HEADER CELL ADHESION 22-APR-08 2JJS TITLE STRUCTURE OF HUMAN CD47 IN COMPLEX WITH HUMAN SIGNAL REGULATORY TITLE 2 PROTEIN (SIRP) ALPHA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: N-TERMINAL ECTODOMAIN, RESIDUES 31-148; COMPND 5 SYNONYM: SIRP ALPHA, SHP SUBSTRATE 1, SHPS-1, INHIBITORY RECEPTOR COMPND 6 SHPS-1, SIGNAL REGULATORY PROTEIN ALPHA-1, SIRP-ALPHA-1, SIRP-ALPHA- COMPND 7 2, SIRP-ALPHA- 3, MYD-1 ANTIGEN, BRAIN IG-LIKE MOLECULE WITH COMPND 8 TYROSINE- BASED ACTIVATION MOTIFS, BIT, MACROPHAGE FUSION RECEPTOR, COMPND 9 P84, CD172A ANTIGEN; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: LEUKOCYTE SURFACE ANTIGEN CD47; COMPND 13 CHAIN: C, D; COMPND 14 FRAGMENT: IMMUNOGLOBULIN-SUPERFAMILY ECTODOMAIN, RESIDUES 19-136; COMPND 15 SYNONYM: CD47, INTEGRIN-ASSOCIATED PROTEIN, IAP, ANTIGENIC SURFACE COMPND 16 DETERMINANT PROTEIN OA3, PROTEIN MER6; COMPND 17 ENGINEERED: YES; COMPND 18 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: LEC3.2.8.1; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: CHO; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PEE14; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 17 EXPRESSION_SYSTEM_VARIANT: LEC3.2.8.1; SOURCE 18 EXPRESSION_SYSTEM_CELL_LINE: CHO; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PEE14 KEYWDS SIGNAL REGULATORY PROTEIN ALPHA, IMMUNOGLOBULIN SUPERFAMILY, KEYWDS 2 TRANSMEMBRANE, PHOSPHOPROTEIN, PAIRED RECEPTOR, POLYMORPHISM, KEYWDS 3 GLYCOPROTEIN, CELL ADHESION, PYRROLIDONE CARBOXYLIC ACID, KEYWDS 4 ALTERNATIVE SPLICING, IMMUNOGLOBULIN DOMAIN, SIRP, CD47, SIRPA, KEYWDS 5 MEMBRANE, SH3-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR D.HATHERLEY,S.C.GRAHAM,J.TURNER,K.HARLOS,D.I.STUART,A.N.BARCLAY REVDAT 7 13-DEC-23 2JJS 1 HETSYN REVDAT 6 29-JUL-20 2JJS 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE REVDAT 5 11-MAR-20 2JJS 1 SEQRES REVDAT 4 03-APR-19 2JJS 1 SOURCE REVDAT 3 13-MAR-19 2JJS 1 TITLE JRNL REMARK LINK REVDAT 2 24-FEB-09 2JJS 1 VERSN REVDAT 1 05-AUG-08 2JJS 0 JRNL AUTH D.HATHERLEY,S.C.GRAHAM,J.TURNER,K.HARLOS,D.I.STUART, JRNL AUTH 2 A.N.BARCLAY JRNL TITL PAIRED RECEPTOR SPECIFICITY EXPLAINED BY STRUCTURES OF JRNL TITL 2 SIGNAL REGULATORY PROTEINS ALONE AND COMPLEXED WITH CD47. JRNL REF MOL. CELL V. 31 266 2008 JRNL REFN ISSN 1097-4164 JRNL PMID 18657508 JRNL DOI 10.1016/J.MOLCEL.2008.05.026 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 89.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 43948 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 + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2345 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3208 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2210 REMARK 3 BIN FREE R VALUE SET COUNT : 168 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3626 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 102 REMARK 3 SOLVENT ATOMS : 540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.50000 REMARK 3 B22 (A**2) : 0.34000 REMARK 3 B33 (A**2) : -0.86000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.09000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.127 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.125 