HEADER IMMUNE SYSTEM 06-JUN-00 1F3R TITLE COMPLEX BETWEEN FV ANTIBODY FRAGMENT AND AN ANALOGUE OF THE MAIN TITLE 2 IMMUNOGENIC REGION OF THE ACETYLCHOLINE RECEPTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACETYLCHOLINE RECEPTOR ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MAIN IMMUNOGENIC REGION (91-100); COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: FV ANTIBODY FRAGMENT; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: FRAGMENT OF MAB198 RAISED AGAINST HUMAN ACETYLCHOLINE COMPND 11 RECEPTOR SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SEQUENCE IS DERIVED FROM ACETYLCHOLINE RECEPTOR OF SOURCE 4 TORPEDO ELECTRIC ORGAN; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 7 ORGANISM_COMMON: NORWAY RAT; SOURCE 8 ORGANISM_TAXID: 10116; SOURCE 9 OTHER_DETAILS: MONOCLONAL ANTIBODY(MAB198) RAISED AGAINST HUMAN SOURCE 10 ACETYLCHOLINE RECEPTOR KEYWDS IG-FOLD, IMMUNO COMPLEX, ANTIBODY-ANTIGEN, BETA-TURN, IMMUNE SYSTEM EXPDTA SOLUTION NMR AUTHOR J.KLEINJUNG,M.-C.PETIT,P.ORLEWSKI,A.MAMALAKI,S.-J.TZARTOS,V.TSIKARIS, AUTHOR 2 M.SAKARELLOS-DAITSIOTIS,C.SAKARELLOS,M.MARRAUD,M.-T.CUNG REVDAT 4 03-NOV-21 1F3R 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1F3R 1 VERSN REVDAT 2 01-APR-03 1F3R 1 JRNL REVDAT 1 15-JUN-00 1F3R 0 JRNL AUTH J.KLEINJUNG,M.C.PETIT,P.ORLEWSKI,A.MAMALAKI,S.J.TZARTOS, JRNL AUTH 2 V.TSIKARIS,M.SAKARELLOS-DAITSIOTIS,C.SAKARELLOS,M.MARRAUD, JRNL AUTH 3 M.T.CUNG JRNL TITL THE THIRD-DIMENSIONAL STRUCTURE OF THE COMPLEX BETWEEN AN FV JRNL TITL 2 ANTIBODY FRAGMENT AND AN ANALOGUE OF THE MAIN IMMUNOGENIC JRNL TITL 3 REGION OF THE ACETYLCHOLINE RECEPTOR: A COMBINED JRNL TITL 4 TWO-DIMENSIONAL NMR, HOMOLOGY, AND MOLECULAR MODELING JRNL TITL 5 APPROACH. JRNL REF BIOPOLYMERS V. 53 113 2000 JRNL REFN ISSN 0006-3525 JRNL PMID 10679615 JRNL DOI 10.1002/(SICI)1097-0282(200002)53:2<113::AID-BIP1>3.3.CO;2-A REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : UXNMR 940501.3, DISCOVER3 97 REMARK 3 AUTHORS : BRUKER (UXNMR), MSI (DISCOVER3) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE PEPTIDE STRUCTURE IS BASED ON 73 REMARK 3 NOE-DERIVED DISTANCE RESTRAINTS. REMARK 3 THE ANTIBODY STRUCTURE IS BASED ON TEMPLATE STRUCTURES REMARK 3 POT IGM AND FAB D1.3 ANTILYSOZYME. REMARK 3 THE COMPLEX STRUCTURE HAS BEEN DERIVED REMARK 3 BY COMPUTATIONAL DOCKING. REMARK 4 REMARK 4 1F3R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-00. REMARK 100 THE DEPOSITION ID IS D_1000011206. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 277 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 0.1 M REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.2 MM MAB198, 10 MM MIR PEPTIDE REMARK 210 ANTIGEN, 0.1 M PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY 1.3, DYANA 1.2 REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING DOCKING MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU B 6 CD GLU B 6 OE2 0.107 REMARK 500 GLU B 16 CD GLU B 16 OE2 0.105 REMARK 500 HIS B 39 CG HIS B 39 CD2 0.057 REMARK 500 GLU B 46 CD GLU B 46 OE2 0.106 REMARK 500 GLU B 180 CD GLU B 180 OE2 0.109 REMARK 500 GLU B 219 CD GLU B 219 OE2 0.107 REMARK 500 GLU B 242 CD GLU B 