LinkDB: 3RY5
Original site: 3RY5
Gene (1) KEGG GENES (1) Protein sequence (3) UniProt (1) SWISS-PROT (1) PDBSTR (1) DNA sequence (1) EMBL (1) Protein domain (7) InterPro (6) PROSITE (1) Literature (1) PubMed (1) All databases (13)
Download RDF
HEADER IMMUNE SYSTEM 11-MAY-11 3RY5
TITLE THREE-DIMENSIONAL STRUCTURE OF GLYCOSYLATED FCGAMMARIIA (HIGH-
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 114-327;
COMPND 5 SYNONYM: IGG FC RECEPTOR II-A, FC-GAMMA RII-A, FC-GAMMA-RIIA, FCRII-
COMPND 6 A, CDW32;
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: FCGR2A, CD32, FCG2, 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, HIGH RESPONDER
KEYWDS 2 POLYMORPHISM, CELL MEMBRANE, IGG-BINDING PROTEIN, IMMUNOGLOBULIN
KEYWDS 3 DOMAIN, MEMBRANE, RECEPTOR, TRANSMEMBRANE, IMMUNE SYSTEM
EXPDTA X-RAY DIFFRACTION
AUTHOR P.A.RAMSLAND,W.FARRUGIA,P.M.HOGARTH
REVDAT 2 21-SEP-11 3RY5 1 JRNL
REVDAT 1 31-AUG-11 3RY5 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. 2.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.0
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) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.43
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 : 7554
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) : 0.206
REMARK 3 FREE R VALUE : 0.275
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 804
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) : 2.30
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.38
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.2370
REMARK 3 BIN FREE R VALUE : 0.2930
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 99
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1350
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 85
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 19.80
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) : 0.25
REMARK 3 ESD FROM SIGMAA (A) : 0.19
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) : 0.36
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.006
REMARK 3 BOND ANGLES (DEGREES) : 1.40
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.00
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.82
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 3RY5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-11.
REMARK 100 THE RCSB ID CODE IS RCSB065521.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 03-JUL-03
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 7.50
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : OSMIC BLUE MIRRORS
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7783
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2
REMARK 200 DATA REDUNDANCY : 4.600
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.10000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0
REMARK 200 DATA REDUNDANCY IN SHELL : 4.30
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.27000
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.900
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: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 45.13
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) PEG 4000, 0.2M AMMONIUM
REMARK 280 SULFATE, PH 7.50, VAPOR DIFFUSION, TEMPERATURE 291.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -X,Y,-Z+1/2
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z
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
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 44.05200
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 44.05200
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 25.01800
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.96750
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 25.01800
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.96750
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 44.05200
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 25.01800
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.96750
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 44.05200
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 25.01800
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.96750
REMARK 290 SMTRY3 8 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 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 -4.27 81.87
REMARK 500 SER A 88 73.47 -105.86
REMARK 500 GLN A 143 84.48 40.86
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3RY4 RELATED DB: PDB
REMARK 900 RELATED ID: 3RY6 RELATED DB: PDB
DBREF 3RY5 A 4 173 UNP P12318 FCG2A_HUMAN 37 206
SEQADV 3RY5 ARG A 134 UNP P12318 HIS 167 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 SER 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 ARG 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
FORMUL 2 HOH *85(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 THR A 28 N LYS A 11
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 GLN A 72 -1 N TYR A 69 O VAL A 82
SHEET 4 B 5 GLN A 41 HIS A 44 -1 N PHE A 43 O THR A 70
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 GLY A 150 O ILE A 170
SHEET 4 D 5 VAL A 119 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 GLY A 150 O ILE A 170
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 2.03
SSBOND 2 CYS A 110 CYS A 154 1555 1555 2.04
CISPEP 1 GLU A 13 PRO A 14 0 -0.49
CRYST1 50.036 77.935 88.104 90.00 90.00 90.00 C 2 2 21 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 0.019986 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012831 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011350 0.00000
(ATOM LINES ARE NOT SHOWN.)
END