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.085 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.986 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3797 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2563 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5158 ; 1.269 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6243 ; 0.842 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 467 ; 6.715 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 156 ;33.176 ;24.615 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 644 ;10.867 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;19.291 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 610 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4232 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 726 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 452 ; 0.187 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2455 ; 0.194 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1731 ; 0.168 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1940 ; 0.098 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 366 ; 0.127 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 6 ; 0.184 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 35 ; 0.222 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.132 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2345 ; 1.708 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3795 ; 2.470 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1566 ; 3.961 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1361 ; 6.381 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 116 REMARK 3 ORIGIN FOR THE GROUP (A): 16.6300 -7.4900 40.6310 REMARK 3 T TENSOR REMARK 3 T11: -0.0958 T22: -0.0566 REMARK 3 T33: -0.1639 T12: -0.0330 REMARK 3 T13: 0.0142 T23: -0.0075 REMARK 3 L TENSOR REMARK 3 L11: 1.1340 L22: 1.0986 REMARK 3 L33: 1.2427 L12: -0.1592 REMARK 3 L13: -0.1886 L23: -0.0676 REMARK 3 S TENSOR REMARK 3 S11: -0.0389 S12: 0.0122 S13: 0.0020 REMARK 3 S21: 0.0253 S22: 0.0127 S23: 0.0214 REMARK 3 S31: 0.0138 S32: -0.1384 S33: 0.0262 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 119 REMARK 3 ORIGIN FOR THE GROUP (A): 19.4240 0.2380 3.7440 REMARK 3 T TENSOR REMARK 3 T11: -0.1249 T22: -0.0875 REMARK 3 T33: -0.1665 T12: -0.0023 REMARK 3 T13: -0.0043 T23: 0.0077 REMARK 3 L TENSOR REMARK 3 L11: 0.7877 L22: 1.2321 REMARK 3 L33: 0.8614 L12: 0.1547 REMARK 3 L13: 0.0180 L23: -0.0631 REMARK 3 S TENSOR REMARK 3 S11: -0.0148 S12: 0.0540 S13: -0.0208 REMARK 3 S21: -0.0405 S22: 0.0004 S23: 0.0205 REMARK 3 S31: 0.0236 S32: -0.0196 S33: 0.0144 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 116 REMARK 3 ORIGIN FOR THE GROUP (A): 31.3700 -21.1630 21.7400 REMARK 3 T TENSOR REMARK 3 T11: -0.1007 T22: -0.0968 REMARK 3 T33: -0.1472 T12: -0.0284 REMARK 3 T13: -0.0062 T23: 0.0009 REMARK 3 L TENSOR REMARK 3 L11: 0.4095 L22: 0.6167 REMARK 3 L33: 2.4153 L12: 0.1615 REMARK 3 L13: -0.0170 L23: 0.2880 REMARK 3 S TENSOR REMARK 3 S11: 0.0373 S12: 0.0010 S13: -0.0316 REMARK 3 S21: 0.0563 S22: -0.0486 S23: -0.0115 REMARK 3 S31: 0.1277 S32: 0.0425 S33: 0.0113 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 