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 5 06-NOV-24 3RY4 1 REMARK
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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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