242 OE2 0.109 REMARK 500 GLU B 247 CD GLU B 247 OE2 0.110 REMARK 500 GLU B 253 CD GLU B 253 OE2 0.108 REMARK 500 GLU B 254 CD GLU B 254 OE2 0.107 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TRP A 67 CD1 - NE1 - CE2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG B 13 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 13 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 38 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 HIS B 39 ND1 - CE1 - NE2 ANGL. DEV. = 8.5 DEGREES REMARK 500 ARG B 50 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP B 54 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP B 54 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG B 66 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG B 66 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 71 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ASP B 72 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP B 72 CB - CG - OD2 ANGL. DEV. = -6.7 DEGREES REMARK 500 ASP B 88 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 88 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG B 97 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ASP B 98 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 TYR B 100 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ASP B 139 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP B 139 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP B 155 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP B 155 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ARG B 156 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG B 199 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 199 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP B 208 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP B 208 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ASP B 220 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP B 220 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 69 100.15 -54.07 REMARK 500 SER B 15 -40.32 84.33 REMARK 500 GLU B 16 -136.17 -84.18 REMARK 500 SER B 31 -75.65 -68.15 REMARK 500 PHE B 32 79.76 -103.90 REMARK 500 SER B 41 90.44 -68.89 REMARK 500 LYS B 43 -70.72 -131.69 REMARK 500 LYS B 64 -79.10 -105.38 REMARK 500 SER B 84 67.24 68.26 REMARK 500 ASP B 89 36.20 -83.39 REMARK 500 TYR B 109 -110.70 88.70 REMARK 500 ASP B 111 -76.36 -115.73 REMARK 500 SER B 122 109.04 -166.49 REMARK 500 SER B 138 96.16 -167.16 REMARK 500 THR B 143 98.75 -68.43 REMARK 500 ASN B 168 -81.10 74.30 REMARK 500 ASN B 169 14.23 -146.97 REMARK 500 TYR B 170 79.97 -109.45 REMARK 500 THR B 189 -74.69 65.26 REMARK 500 THR B 194 105.34 -56.00 REMARK 500 ARG B 199 -47.66 -136.61 REMARK 500 SER B 214 -80.89 -75.54 REMARK 500 ASN B 230 -63.09 -148.56 REMARK 500 ASN B 231 -90.92 -86.