116 REMARK 3 ORIGIN FOR THE GROUP (A): 31.0470 14.7340 25.1970 REMARK 3 T TENSOR REMARK 3 T11: -0.1161 T22: -0.0866 REMARK 3 T33: -0.1450 T12: 0.0002 REMARK 3 T13: 0.0028 T23: 0.0094 REMARK 3 L TENSOR REMARK 3 L11: 0.6687 L22: 0.8509 REMARK 3 L33: 2.0707 L12: -0.3992 REMARK 3 L13: -0.1681 L23: 0.4135 REMARK 3 S TENSOR REMARK 3 S11: -0.0510 S12: -0.0947 S13: 0.0581 REMARK 3 S21: 0.0374 S22: 0.0883 S23: -0.0225 REMARK 3 S31: -0.1219 S32: 0.0458 S33: -0.0373 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. B VALUES INCLUDE TLS CONTRIBUTIONS. REMARK 4 REMARK 4 2JJS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-APR-08. REMARK 100 THE DEPOSITION ID IS D_1290036000. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-07; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; NULL REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ESRF; ESRF REMARK 200 BEAMLINE : ID23-2; BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.873; 1.5498 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR; NULL REMARK 200 OPTICS : MIRRORS; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; NULL REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46373 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 29.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : 0.79000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2UV3 FOR CHAINS A AND B, PDB ENTRY 2ICC REMARK 200 FOR CHAINS C AND D REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 NL SIRP ALPHA / CD47 COMPLEX (1:1 REMARK 280 RATIO, EACH PROTEIN AT APPROX. 0.375 UM) PLUS 100 NL RESERVOIR REMARK 280 (0.2 M POTASSIUM IODIDE, 20% W/V PEG 3350) EQUILIBRATED AGAINST REMARK 280 95 UL OF RESERVOIR AT 5 C., PH 7.4, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 36.20500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN C, CYS 33 TO GLY REMARK 400 ENGINEERED RESIDUE IN CHAIN D, CYS 33 TO GLY 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 PRO A 117 REMARK 465 SER A 118 REMARK 465 THR A 119 REMARK 465 ARG A 120 REMARK 465 HIS A 121 REMARK 465 HIS A 122 REMARK 465 HIS A 123 REMARK 465 HIS A 124 REMARK 465 HIS A 125 REMARK 465 HIS A 126 REMARK 465 ARG B 120 REMARK 465 HIS B 121 REMARK 465 HIS B 122 REMARK 465 HIS B 123 REMARK 465 HIS B 124 REMARK 465 HIS B 125 REMARK 465 HIS B 126 REMARK 465 SER C 117 REMARK 465 TRP C 118 REMARK 465 SER C 119 REMARK 465 THR C 120 REMARK 465 ARG C 121 REMARK 465 HIS C 122 REMARK 465 HIS C 123 REMARK 465 HIS C 124 REMARK 465 HIS C 125 REMARK 465 HIS C 126 REMARK 465 HIS C 127 REMARK 465 SER D 117 REMARK 465 TRP D 118 REMARK 465 SER D 119 REMARK 465 THR D 120 REMARK 465 ARG D 121 REMARK 465 HIS D 122 REMARK 465 HIS D 123 REMARK 465 HIS D 124 REMARK 465 HIS D 125 REMARK 465 HIS D 126 REMARK 465 HIS D 127 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 116 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG1 THR B 88 OE1 GLU B 110 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 LEU C 101 -109.21 52.76 REMARK 500 LEU D 101 -108.28 56.