HEADER CELL ADHESION 23-JAN-12 4DFI TITLE CRYSTAL STRUCTURE OF CELL ADHESION MOLECULE NECTIN-2/CD112 MUTANT FAMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLIOVIRUS RECEPTOR-RELATED PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: IG-LIKE V-TYPE DOMAIN, UNP RESIDUES 32-158; COMPND 5 SYNONYM: HERPES VIRUS ENTRY MEDIATOR B, HERPESVIRUS ENTRY MEDIATOR B, COMPND 6 HVEB, NECTIN-2; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PVRL2, HVEB, PRR2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-21A KEYWDS CELL ADHESION, CD226, CELL SURFACE EXPDTA X-RAY DIFFRACTION AUTHOR J.LIU,X.QIAN,Z.CHEN,X.XU,F.GAO,S.ZHANG,R.ZHANG,J.QI,G.F.GAO,J.YAN REVDAT 2 08-NOV-23 4DFI 1 SEQADV REVDAT 1 06-JUN-12 4DFI 0 JRNL AUTH J.LIU,X.QIAN,Z.CHEN,X.XU,F.GAO,S.ZHANG,R.ZHANG,J.QI,G.F.GAO, JRNL AUTH 2 J.YAN JRNL TITL CRYSTAL STRUCTURE OF CELL ADHESION MOLECULE NECTIN-2/CD112 JRNL TITL 2 AND ITS BINDING TO IMMUNE RECEPTOR DNAM-1/CD226 JRNL REF J.IMMUNOL. V. 188 5511 2012 JRNL REFN ISSN 0022-1767 JRNL PMID 22547693 JRNL DOI 10.4049/JIMMUNOL.1200324 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 9250 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 447 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 34.5505 - 2.5948 0.98 3286 158 0.1896 0.2192 REMARK 3 2 2.5948 - 2.0597 0.94 2952 171 0.2051 0.2433 REMARK 3 3 2.0597 - 1.7993 0.81 2565 118 0.2122 0.2879 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 : 0.38 REMARK 3 B_SOL : 47.91 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.50060 REMARK 3 B22 (A**2) : -4.10110 REMARK 3 B33 (A**2) : -4.39950 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 : 0.016 978 REMARK 3 ANGLE : 1.067 1334 REMARK 3 CHIRALITY : 0.065 149 REMARK 3 PLANARITY : 0.007 177 REMARK 3 DIHEDRAL : 19.051 359 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -9.2438 2.6187 -8.0156 REMARK 3 T TENSOR REMARK 3 T11: 0.0882 T22: 0.0914 REMARK 3 T33: 0.0868 T12: 0.0072 REMARK 3 T13: 0.0089 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: 0.5468 L22: 0.5132 REMARK 3 L33: 0.7130 L12: 0.0061 REMARK 3 L13: -0.3384 L23: 0.3067 REMARK 3 S TENSOR REMARK 3 S11: 0.0030 S12: 0.0190 S13: 0.0193 REMARK 3 S21: 0.0068 S22: -0.0054 S23: 0.0265 REMARK 3 S31: 0.0120 S32: -0.0334 S33: -0.0090 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 4DFI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070264. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9783 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9858 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 35.419 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 4DFH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 0.1M TRIS (PH REMARK 280 8.5), 25% (W/V) PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 21.63600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.32050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.89000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.32050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.63600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.89000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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 