TUMOUR MARKER, IMMUNOGLOBULIN-FOLD EXPDTA SOLUTION SCATTERING MDLTYP CA ATOMS ONLY, CHAIN A AUTHOR M.K.BOEHM,S.J.PERKINS REVDAT 8 09-OCT-19 1E07 1 JRNL REVDAT 7 28-DEC-11 1E07 1 REMARK VERSN REVDAT 6 07-APR-10 1E07 1 VERSN REVDAT 5 24-MAR-09 1E07 1 REMARK MASTER REVDAT 4 24-FEB-09 1E07 1 VERSN REVDAT 3 17-JAN-06 1E07 1 TITLE REVDAT 2 17-OCT-05 1E07 1 EXPDTA REMARK REVDAT 1 04-JUL-00 1E07 0 JRNL AUTH M.K.BOEHM,S.J.PERKINS JRNL TITL STRUCTURAL MODELS FOR CARCINOEMBRYONIC ANTIGEN AND ITS JRNL TITL 2 COMPLEX WITH THE SINGLE-CHAIN FV ANTIBODY MOLECULE MFE23. JRNL REF FEBS LETT. V. 475 11 2000 JRNL REFN ISSN 0014-5793 JRNL PMID 10854848 JRNL DOI 10.1016/S0014-5793(00)01612-4 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.K.BOEHM,A.L.CORPER,T.WAN,M.K.SOHI,B.J.SUTTON,J.D.THORNTON, REMARK 1 AUTH 2 P.A.KEEP,K.A.CHESTER,R.H.BEGENT,S.J.PERKINS REMARK 1 TITL CRYSTAL STRUCTURE OF THE ANTI-(CARCINOEMBRYONIC ANTIGEN) REMARK 1 TITL 2 SINGLE-CHAIN FV ANTIBODY MFE-23 AND A MODEL FOR ANTIGEN REMARK 1 TITL 3 BINDING BASED ON INTERMOLECULAR CONTACTS. REMARK 1 REF BIOCHEM.J. V. 346 519 2000 REMARK 1 REFN ISSN 0264-6021 REMARK 1 PMID 10677374 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.K.BOEHM,M.O.MAYANS,J.D.THORNTON,R.H.BEGENT,P.A.KEEP, REMARK 1 AUTH 2 S.J.PERKINS REMARK 1 TITL EXTENDED GLYCOPROTEIN STRUCTURE OF THE SEVEN DOMAINS IN REMARK 1 TITL 2 HUMAN CARCINOEMBRYONIC ANTIGEN BY X-RAY AND NEUTRON SOLUTION REMARK 1 TITL 3 SCATTERING AND AN AUTOMATED CURVE FITTING PROCEDURE: REMARK 1 TITL 4 IMPLICATIONS FOR CELLULAR ADHESION. REMARK 1 REF J.MOL.BIOL. V. 259 718 1996 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 8683578 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVERY REMARK 3 AUTHORS : REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 642 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ENERGY MINIMIZATION. DETAILS ARE GIVEN REMARK 3 IN THE PRIMARY REFERENCE. REMARK 4 REMARK 4 1E07 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-MAR-00. REMARK 100 THE DEPOSITION ID IS D_1290001611. 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 : ESRF BEAMLINE ID02 REMARK 265 SYNCHROTRON (Y/N) : Y REMARK 265 BEAMLINE TYPE : NULL REMARK 265 BEAMLINE INSTRUMENT : NULL REMARK 265 DETECTOR TYPE : QUADRANT DETECTOR REMARK 265 DETECTOR MANUFACTURER DETAILS : NULL REMARK 265 TEMPERATURE (KELVIN) : 288 REMARK 265 PH : NULL REMARK 265 NUMBER OF TIME FRAMES USED : 10 REMARK 265 PROTEIN CONCENTRATION RANGE (MG/ML) : 1.2-7.0 REMARK 265 SAMPLE BUFFER : 12 MM NA, K REMARK 265 PHOSPHATE, 140 MM NACL REMARK 265 DATA REDUCTION SOFTWARE : OTOKO REMARK 265 GUINIER MEAN RADIUS OF GYRATION (NM) : 8.0 REMARK 265 SIGMA MEAN RADIUS OF GYRATION : 0.6 REMARK 265 R(XS-1) MEAN CROSS SECTIONAL RADII (NM) : 2.1 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) : 33 REMARK 265 REMARK 265 EXPERIMENT TYPE : SMALL ANGLE NEUTRON SCATTERING REMARK 265 DATA ACQUISITION REMARK 265 RADIATION/NEUTRON SOURCE : ISIS RUTHERFORD LOQ REMARK 265 SYNCHROTRON (Y/N) : N REMARK 265 BEAMLINE TYPE : NULL REMARK 265 BEAMLINE INSTRUMENT : NULL REMARK 265 DETECTOR TYPE : HE-3 ORDELA DETECTOR REMARK 265 DETECTOR MANUFACTURER DETAILS : NULL REMARK 265 TEMPERATURE (KELVIN) : 288 REMARK 265 PH : NULL REMARK 265 NUMBER OF TIME FRAMES USED : 1 REMARK 265 PROTEIN CONCENTRATION RANGE (MG/ML) : 3.6-7.3 REMARK 265 SAMPLE BUFFER : 12 MM NA, K REMARK 265 PHOSPHATE, 140 MM REMARK 265 NACL 99.9% D2O REMARK 265 DATA REDUCTION SOFTWARE : COLETTE REMARK 265 GUINIER MEAN RADIUS OF GYRATION (NM) : 8.8 REMARK 265 SIGMA MEAN RADIUS OF GYRATION : 0.5 REMARK 265 R(XS-1) MEAN CROSS SECTIONAL RADII (NM) : 2.3 REMARK 265 R(XS-1) SIGMA MEAN CROSS SECTIONAL RADII : 0.3 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) : 29 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, SCTPL4, GNOM REMARK 265 SOFTWARE AUTHORS : BIOSYM/MSI REMARK 265 STARTING MODEL : PDB CODE 3CD4, 1CD8 REMARK 265 REMARK 265 CONFORMERS, NUMBER CALCULATED : NULL REMARK 265 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 265 CONFORMERS, SELECTION CRITERIA : NULL REMARK 265 REMARK 265 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 265 REMARK 265 OTHER DETAILS: HUMAN CARCINOEMBRYONIC ANTIGEN (CEA) CONTAINS REMARK 265 SEVEN EXTRACELLULAR IMMUNOGLOBULIN (IG) FOLD DOMAINS. THE N- REMARK 265 TERMINAL DOMAIN IS PREDICTED TO HAVE A V-TYPE IG FOLD, AND WAS REMARK 265 MODELLED USING THE V-TYPE DOMAIN STRUCTURES FROM HUMAN CD2 (CODE: REMARK 265 1HNF), HUMAN CD4 (CODE: 3CD4) AND HUMAN CD8 (CODE: 1CD8) . THE REMARK 265 SECOND, FOURTH AND SIXTH DOMAINS (COMMONLY REFERRED TO AS IA, REMARK 265 IIA AND IIIA) ARE PREDICTED TO HAVE I-TYPE IG FOLDS, AND WERE REMARK 265 MODELLED USING THE I-TYPE DOMAIN STRUCTURE FROM HUMAN VCAM-1 REMARK 265 (CODE: 1VCA). THE THIRD, FIFTH AND SEVENTH DOMAINS (COMMONLY REMARK 265 REFERRED TO AS IB, IIB AND IIIB) ARE PREDICTED TO HAVE C2-TYPE REMARK 265 IG FOLDS, AND WERE MODELLED USING THE C2-TYPE DOMAIN STRUCTURE REMARK 265 FROM HUMAN CD2 (CODE: 1HNF). FURTHER DETAILS OF THE HOMOLOGY REMARK 265 MODELLING ARE GIVEN IN THE PRIMARY REFERENCE. IN THE COMPLETE REMARK 265 CEA MODEL, ALL INTER-DOMAIN ORIENTATIONS BETWEEN NEIGHBOURING REMARK 265 DOMAINS ARE BASED ON THAT BETWEEN THE TWO DOMAINS IN HUMAN CD2. REMARK 265 SUCH AN ARRANGEMENT OF THE DOMAINS WAS SHOWN TO BE COMPATIBLE REMARK 265 WITH THE SOLUTION STRUCTURE OF CEA BY X- RAY AND NEUTRON REMARK 265 SCATTERING (SEE REFERENCE TWO). 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 CA TYR A 285 CA SER A 366 1.94 REMARK 500 CA SER A 463 CA SER A 544 2.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CARCINOEMBRYONIC ANTIGEN PRECURSOR CONTAINS A REMARK 999 34-RESIDUE N-TERMINAL SIGNAL PEPTIDE AND A 26-RESIDUE REMARK 999 C-TERMINAL HYDROPHOBIC PEPTIDE, BOTH OF WHICH ARE REMARK 999 POST-TRANSLATIONALLY CLEAVED. DBREF 1E07 A 1 642 UNP P06731 CCEM_HUMAN 35 676 SEQRES 1 A 642 LYS LEU THR ILE GLU SER THR PRO PHE ASN VAL ALA GLU SEQRES 2 A 642 GLY LYS GLU VAL LEU LEU LEU VAL HIS ASN LEU PRO GLN SEQRES 3 A 642 HIS LEU PHE GLY TYR SER TRP TYR LYS GLY GLU ARG VAL SEQRES 4 A 642 ASP GLY ASN ARG GLN ILE ILE GLY TYR VAL ILE GLY THR SEQRES 5 A 642 GLN GLN ALA THR PRO GLY PRO ALA TYR