HEADER IMMUNE SYSTEM 30-MAY-07 2Q3A TITLE CRYSTAL STRUCTURE OF RHESUS MACAQUE CD8 ALPHA-ALPHA HOMODIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: CD8; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 3 ORGANISM_COMMON: RHESUS MONKEY; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS RHESUS MACAQUE, CD8 HOMODIMER, IMMUNOGLOBULIN, MHC, COMPLEX, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR H.PENG,Y.CHEN,L.ZONG,F.GAO,Y.LIU,G.F.GAO REVDAT 3 30-AUG-23 2Q3A 1 REMARK REVDAT 2 24-FEB-09 2Q3A 1 VERSN REVDAT 1 17-JUN-08 2Q3A 0 JRNL AUTH L.ZONG,Y.CHEN,H.PENG,D.K.COLE,F.GAO,Y.LIU,G.F.GAO JRNL TITL CRYSTAL STRUCTURE OF RHESUS MACAQUE CD8 HOMODIMER SHEDS THE JRNL TITL 2 LIGHTS ON THE MOLECULAR BASIS OF RHESUS MACAQUE MHC CLASS I JRNL TITL 3 WITH CD8 COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL 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 : 7018 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) : 0.213 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 719 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1851 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 133 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.30 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.335 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 2Q3A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000043094. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 24 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 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS VII REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11313 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.13600 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) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.63700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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 1AKJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M POTASSIUM PHOSPHATE MONOBASIC, REMARK 280 20% W/V POLYETHYLENE GLYCOL 8,000, PH 8.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291.15K 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 23.27150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.15700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.12950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.15700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.27150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.12950 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 THR A 118 REMARK 465 THR A 119 REMARK 465 PRO A 120 REMARK 465 LYS B 115 REMARK 465 PRO B 116 REMARK 465 THR B 117 REMARK 465 THR B 118 REMARK 465 THR B 119 REMARK 465 PRO B 120 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 THR A 30 41.45 -109.01 REMARK 500 SER A 31 162.38 177.55 REMARK 500 SER A 53 -157.03 -179.06 REMARK 500 ASN A 55 -98.86 -58.18 REMARK 500 ASP A 64 82.04 -55.03 REMARK 500 ASN A 99 74.13 53.66 REMARK 500 SER A 100 -16.04 67.89 REMARK 500 PRO B 39 -177.27 -61.05 REMARK 500 LEU B 49 -68.88 -102.88 REMARK 500 ASN B 55 -103.80 -75.46 REMARK 500 ASP B 64 88.79 -65.66 REMARK 500 ASP B 83 77.57 48.39 REMARK 500 SER B 100 -15.19 74.