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VSC RELATED DB: PDB REMARK 900 STRUCTURE OF THE IMMUNOGLOBULIN-SUPERFAMILY ECTODOMAIN OF HUMAN CD47 REMARK 900 RELATED ID: 2JJT RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN CD47 IN COMPLEX WITH HUMAN SIGNAL RECEPTOR REMARK 900 PEPTIDE (SIRP) ALPHA REMARK 900 RELATED ID: 2UV3 RELATED DB: PDB REMARK 900 STRUCTURE OF THE SIGNAL-REGULATORY PROTEIN ( SIRP) ALPHA DOMAIN REMARK 900 THAT BINDS CD47. REMARK 999 REMARK 999 SEQUENCE REMARK 999 SIRP ALPHA (CHAINS A AND B) RESIDUE NUMBERING IS FOR THE REMARK 999 MATURE PROTEIN (LACKING N-TERMINAL 30 AMINO ACID SIGNAL REMARK 999 SEQUENCE). C-TERMINAL PURIFICATION TAG (TRHHHHHH) IS REMARK 999 ADDED. REMARK 999 CD47 RESIDUE NUMBERING IS FOR MATURE PROTEIN (LACKING N- REMARK 999 TERMINAL 18 AMINO ACID SIGNAL SEQUENCE). RESIDUE 1 (GLN) REMARK 999 CYCLISES TO FORM A PYROGLUTAMIC ACID. RESIDUE 15 WAS REMARK 999 MUTATED FROM CYS TO GLY. C-TERMINAL PURIFICATION TAG ( REMARK 999 STRHHHHHH) IS ADDED. DBREF 2JJS A 1 118 UNP P78324 SHPS1_HUMAN 31 148 DBREF 2JJS A 119 126 PDB 2JJS 2JJS 119 126 DBREF 2JJS B 1 118 UNP P78324 SHPS1_HUMAN 31 148 DBREF 2JJS B 119 126 PDB 2JJS 2JJS 119 126 DBREF 2JJS C 1 118 UNP Q08722 CD47_HUMAN 19 136 DBREF 2JJS C 119 127 PDB 2JJS 2JJS 119 127 DBREF 2JJS D 1 118 UNP Q08722 CD47_HUMAN 19 136 DBREF 2JJS D 119 127 PDB 2JJS 2JJS 119 127 SEQADV 2JJS GLY C 15 UNP Q08722 CYS 33 ENGINEERED MUTATION SEQADV 2JJS GLY D 15 UNP Q08722 CYS 33 ENGINEERED MUTATION SEQRES 1 A 126 GLU GLU GLU LEU GLN VAL ILE GLN PRO ASP LYS SER VAL SEQRES 2 A 126 SER VAL ALA ALA GLY GLU SER ALA ILE LEU HIS CYS THR SEQRES 3 A 126 VAL THR SER LEU ILE PRO VAL GLY PRO ILE GLN TRP PHE SEQRES 4 A 126 ARG GLY ALA GLY PRO ALA ARG GLU LEU ILE TYR ASN GLN SEQRES 5 A 126 LYS GLU GLY HIS PHE PRO ARG VAL THR THR VAL SER GLU SEQRES 6 A 126 SER THR LYS ARG GLU ASN MET ASP PHE SER ILE SER ILE SEQRES 7 A 126 SER ASN ILE THR PRO ALA ASP ALA GLY THR TYR TYR CYS SEQRES 8 A 126 VAL LYS PHE ARG LYS GLY SER PRO ASP THR GLU PHE LYS SEQRES 9 A 126 SER GLY ALA GLY THR GLU LEU SER VAL ARG ALA LYS PRO SEQRES 10 A 126 SER THR ARG HIS HIS HIS HIS HIS HIS SEQRES 1 B 126 GLU GLU GLU LEU GLN VAL ILE GLN PRO ASP LYS SER VAL SEQRES 2 B 126 SER VAL ALA ALA GLY GLU SER ALA ILE LEU HIS CYS THR SEQRES 3 B 126 VAL THR SER LEU ILE PRO VAL GLY PRO ILE GLN TRP PHE SEQRES 4 B 126 ARG GLY ALA GLY PRO ALA ARG GLU LEU ILE TYR ASN GLN SEQRES 5 B 126 LYS GLU GLY HIS PHE PRO ARG VAL THR THR VAL SER GLU SEQRES 6 B 126 SER THR LYS ARG GLU ASN MET ASP PHE SER ILE SER ILE SEQRES 7 B 126 SER ASN ILE THR PRO ALA ASP ALA GLY THR TYR TYR CYS SEQRES 8 B 126 VAL LYS PHE ARG LYS GLY SER PRO ASP THR GLU PHE LYS SEQRES 9 B 126 SER GLY ALA GLY THR GLU LEU SER VAL ARG ALA LYS PRO SEQRES 10 B 126 SER THR ARG HIS HIS HIS HIS HIS HIS SEQRES 1 C 127 PCA LEU LEU PHE ASN LYS THR LYS SER VAL GLU PHE THR SEQRES 2 C 127 PHE GLY ASN ASP THR VAL VAL ILE PRO CYS PHE VAL THR SEQRES 3 C 127 ASN MET GLU ALA GLN ASN THR THR GLU VAL TYR VAL LYS SEQRES 4 C 127 TRP LYS PHE LYS GLY ARG ASP ILE TYR THR PHE ASP GLY SEQRES 5 C 127 ALA LEU ASN LYS SER THR VAL PRO THR ASP PHE SER SER SEQRES 6 C 127 ALA LYS ILE GLU VAL SER GLN LEU LEU LYS GLY ASP ALA SEQRES 7 C 127 SER LEU LYS MET ASP LYS SER ASP ALA VAL SER HIS THR SEQRES 8 C 127 GLY ASN TYR THR