SER GLY ARG GLU SEQRES 6 A 642 ILE ILE TYR PRO ASN ALA SER LEU LEU ILE GLN ASN ILE SEQRES 7 A 642 ILE GLN ASN ASP THR GLY PHE TYR THR LEU HIS VAL ILE SEQRES 8 A 642 LYS SER ASP LEU VAL ASN GLU GLU ALA THR GLY GLN PHE SEQRES 9 A 642 ARG VAL TYR PRO GLU LEU PRO LYS PRO SER ILE SER SER SEQRES 10 A 642 ASN ASN SER LYS PRO VAL GLU ASP LYS ASP ALA VAL ALA SEQRES 11 A 642 PHE THR CYS GLU PRO GLU THR GLN ASP ALA THR TYR LEU SEQRES 12 A 642 TRP TRP VAL ASN ASN GLN SER LEU PRO VAL SER PRO ARG SEQRES 13 A 642 LEU GLN LEU SER ASN GLY ASN ARG THR LEU THR LEU PHE SEQRES 14 A 642 ASN VAL THR ARG ASN ASP THR ALA SER TYR LYS CYS GLU SEQRES 15 A 642 THR GLN ASN PRO VAL SER ALA ARG ARG SER ASP SER VAL SEQRES 16 A 642 ILE LEU ASN VAL LEU TYR GLY PRO ASP ALA PRO THR ILE SEQRES 17 A 642 SER PRO LEU ASN THR SER TYR ARG SER GLY GLU ASN LEU SEQRES 18 A 642 ASN LEU SER CYS HIS ALA ALA SER ASN PRO PRO ALA GLN SEQRES 19 A 642 TYR SER TRP PHE VAL ASN GLY THR PHE GLN GLN SER THR SEQRES 20 A 642 GLN GLU LEU PHE ILE PRO ASN ILE THR VAL ASN ASN SER SEQRES 21 A 642 GLY SER TYR THR CYS GLN ALA HIS ASN SER ASP THR GLY SEQRES 22 A 642 LEU ASN ARG THR THR VAL THR THR ILE THR VAL TYR ALA SEQRES 23 A 642 GLU PRO PRO LYS PRO PHE ILE THR SER ASN ASN SER ASN SEQRES 24 A 642 PRO VAL GLU ASP GLU ASP ALA VAL ALA LEU THR CYS GLU SEQRES 25 A 642 PRO GLU ILE GLN ASN THR THR TYR LEU TRP TRP VAL ASN SEQRES 26 A 642 ASN GLN SER LEU PRO VAL SER PRO ARG LEU GLN LEU SER SEQRES 27 A 642 ASN ASP ASN ARG THR LEU THR LEU LEU SER VAL THR ARG SEQRES 28 A 642 ASN ASP VAL GLY PRO TYR GLU CYS GLY ILE GLN ASN GLU SEQRES 29 A 642 LEU SER VAL ASP HIS SER ASP PRO VAL ILE LEU ASN VAL SEQRES 30 A 642 LEU TYR GLY PRO ASP ASP PRO THR ILE SER PRO SER TYR SEQRES 31 A 642 THR TYR TYR ARG PRO GLY VAL ASN LEU SER LEU SER CYS SEQRES 32 A 642 HIS ALA ALA SER ASN PRO PRO ALA GLN TYR SER TRP LEU SEQRES 33 A 642 ILE ASP GLY ASN ILE GLN GLN HIS THR GLN GLU LEU PHE SEQRES 34 A 642 ILE SER ASN ILE THR GLU LYS ASN SER GLY LEU TYR THR SEQRES 35 A 642 CYS GLN ALA ASN ASN SER ALA SER GLY HIS SER ARG THR SEQRES 36 A 642 THR VAL LYS THR ILE THR VAL SER ALA GLU LEU PRO LYS SEQRES 37 A 642 PRO SER ILE SER SER ASN ASN SER LYS PRO VAL GLU ASP SEQRES 38 A 642 LYS ASP ALA VAL ALA PHE THR CYS GLU PRO GLU ALA GLN SEQRES 39 A 642 ASN THR THR TYR LEU TRP TRP VAL ASN GLY GLN SER LEU SEQRES 40 A 642 PRO VAL SER PRO ARG LEU GLN LEU SER ASN GLY ASN ARG SEQRES 41 A 642 THR LEU THR LEU PHE ASN VAL THR ARG ASN ASP ALA ARG SEQRES 42 A 642 ALA TYR VAL CYS GLY ILE GLN ASN SER VAL SER ALA ASN SEQRES 43 A 642 ARG SER ASP PRO VAL THR LEU ASP VAL LEU TYR GLY PRO SEQRES 44 A 642 ASP THR PRO ILE ILE SER PRO PRO ASP SER SER TYR LEU SEQRES 45 A 642 SER GLY ALA ASN LEU ASN LEU SER CYS HIS SER ALA SER SEQRES 46 A 642 ASN PRO SER PRO GLN TYR SER TRP ARG ILE ASN GLY ILE SEQRES 47 A 642 PRO GLN GLN HIS THR GLN VAL LEU PHE ILE ALA LYS ILE SEQRES 48 A 642 THR PRO ASN ASN ASN GLY THR TYR ALA CYS PHE VAL SER SEQRES 49 A 642 ASN LEU ALA THR GLY ARG ASN ASN SER ILE VAL LYS SER SEQRES 50 A 642 ILE THR VAL SER ALA 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