GLY A 83 REMARK 465 GLN A 84 REMARK 465 ASP A 85 REMARK 465 THR A 86 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 O HOH A 210 O HOH A 312 1.83 REMARK 500 O HOH A 284 O HOH A 305 1.85 REMARK 500 O HOH A 237 O HOH A 301 1.89 REMARK 500 O HOH A 286 O HOH A 303 1.90 REMARK 500 OXT VAL A 128 O HOH A 298 1.93 REMARK 500 O HOH A 318 O HOH A 324 1.96 REMARK 500 O HOH A 254 O HOH A 304 2.06 REMARK 500 OE1 GLN A 91 O HOH A 304 2.06 REMARK 500 O HOH A 301 O HOH A 315 2.10 REMARK 500 O HOH A 211 O HOH A 312 2.14 REMARK 500 O HOH A 272 O HOH A 276 2.17 REMARK 500 O HOH A 290 O HOH A 314 2.18 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 ALA A 47 -70.62 -34.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DFH RELATED DB: PDB DBREF 4DFI A 2 128 UNP Q92692 PVRL2_HUMAN 32 158 SEQADV 4DFI MET A 1 UNP Q92692 EXPRESSION TAG SEQADV 4DFI SER A 59 UNP Q92692 MET 89 ENGINEERED MUTATION SEQADV 4DFI SER A 64 UNP Q92692 PRO 94 ENGINEERED MUTATION SEQADV 4DFI SER A 113 UNP Q92692 ALA 143 ENGINEERED MUTATION SEQADV 4DFI SER A 115 UNP Q92692 PHE 145 ENGINEERED MUTATION SEQRES 1 A 128 MET GLN ASP VAL ARG VAL GLN VAL LEU PRO GLU VAL ARG SEQRES 2 A 128 GLY GLN LEU GLY GLY THR VAL GLU LEU PRO CYS HIS LEU SEQRES 3 A 128 LEU PRO PRO VAL PRO GLY LEU TYR ILE SER LEU VAL THR SEQRES 4 A 128 TRP GLN ARG PRO ASP ALA PRO ALA ASN HIS GLN ASN VAL SEQRES 5 A 128 ALA ALA PHE HIS PRO LYS SER GLY PRO SER PHE SER SER SEQRES 6 A 128 PRO LYS PRO GLY SER GLU ARG LEU SER PHE VAL SER ALA SEQRES 7 A 128 LYS GLN SER THR GLY GLN ASP THR GLU ALA GLU LEU GLN SEQRES 8 A 128 ASP ALA THR LEU ALA LEU HIS GLY LEU THR VAL GLU ASP SEQRES 9 A 128 GLU GLY ASN TYR THR CYS GLU PHE SER THR SER PRO LYS SEQRES 10 A 128 GLY SER VAL ARG GLY MET THR TRP LEU ARG VAL FORMUL 2 HOH *124(H2 O) HELIX 1 1 PRO A 46 HIS A 49 5 4 HELIX 2 2 GLY A 69 GLU A 71 5 3 HELIX 3 3 THR A 101 GLU A 105 5 5 SHEET 1 A 2 ARG A 5 GLN A 7 0 SHEET 2 A 2 HIS A 25 LEU A 27 -1 O LEU A 27 N ARG A 5 SHEET 1 B 6 GLU A 11 ARG A 13 0 SHEET 2 B 6 GLY A 118 ARG A 127 1 O ARG A 127 N VAL A 12 SHEET 3 B 6 GLY A 106 SER A 115 -1 N TYR A 108 O THR A 124 SHEET 4 B 6 TYR A 34 GLN A 41 -1 N TYR A 34 O SER A 115 SHEET 5 B 6 ASN A 51 HIS A 56 -1 O ALA A 53 N TRP A 40 SHEET 6 B 6 GLY A 60 SER A 62 -1 O SER A 62 N ALA A 54 SHEET 1 C 3 VAL A 20 LEU A 22 0 SHEET 2 C 3 LEU A 95 LEU A 97 -1 O LEU A 95 N LEU A 22 SHEET 3 C 3 LEU A 73 PHE A 75 -1 N SER A 74 O ALA A 96 SSBOND 1 CYS A 24 CYS A 110 1555 1555 2.03 CISPEP 1 LEU A 27 PRO A 28 0 -7.38 CISPEP 2 LYS A 67 PRO A 68 0 1.04 CISPEP 3 SER A 115 PRO A 116 0 9.53 CRYST1 43.272 45.780 52.641 90.00 90.00 90.00 P 21 21 21 4 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 0.023110 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021844 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018997 0.00000