HEADER IMMUNE SYSTEM 17-AUG-01 1JSK OBSLTE 09-APR-14 1JSK 4PP8 TITLE CRYSTAL STRUCTURE OF MURINE NK CELL LIGAND RAE-1 BETA IN COMPLEX WITH TITLE 2 NKG2D COMPND MOL_ID: 1; COMPND 2 MOLECULE: NKG2-D; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN, RESIDUES 110-232; COMPND 5 SYNONYM: MOUSE NK CELL RECEPTOR NKG2D; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RAE-1 BETA; COMPND 9 CHAIN: C; COMPND 10 FRAGMENT: RECEPTOR BINDING DOMAIN, RESIDUES 31-204; COMPND 11 SYNONYM: RETINOIC ACID EARLY TRANSCRIPT BETA; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: NKG2D; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B(+); SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 14 ORGANISM_TAXID: 10090; SOURCE 15 GENE: RAE-1 BETA; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 RIL; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET22B(+) KEYWDS MURINE NK CELL LIGAND, RAE-1 BETA, NKG2D, MHC-I PLATFORM, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION MDLTYP CA ATOMS ONLY, CHAIN A, B, C AUTHOR P.LI,R.K.STRONG REVDAT 4 09-APR-14 1JSK 1 OBSLTE VERSN REVDAT 3 24-FEB-09 1JSK 1 VERSN REVDAT 2 01-APR-03 1JSK 1 JRNL REVDAT 1 20-FEB-02 1JSK 0 JRNL AUTH P.LI,G.MCDERMOTT,R.K.STRONG JRNL TITL CRYSTAL STRUCTURES OF RAE-1BETA AND ITS COMPLEX WITH THE JRNL TITL 2 ACTIVATING IMMUNORECEPTOR NKG2D. JRNL REF IMMUNITY V. 16 77 2002 JRNL REFN ISSN 1074-7613 JRNL PMID 11825567 JRNL DOI 10.1016/S1074-7613(02)00258-3 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.CERWENKA,A.B.BAKKER,T.MCCLANHAN,J.WAGNER,J.WU,J.H.PHILIPS, REMARK 1 AUTH 2 L.L.LANIER REMARK 1 TITL RITINOIC ACID EARLY INDUCIBLE GENES DEFINE A LIGAND 2 REMARK 1 TITL 2 ACTIVATING NKG2D RECEPTOR IN MOUSE REMARK 1 REF IMMUNITY V. 12 721 2000 REMARK 1 REFN ISSN 1074-7613 REMARK 1 DOI 10.1016/S1074-7613(00)80222-8 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.DIEFENBACH,A.M.JAMIESON,S.D.LIU,N.SHASTRI,D.H.RAULET REMARK 1 TITL LIGANDS FOR THE MURINE NKG2D RECEPTOR:EXPRESSION BY CELLS REMARK 1 TITL 2 AND MACROPHAGES REMARK 1 REF NAT.IMMUNOL. V. 1 119 2000 REMARK 1 REFN ISSN 1529-2908 REMARK 1 DOI 10.1038/77793 REMARK 2 REMARK 2 RESOLUTION. 3.50 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) : 3.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 70458.430 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 8115 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) : 0.314 REMARK 3 FREE R VALUE : 0.330 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 16.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1373 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.72 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1112 REMARK 3 BIN R VALUE (WORKING SET) : 0.3230 REMARK 3 BIN FREE R VALUE : 0.3710 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 15.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 208 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 420 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 58.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.93000 REMARK 3 B22 (A**2) : 10.93000 REMARK 3 B33 (A**2) : -21.85000 REMARK 3 B12 (A**2) : 0.36000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.54 REMARK 3 ESD FROM SIGMAA (A) : 0.35 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) : 0.60 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.69 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 2.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.400 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.110 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : GROUP 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 : FLAT MODEL REMARK 3 KSOL : 0.25 REMARK 3 BSOL : 30.00 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THIS IS A PARTIALLY REFINED MODEL AT REMARK 3 3.50A REMARK 4 REMARK 4 1JSK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 99 REMARK 99 THE ENTRY CONTAINS COORDINATES WITH THE REMARK 99 ALPHA CARBONS ONLY. REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-AUG-01. REMARK 100 THE RCSB ID CODE IS RCSB014135. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-APR-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : DOUBLE CRYSTAL 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 : 8417 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.500 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : 0.10100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.22900 REMARK 200 R SYM FOR SHELL (I) : 0.22900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE, MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1HQ8, MOUSE NKG2D; PDB ENTRY 1JFM, RAE- REMARK 200 1 BETA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG8000 + 0.300M AS, PH 6.50, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 116.58267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 233.16533 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 174.87400 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 291.45667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.29133 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 DBREF 1JSK A 110 232 UNP O54709 NKG2D_MOUSE 110 232 DBREF 1JSK B 110 232 UNP O54709 NKG2D_MOUSE 110 232 DBREF 1JSK C 1 174 UNP O08603 RAE1B_MOUSE 31 204 SEQRES 1 A 123 GLY TYR CYS GLY PRO CYS PRO ASN ASN TRP ILE CYS HIS SEQRES 2 A 123 ARG ASN ASN CYS TYR GLN PHE PHE ASN GLU GLU LYS THR SEQRES 3 A 123 TRP ASN GLN SER GLN ALA SER CYS LEU SER GLN ASN SER SEQRES 4 A 123 SER LEU LEU LYS ILE TYR SER LYS GLU GLU GLN ASP PHE SEQRES 5 A 123 LEU LYS LEU VAL LYS SER TYR HIS TRP MET GLY LEU VAL SEQRES 6 A 123 GLN ILE PRO ALA ASN GLY SER TRP GLN TRP GLU ASP GLY SEQRES 7 A 123 SER SER LEU SER TYR ASN GLN LEU THR LEU VAL GLU ILE SEQRES 8 A 123 PRO LYS GLY SER CYS ALA VAL TYR GLY SER SER PHE LYS SEQRES 9 A 123 ALA TYR THR GLU ASP CYS ALA ASN LEU ASN THR TYR ILE SEQRES 10 A 123 CYS MET LYS ARG ALA VAL SEQRES 1 B 123 GLY TYR CYS GLY PRO CYS PRO ASN ASN TRP ILE CYS HIS SEQRES 2 B 123 ARG ASN ASN CYS TYR GLN PHE PHE ASN GLU GLU LYS THR SEQRES 3 B 123 TRP ASN GLN SER GLN ALA SER CYS LEU SER GLN ASN SER SEQRES 4 B 123 SER LEU LEU LYS ILE TYR SER LYS GLU GLU GLN ASP PHE SEQRES 5 B 123 LEU LYS LEU VAL LYS SER TYR HIS TRP MET GLY LEU VAL SEQRES 6 B 123 GLN ILE PRO ALA ASN GLY SER TRP GLN TRP GLU ASP GLY SEQRES 7 B 123 SER SER LEU SER TYR ASN GLN LEU THR LEU VAL GLU ILE SEQRES 8 B 123 PRO LYS GLY SER CYS ALA VAL TYR GLY SER SER PHE LYS SEQRES 9 B 123 ALA TYR THR GLU ASP CYS ALA ASN LEU ASN THR TYR ILE SEQRES 10 B 123 CYS MET LYS ARG ALA VAL SEQRES 1 C 174 ASP ALA HIS SER LEU ARG CYS ASN LEU THR ILE LYS ASP SEQRES 2 C 174 PRO THR PRO ALA ASP PRO LEU TRP TYR GLU ALA LYS CYS SEQRES 3 C 174 PHE VAL GLY GLU ILE LEU ILE LEU HIS LEU SER ASN ILE SEQRES 4 C 174 ASN LYS THR MET THR SER GLY ASP PRO GLY GLU THR ALA SEQRES 5 C 174 ASN ALA THR GLU VAL LYS LYS CYS LEU THR GLN PRO LEU SEQRES 6 C 174 LYS ASN LEU CYS GLN LYS LEU ARG ASN LYS VAL SER ASN SEQRES 7 C 174 THR LYS VAL ASP THR HIS LYS THR ASN GLY TYR PRO HIS SEQRES 8 C 174 LEU GLN VAL THR MET ILE TYR PRO GLN SER GLN GLY ARG SEQRES 9 C 174 THR PRO SER ALA THR TRP GLU PHE ASN ILE SER ASP SER SEQRES 10 C 174 TYR PHE PHE THR PHE TYR THR GLU ASN MET SER TRP ARG SEQRES 11 C 174 SER ALA ASN ASP GLU SER GLY VAL ILE MET ASN LYS TRP SEQRES 12 C 174 LYS ASP ASP GLY GLU PHE VAL LYS GLN LEU LYS PHE LEU SEQRES 13 C 174 ILE HIS GLU CYS SER GLN LYS MET ASP GLU PHE LEU LYS SEQRES 14 C 174 GLN SER LYS GLU LYS CRYST1 58.467 58.467 349.748 90.00 90.00 120.00 P 61 12 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 0.017104 0.009875 0.000000 0.00000 SCALE2 0.000000 0.019750 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002859 0.00000