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE REMARK 999 IN THE UNP DATABASE AT THE TIME OF PROCESSING. REMARK 999 AUTHOR STATED THE SEQUENCE OF THIS PROTEIN IS REMARK 999 UNDER GENEBANK ACCESSION CODE: XP_001092778 DBREF 2Q3A A 1 120 PDB 2Q3A 2Q3A 1 120 DBREF 2Q3A B 1 120 PDB 2Q3A 2Q3A 1 120 SEQRES 1 A 120 ASN GLN PHE ARG VAL SER PRO LEU GLY ARG THR TRP ASN SEQRES 2 A 120 LEU GLY GLU THR VAL GLU LEU LYS CYS GLN VAL LEU LEU SEQRES 3 A 120 SER ASN PRO THR SER GLY CYS SER TRP LEU PHE GLN PRO SEQRES 4 A 120 ARG GLY THR ALA ALA ARG PRO THR PHE LEU LEU TYR LEU SEQRES 5 A 120 SER GLN ASN LYS PRO LYS ALA ALA GLU GLY LEU ASP THR SEQRES 6 A 120 GLN ARG PHE SER GLY LYS ARG LEU GLY ASP THR PHE VAL SEQRES 7 A 120 LEU THR LEU ARG ASP PHE ARG GLN GLU ASN GLU GLY TYR SEQRES 8 A 120 TYR PHE CYS SER ALA LEU SER ASN SER ILE MET TYR PHE SEQRES 9 A 120 SER HIS PHE VAL PRO VAL PHE LEU PRO ALA LYS PRO THR SEQRES 10 A 120 THR THR PRO SEQRES 1 B 120 ASN GLN PHE ARG VAL SER PRO LEU GLY ARG THR TRP ASN SEQRES 2 B 120 LEU GLY GLU THR VAL GLU LEU LYS CYS GLN VAL LEU LEU SEQRES 3 B 120 SER ASN PRO THR SER GLY CYS SER TRP LEU PHE GLN PRO SEQRES 4 B 120 ARG GLY THR ALA ALA ARG PRO THR PHE LEU LEU TYR LEU SEQRES 5 B 120 SER GLN ASN LYS PRO LYS ALA ALA GLU GLY LEU ASP THR SEQRES 6 B 120 GLN ARG PHE SER GLY LYS ARG LEU GLY ASP THR PHE VAL SEQRES 7 B 120 LEU THR LEU ARG ASP PHE ARG GLN GLU ASN GLU GLY TYR SEQRES 8 B 120 TYR PHE CYS SER ALA LEU SER ASN SER ILE MET TYR PHE SEQRES 9 B 120 SER HIS PHE VAL PRO VAL PHE LEU PRO ALA LYS PRO THR SEQRES 10 B 120 THR THR PRO FORMUL 3 HOH *133(H2 O) HELIX 1 1 ARG A 85 ASN A 88 5 4 HELIX 2 2 ARG B 85 GLU B 89 5 5 SHEET 1 A 4 PHE A 3 SER A 6 0 SHEET 2 A 4 VAL A 18 VAL A 24 -1 O GLN A 23 N ARG A 4 SHEET 3 A 4 THR A 76 LEU A 81 -1 O LEU A 81 N VAL A 18 SHEET 4 A 4 PHE A 68 LEU A 73 -1 N SER A 69 O THR A 80 SHEET 1 B 5 LYS A 58 ALA A 59 0 SHEET 2 B 5 THR A 47 LEU A 52 -1 N TYR A 51 O LYS A 58 SHEET 3 B 5 CYS A 33 PRO A 39 -1 N CYS A 33 O LEU A 52 SHEET 4 B 5 GLY A 90 SER A 98 -1 O PHE A 93 N LEU A 36 SHEET 5 B 5 ILE A 101 PHE A 104 -1 O ILE A 101 N SER A 98 SHEET 1 C 5 LYS A 58 ALA A 59 0 SHEET 2 C 5 THR A 47 LEU A 52 -1 N TYR A 51 O LYS A 58 SHEET 3 C 5 CYS A 33 PRO A 39 -1 N CYS A 33 O LEU A 52 SHEET 4 C 5 GLY A 90 SER A 98 -1 O PHE A 93 N LEU A 36 SHEET 5 C 5 VAL A 108 VAL A 110 -1 O VAL A 110 N GLY A 90 SHEET 1 D 4 PHE B 3 SER B 6 0 SHEET 2 D 4 VAL B 18 VAL B 24 -1 O LYS B 21 N SER B 6 SHEET 3 D 4 THR B 76 LEU B 81 -1 O LEU B 81 N VAL B 18 SHEET 4 D 4 PHE B 68 LEU B 73 -1 N LYS B 71 O VAL B 78 SHEET 1 E 5 LYS B 58 ALA B 59 0 SHEET 2 E 5 THR B 47 LEU B 52 -1 N TYR B 51 O LYS B 58 SHEET 3 E 5 CYS B 33 GLN B 38 -1 N CYS B 33 O LEU B 52 SHEET 4 E 5 GLY B 90 SER B 98 -1 O PHE B 93 N LEU B 36 SHEET 5 E 5 ILE B 101 PHE B 104 -1 O TYR B 103 N ALA B 96 SHEET 1 F 5 LYS B 58 ALA B 59 0 SHEET 2 F 5 THR B 47 LEU B 52 -1 N TYR B 51 O LYS B 58 SHEET 3 F 5 CYS B 33 GLN B 38 -1 N CYS B 33 O LEU B 52 SHEET 4 F 5 GLY B 90 SER B 98 -1 O PHE B 93 N LEU B 36 SHEET 5 F 5 VAL B 108 VAL B 110 -1 O VAL B 110 N GLY B 90 SSBOND 1 CYS A 22 CYS A 94 1555 1555 2.05 SSBOND 2 CYS B 22 CYS B 94 1555 1555 2.07 CISPEP 1 SER A 6 PRO A 7 0 0.27 CISPEP 2 SER B 6 PRO B 7 0 -0.05 CRYST1 46.543 56.259 82.314 90.00 90.00 90.00 P 21 21 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 0.021486 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017775 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012149 0.00000