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR B 59 0.07 SIDE CHAIN REMARK 500 TYR B 100 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1F3R A 67 76 GB 223528 223528 91 100 DBREF 1F3R B 1 123 GB 404506 AAB27717 1 123 DBREF 1F3R B 139 244 GB 404508 AAB27718 1 106 SEQADV 1F3R GLY A 70 GB 223528 ALA 94 ENGINEERED MUTATION SEQADV 1F3R NLE A 76 GB 223528 LYS 100 ENGINEERED MUTATION SEQRES 1 A 10 TRP ASN PRO GLY ASP TYR GLY GLY ILE NLE SEQRES 1 B 257 GLN VAL GLN LEU LEU GLU SER GLY PRO GLY LEU VAL ARG SEQRES 2 B 257 PRO SER GLU THR LEU SER LEU THR CYS THR VAL SER GLY SEQRES 3 B 257 PHE SER LEU THR SER PHE SER VAL SER TRP VAL ARG HIS SEQRES 4 B 257 PRO SER GLY LYS GLY PRO GLU TRP MET GLY ARG MET TRP SEQRES 5 B 257 TYR ASP GLY TYR THR ALA TYR ASN SER ALA LEU LYS SER SEQRES 6 B 257 ARG LEU SER ILE SER ARG ASP THR SER LYS ASN GLN VAL SEQRES 7 B 257 PHE LEU LYS MET ASN SER LEU GLN THR ASP ASP THR GLY SEQRES 8 B 257 THR TYR TYR CYS THR ARG ASP LEU TYR GLY GLY TYR PRO SEQRES 9 B 257 LEU GLY PHE TRP TYR PHE ASP PHE TRP GLY PRO GLY THR SEQRES 10 B 257 MET VAL THR VAL SER SER GLY GLY GLY GLY SER GLY GLY SEQRES 11 B 257 GLY GLY SER GLY GLY GLY GLY SER ASP ILE LYS LEU THR SEQRES 12 B 257 GLN SER PRO SER LEU LEU SER ALA SER VAL GLY ASP ARG SEQRES 13 B 257 VAL THR LEU SER CYS LYS GLY SER GLN ASN ILE ASN ASN SEQRES 14 B 257 TYR LEU ALA TRP TYR GLN GLN LYS LEU GLY GLU ALA PRO SEQRES 15 B 257 LYS LEU LEU ILE TYR ASN THR ASN SER LEU GLN THR GLY SEQRES 16 B 257 ILE PRO SER ARG PHE SER GLY SER GLY SER GLY THR ASP SEQRES 17 B 257 TYR THR LEU THR ILE SER SER LEU GLN PRO GLU ASP VAL SEQRES 18 B 257 ALA THR TYR PHE CYS TYR GLN TYR ASN ASN GLY TYR THR SEQRES 19 B 257 PHE GLY ALA GLY THR LYS LEU GLU LEU LYS ALA ALA GLU SEQRES 20 B 257 GLN LYS LEU ILE SER GLU GLU ASP LEU ASN MODRES 1F3R NLE A 76 LEU NORLEUCINE HET NLE A 76 20 HETNAM NLE NORLEUCINE FORMUL 1 NLE C6 H13 N O2 HELIX 1 1 GLN B 217 VAL B 221 5 5 SHEET 1 A 4 GLN B 3 SER B 7 0 SHEET 2 A 4 THR B 17 SER B 25 -1 O THR B 21 N SER B 7 SHEET 3 A 4 GLN B 77 ASN B 83 -1 O VAL B 78 N CYS B 22 SHEET 4 A 4 LEU B 67 ASP B 72 -1 O SER B 68 N LYS B 81 SHEET 1 B 5 THR B 57 TYR B 59 0 SHEET 2 B 5 GLU B 46 MET B 51 -1 N ARG B 50 O ALA B 58 SHEET 3 B 5 SER B 35 PRO B 40 -1 N TRP B 36 O GLY B 49 SHEET 4 B 5 GLY B 91 ASP B 98 -1 N THR B 92 O HIS B 39 SHEET 5 B 5 PHE B 110 TRP B 113 -1 N ASP B 111 O ARG B 97 SHEET 1 C 6 THR B 57 TYR B 59 0 SHEET 2 C 6 GLU B 46 MET B 51 -1 N ARG B 50 O ALA B 58 SHEET 3 C 6 SER B 35 PRO B 40 -1 N TRP B 36 O GLY B 49 SHEET 4 C 6 GLY B 91 ASP B 98 -1 N THR B 92 O HIS B 39 SHEET 5 C 6 THR B 117 VAL B 121 -1 N THR B 117 O TYR B 93 SHEET 6 C 6 LEU B 11 VAL B 12 1 N VAL B 12 O THR B 120 SHEET 1 D 2 ASP B 139 ILE B 140 0 SHEET 2 D 2 GLU B 254 ASP B 255 1 N ASP B 255 O ASP B 139 SHEET 1 E 4 GLN B 144 SER B 145 0 SHEET 2 E 4 VAL B 157 LYS B 162 -1 N SER B 160 O SER B 145 SHEET 3 E 4 ASP B 208 ILE B 213 -1 O TYR B 209 N CYS B 161 SHEET 4 E 4 PHE B 200 SER B 205 -1 O SER B 201 N THR B 212 SHEET 1 F 2 LEU B 148 LEU B 149 0 SHEET 2 F 2 LYS B 240 LEU B 241 1 O LYS B 240 N LEU B 149 SHEET 1 G 5 SER B 191 LEU B 192 0 SHEET 2 G 5 LYS B 183 TYR B 187 -1 N TYR B 187 O SER B 191 SHEET 3 G 5 LEU B 171 GLN B 176 -1 O TRP B 173 N LEU B 185 SHEET 4 G 5 THR B 223 TYR B 229 -1 O THR B 223 N GLN B 176 SHEET 5 G 5 TYR B 233 PHE B 235 -1 O THR B 234 N GLN B 228 SSBOND 1 CYS B 22 CYS B 95 1555 1555 2.95 LINK C ILE A 75 N NLE A 76 1555 1555 1.35 CISPEP 1 SER B 145 PRO B 146 0 -0.89 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