HEADER IMMUNE SYSTEM 11-MAY-11 3RY4 TITLE 1.5 ANGSTROM RESOLUTION STRUCTURE OF GLYCOSYLATED FCGAMMARIIA (LOW- TITLE 2 RESPONDER POLYMORPHISM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOW AFFINITY IMMUNOGLOBULIN GAMMA FC REGION RECEPTOR II-A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN, RESIDUES 37-206; COMPND 5 SYNONYM: IGG FC RECEPTOR II-A, CDW32, FC-GAMMA RII-A, FC-GAMMA-RIIA, COMPND 6 FCRII-A; 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 TISSUE: BLOOD; SOURCE 6 GENE: CD32, FCG2, FCGR2A, FCGR2A1, IGFR2; SOURCE 7 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 8 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: SF21; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PVL1392 KEYWDS FC RECEPTOR, CD32, IMMUNOGLOBULIN SUPERFAMILY, LOW RESPONDER KEYWDS 2 POLYMORPHISM, CELL MEMBRANE, GLYCOPROTEIN, IGG-BINDING PROTEIN, KEYWDS 3 IMMUNOGLOBULIN DOMAIN, MEMBRANE, PHOSPHOPROTEIN, RECEPTOR, KEYWDS 4 TRANSMEMBRANE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR P.A.RAMSLAND,W.FARRUGIA,P.M.HOGARTH REVDAT 4 13-SEP-23 3RY4 1 HETSYN REVDAT 3 29-JUL-20 3RY4 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 LINK SITE REVDAT 2 21-SEP-11 3RY4 1 JRNL REVDAT 1 31-AUG-11 3RY4 0 JRNL AUTH P.A.RAMSLAND,W.FARRUGIA,T.M.BRADFORD,C.T.SARDJONO,S.ESPARON, JRNL AUTH 2 H.M.TRIST,M.S.POWELL,P.S.TAN,A.C.CENDRON,B.D.WINES, JRNL AUTH 3 A.M.SCOTT,P.M.HOGARTH JRNL TITL STRUCTURAL BASIS FOR FC{GAMMA}RIIA RECOGNITION OF HUMAN IGG JRNL TITL 2 AND FORMATION OF INFLAMMATORY SIGNALING COMPLEXES. JRNL REF J.IMMUNOL. V. 187 3208 2011 JRNL REFN ISSN 0022-1767 JRNL PMID 21856937 JRNL DOI 10.4049/JIMMUNOL.1101467 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 34590 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1769 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE : 0.3550 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 135 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1354 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 267 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.20 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.830 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3RY4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065520. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : BENT GE(111) MONOCHROMATOR REMARK 200 OPTICS : BENT CONICAL SI-MIRROR (RH REMARK 200 COATED) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35275 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 21.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.32000 REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1FCG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) PEG 4000, 0.2M AMMONIUM REMARK 280 ACETATE, 0.1M SODIUM CITRATE, PH 5.60, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 291.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z 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 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 39.67150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.20350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.67150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.20350 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 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 A1062 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1066 LIES ON A SPECIAL POSITION. 