HEADER CELL ADHESION 13-OCT-09 2WV3 TITLE NEUROPLASTIN-55 BINDS TO AND SIGNALS THROUGH THE FIBROBLAST GROWTH TITLE 2 FACTOR RECEPTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPLASTIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: IG2 AND IG3 OF NEUROPLASTIN-65, RESIDUES 29-217; COMPND 5 SYNONYM: STROMAL CELL-DERIVED RECEPTOR 1, GLYCOPROTEIN 55/65, SDR-1, COMPND 6 GP55/65, NEUROPLASTIN-55; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 644223; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: GS115; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HIS 4; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPIC9K KEYWDS IGCAM, MEMBRANE, GLYCOPROTEIN, CELL MEMBRANE, CELL ADHESION, KEYWDS 2 TRANSMEMBRANE, DISULFIDE BOND, ALTERNATIVE SPLICING, IMMUNOGLOBULIN KEYWDS 3 DOMAIN EXPDTA X-RAY DIFFRACTION AUTHOR V.SOROKA,S.OWCZAREK,J.S.KASTRUP,V.BEREZIN,E.BOCK,M.GAJHEDE REVDAT 4 29-JUL-20 2WV3 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 24-JUL-19 2WV3 1 REMARK LINK REVDAT 2 14-APR-10 2WV3 1 JRNL REMARK REVDAT 1 15-DEC-09 2WV3 0 JRNL AUTH S.OWCZAREK,D.KIRYUSHKO,M.H.LARSEN,J.S.KASTRUP,M.GAJHEDE, JRNL AUTH 2 C.SANDI,V.BEREZIN,E.BOCK,V.SOROKA JRNL TITL NEUROPLASTIN-55 BINDS TO AND SIGNALS THROUGH THE FIBROBLAST JRNL TITL 2 GROWTH FACTOR RECEPTOR JRNL REF FASEB J. V. 24 1139 2010 JRNL REFN ISSN 0892-6638 JRNL PMID 19952283 JRNL DOI 10.1096/FJ.09-140509 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.450 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 20427 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1044 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.6064 - 3.7289 0.98 2864 157 0.1861 0.1999 REMARK 3 2 3.7289 - 2.9603 1.00 2803 148 0.1871 0.2507 REMARK 3 3 2.9603 - 2.5863 1.00 2772 150 0.2262 0.2804 REMARK 3 4 2.5863 - 2.3499 1.00 2751 158 0.2317 0.3196 REMARK 3 5 2.3499 - 2.1815 1.00 2743 142 0.2280 0.2775 REMARK 3 6 2.1815 - 2.0529 0.99 2721 147 0.2352 0.2652 REMARK 3 7 2.0529 - 1.9501 0.99 2729 142 0.2622 0.3252 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 71.63 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 13.63880 REMARK 3 B22 (A**2) : 2.04330 REMARK 3 B33 (A**2) : -15.68220 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1596 REMARK 3 ANGLE : 1.057 2166 REMARK 3 CHIRALITY : 0.071 234 REMARK 3 PLANARITY : 0.004 277 REMARK 3 DIHEDRAL : 16.640 621 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2WV3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1290041394. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 288 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X12 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20597 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 33.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.450 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL2MAP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NEUROPLASTIN-55 AT A CONCENTRATION OF REMARK 280 4 MG/ML IN 5 MM SODIUM PHOSPHATE AND 150 MM NACL, PH 7.4, WAS REMARK 280 MIXED WITH THE RESERVOIR SOLUTION CONTAINING 13-15% W/V PEG 4000, REMARK 280 0.2 M AMMONIUM SULFATE, AND 0.1 M SODIUM ACETATE, PH 4.6. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 24.69500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.54000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.77000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.69500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.54000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 68.77000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.69500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.54000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 68.77000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.69500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 40.54000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 68.77000 REMARK 290 REMARK 290 REMARK: NULL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2020 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLN A 1 REMARK 465 ASN A 2 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 ND2 ASN A 26 O5 NAG A 1201 2.13 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 ASN A 52 71.32 -100.56 REMARK 500 REMARK 500 REMARK: NULL DBREF 2WV3 A 1 189 UNP P97546 NPTN_RAT 29 217 DBREF 2WV3 A 190 190 PDB 2WV3 2WV3 190 190 SEQRES 1 A 190 GLN ASN GLU PRO ARG ILE VAL THR SER GLU GLU VAL ILE SEQRES 2 A 190 ILE ARG ASP SER LEU LEU PRO VAL THR LEU GLN CYS ASN SEQRES 3 A 190 LEU THR SER SER SER HIS THR LEU MET TYR SER TYR TRP SEQRES 4 A 190 THR LYS ASN GLY VAL GLU LEU THR ALA THR ARG LYS ASN SEQRES 5 A 190 ALA SER ASN MET GLU TYR ARG ILE ASN LYS PRO ARG ALA SEQRES 6 A 190 GLU ASP SER GLY GLU TYR HIS CYS VAL TYR HIS PHE VAL SEQRES 7 A 190 SER ALA PRO LYS ALA ASN ALA THR ILE GLU VAL LYS ALA SEQRES 8 A 190 ALA PRO ASP ILE THR GLY HIS LYS ARG SER GLU ASN LYS SEQRES 9 A 190 ASN GLU GLY GLN ASP ALA MET MET TYR CYS LYS SER VAL SEQRES 10 A 190 GLY TYR PRO HIS PRO GLU TRP MET TRP ARG LYS LYS GLU SEQRES 11 A 190 ASN GLY VAL PHE GLU GLU ILE SER ASN SER SER GLY ARG SEQRES 12 A 190 PHE PHE ILE ILE ASN LYS GLU ASN TYR THR GLU LEU ASN SEQRES 13 A 190 ILE VAL ASN LEU GLN ILE THR GLU ASP PRO GLY GLU TYR SEQRES 14 A 190 GLU CYS ASN ALA THR ASN SER ILE GLY SER ALA SER VAL SEQRES 15 A 190 SER THR VAL LEU ARG VAL ARG VAL MODRES 2WV3 ASN A 26 ASN GLYCOSYLATION SITE MODRES 2WV3 ASN A 139 ASN GLYCOSYLATION SITE HET NAG A1201 14 HET NAG A1203 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 4 HOH *113(H2 O) HELIX 1 1 ARG A 64 SER A 68 5 5 SHEET 1 AA 3 ARG A 5 THR A 8 0 SHEET 2 AA 3 VAL A 21 SER A 29 -1 O ASN A 26 N VAL A 7 SHEET 3 AA 3 ASN A 55 ILE A 60 -1 O MET A 56 N CYS A 25 SHEET 1 AB 5 VAL A 12 ILE A 13 0 SHEET 2 AB 5 ALA A 80 LYS A 90 1 O GLU A 88 N VAL A 12 SHEET 3 AB 5 GLY A 69 PHE A 77 -1 O GLY A 69 N VAL A 89 SHEET 4 AB 5 LEU A 34 LYS A 41 -1 N MET A 35 O HIS A 76 SHEET 5 AB 5 VAL A 44 GLU A 45 -1 O VAL A 44 N LYS A 41 SHEET 1 AC 4 ASP A 94 HIS A 98 0 SHEET 2 AC 4 ALA A 110 VAL A 117 -1 O LYS A 115 N THR A 96 SHEET 3 AC 4 TYR A 152 ILE A 157 -1 O THR A 153 N CYS A 114 SHEET 4 AC 4 PHE A 144 ASN A 148 -1 O PHE A 145 N ASN A 156 SHEET 1 AD 5 SER A 101 ASN A 105 0 SHEET 2 AD 5 SER A 179 ARG A 189 1 O VAL A 185 N GLU A 102 SHEET 3 AD 5 GLY A 167 THR A 174 -1 O GLY A 167 N LEU A 186 SHEET 4 AD 5 GLU A 123 GLU A 130 -1 O GLU A 123 N THR A 174 SHEET 5 AD 5 VAL A 133 GLU A 136 -1 O VAL A 133 N GLU A 130 SSBOND 1 CYS A 25 CYS A 73 1555 1555 2.01 SSBOND 2 CYS A 114 CYS A 171 1555 1555 2.02 LINK ND2 ASN A 26 C1 NAG A1201 1555 1555 1.45 LINK ND2 ASN A 139 C1 NAG A1203 1555 1555 1.45 CISPEP 1 TYR A 119 PRO A 120 0 1.98 CRYST1 49.390 81.080 137.540 90.00 90.00 90.00 I 2 2 2 8 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 0.020247 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012333 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007271 0.00000