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 GLU A 22 -11.10 89.85 REMARK 500 GLN A 143 83.27 45.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RY5 RELATED DB: PDB REMARK 900 RELATED ID: 3RY6 RELATED DB: PDB DBREF 3RY4 A 4 173 UNP P12318 FCG2A_HUMAN 37 206 SEQADV 3RY4 PHE A 88 UNP P12318 SER 121 ENGINEERED MUTATION SEQRES 1 A 170 ALA PRO PRO LYS ALA VAL LEU LYS LEU GLU PRO PRO TRP SEQRES 2 A 170 ILE ASN VAL LEU GLN GLU ASP SER VAL THR LEU THR CYS SEQRES 3 A 170 GLN GLY ALA ARG SER PRO GLU SER ASP SER ILE GLN TRP SEQRES 4 A 170 PHE HIS ASN GLY ASN LEU ILE PRO THR HIS THR GLN PRO SEQRES 5 A 170 SER TYR ARG PHE LYS ALA ASN ASN ASN ASP SER GLY GLU SEQRES 6 A 170 TYR THR CYS GLN THR GLY GLN THR SER LEU SER ASP PRO SEQRES 7 A 170 VAL HIS LEU THR VAL LEU PHE GLU TRP LEU VAL LEU GLN SEQRES 8 A 170 THR PRO HIS LEU GLU PHE GLN GLU GLY GLU THR ILE MET SEQRES 9 A 170 LEU ARG CYS HIS SER TRP LYS ASP LYS PRO LEU VAL LYS SEQRES 10 A 170 VAL THR PHE PHE GLN ASN GLY LYS SER GLN LYS PHE SER SEQRES 11 A 170 HIS LEU ASP PRO THR PHE SER ILE PRO GLN ALA ASN HIS SEQRES 12 A 170 SER HIS SER GLY ASP TYR HIS CYS THR GLY ASN ILE GLY SEQRES 13 A 170 TYR THR LEU PHE SER SER LYS PRO VAL THR ILE THR VAL SEQRES 14 A 170 GLN MODRES 3RY4 ASN A 145 ASN GLYCOSYLATION SITE HET NAG A 200 14 HET GOL A 600 6 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM GOL GLYCEROL HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NAG C8 H15 N O6 FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *267(H2 O) HELIX 1 1 ASN A 62 SER A 66 5 5 HELIX 2 2 LYS A 114 LYS A 116 5 3 HELIX 3 3 ASN A 145 SER A 149 5 5 SHEET 1 A 3 VAL A 9 GLU A 13 0 SHEET 2 A 3 SER A 24 GLN A 30 -1 O GLN A 30 N VAL A 9 SHEET 3 A 3 SER A 56 LYS A 60 -1 O TYR A 57 N LEU A 27 SHEET 1 B 5 ASN A 18 LEU A 20 0 SHEET 2 B 5 VAL A 82 LEU A 87 1 O LEU A 87 N VAL A 19 SHEET 3 B 5 GLY A 67 THR A 73 -1 N GLY A 67 O LEU A 84 SHEET 4 B 5 ILE A 40 HIS A 44 -1 N GLN A 41 O GLN A 72 SHEET 5 B 5 ASN A 47 LEU A 48 -1 O ASN A 47 N HIS A 44 SHEET 1 C 3 LEU A 91 GLN A 94 0 SHEET 2 C 3 ILE A 106 SER A 112 -1 O ARG A 109 N GLN A 94 SHEET 3 C 3 THR A 138 ILE A 141 -1 O PHE A 139 N LEU A 108 SHEET 1 D 5 GLU A 99 PHE A 100 0 SHEET 2 D 5 VAL A 168 VAL A 172 1 O THR A 171 N PHE A 100 SHEET 3 D 5 GLY A 150 ILE A 158 -1 N TYR A 152 O VAL A 168 SHEET 4 D 5 LEU A 118 GLN A 125 -1 N PHE A 124 O HIS A 153 SHEET 5 D 5 LYS A 128 SER A 133 -1 O GLN A 130 N PHE A 123 SHEET 1 E 4 GLU A 99 PHE A 100 0 SHEET 2 E 4 VAL A 168 VAL A 172 1 O THR A 171 N PHE A 100 SHEET 3 E 4 GLY A 150 ILE A 158 -1 N TYR A 152 O VAL A 168 SHEET 4 E 4 THR A 161 SER A 164 -1 O PHE A 163 N GLY A 156 SSBOND 1 CYS A 29 CYS A 71 1555 1555 2.05 SSBOND 2 CYS A 110 CYS A 154 1555 1555 2.06 LINK ND2 ASN A 145 C1 NAG A 200 1555 1555 1.45 CISPEP 1 GLU A 13 PRO A 14 0 -0.72 CRYST1 79.343 100.407 27.937 90.00 90.00 90.00 P 21 21 2 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 0.012604 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009959 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035795 0.00000