CYS GLU VAL THR GLU LEU THR ARG GLU SEQRES 9 C 127 GLY GLU THR ILE ILE GLU LEU LYS TYR ARG VAL VAL SER SEQRES 10 C 127 TRP SER THR ARG HIS HIS HIS HIS HIS HIS SEQRES 1 D 127 PCA LEU LEU PHE ASN LYS THR LYS SER VAL GLU PHE THR SEQRES 2 D 127 PHE GLY ASN ASP THR VAL VAL ILE PRO CYS PHE VAL THR SEQRES 3 D 127 ASN MET GLU ALA GLN ASN THR THR GLU VAL TYR VAL LYS SEQRES 4 D 127 TRP LYS PHE LYS GLY ARG ASP ILE TYR THR PHE ASP GLY SEQRES 5 D 127 ALA LEU ASN LYS SER THR VAL PRO THR ASP PHE SER SER SEQRES 6 D 127 ALA LYS ILE GLU VAL SER GLN LEU LEU LYS GLY ASP ALA SEQRES 7 D 127 SER LEU LYS MET ASP LYS SER ASP ALA VAL SER HIS THR SEQRES 8 D 127 GLY ASN TYR THR CYS GLU VAL THR GLU LEU THR ARG GLU SEQRES 9 D 127 GLY GLU THR ILE ILE GLU LEU LYS TYR ARG VAL VAL SER SEQRES 10 D 127 TRP SER THR ARG HIS HIS HIS HIS HIS HIS MODRES 2JJS ASN C 16 ASN GLYCOSYLATION SITE MODRES 2JJS ASN C 32 ASN GLYCOSYLATION SITE MODRES 2JJS ASN C 93 ASN GLYCOSYLATION SITE MODRES 2JJS ASN D 16 ASN GLYCOSYLATION SITE MODRES 2JJS ASN D 32 ASN GLYCOSYLATION SITE MODRES 2JJS ASN D 93 ASN GLYCOSYLATION SITE MODRES 2JJS PCA C 1 GLU PYROGLUTAMIC ACID MODRES 2JJS PCA D 1 GLU PYROGLUTAMIC ACID HET PCA C 1 8 HET PCA D 1 8 HET NAG A1117 14 HET IOD A1118 1 HET IOD A1119 1 HET IOD A1120 1 HET IOD A1121 1 HET IOD A1122 1 HET NAG B1120 14 HET IOD B1121 1 HET IOD B1122 1 HET IOD B1123 1 HET IOD B1124 1 HET IOD B1125 1 HET NAG C1117 14 HET NAG C1118 14 HET IOD C1119 1 HET IOD C1120 1 HET IOD C1121 1 HET IOD C1122 1 HET NAG D1117 14 HET NAG D1118 14 HET IOD D1119 1 HET IOD D1120 1 HET IOD D1121 1 HET IOD D1122 1 HETNAM PCA PYROGLUTAMIC ACID HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM IOD IODIDE ION 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 FORMUL 3 PCA 2(C5 H7 N O3) FORMUL 5 NAG 6(C8 H15 N O6) FORMUL 6 IOD 18(I 1-) FORMUL 29 HOH *540(H2 O) HELIX 1 1 PRO A 83 ASP A 85 5 3 HELIX 2 2 PRO B 83 ASP B 85 5 3 HELIX 3 6 VAL C 70 LYS C 75 5 6 HELIX 4 7 LYS C 84 VAL C 88 1 5 HELIX 5 10 VAL D 70 LYS D 75 5 6 HELIX 6 11 LYS D 84 VAL D 88 1 5 SHEET 1 AA 2 VAL A 6 ILE A 7 0 SHEET 2 AA 2 THR A 26 VAL A 27 -1 O THR A 26 N ILE A 7 SHEET 1 AB 5 SER A 12 ALA A 16 0 SHEET 2 AB 5 THR A 109 ARG A 114 1 O GLU A 110 N VAL A 13 SHEET 3 AB 5 GLY A 87 ARG A 95 -1 O GLY A 87 N LEU A 111 SHEET 4 AB 5 ILE A 36 ARG A 40 -1 O GLN A 37 N VAL A 92 SHEET 5 AB 5 GLU A 47 TYR A 50 -1 O GLU A 47 N ARG A 40 SHEET 1 AC 4 SER A 12 ALA A 16 0 SHEET 2 AC 4 THR A 109 ARG A 114 1 O GLU A 110 N VAL A 13 SHEET 3 AC 4 GLY A 87 ARG A 95 -1 O GLY A 87 N LEU A 111 SHEET 4 AC 4 THR A 101 SER A 105 -1 O THR A 101 N ARG A 95 SHEET 1 AD 3 ALA A 21 LEU A 23 0 SHEET 2 AD 3 ILE A 76 ILE A 78 -1 O ILE A 76 N LEU A 23 SHEET 3 AD 3 VAL A 60 THR A 62 -1 O THR A 61 N SER A 77 SHEET 1 BA 2 VAL B 6 ILE B 7 0 SHEET 2 BA 2 THR B 26 VAL B 27 -1 O THR B 26 N ILE B 7 SHEET 1 BB 5 SER B 12 ALA B 16 0 SHEET 2 BB 5 THR B 109 ARG B 114 1 O GLU B 110 N VAL B 13 SHEET 3 BB 5 GLY B 87 ARG B 95 -1 O GLY B 87 N LEU B 111 SHEET 4 BB 5 ILE B 36 ARG B 40 -1 O GLN B 37 N VAL B 92 SHEET 5 BB 5 GLU B 47 TYR B 50 -1 O GLU B 47 N ARG B 40 SHEET 1 BC 4 SER B 12 ALA B 16 0 SHEET 2 BC 4 THR B 109 ARG B 114 1 O GLU B 110 N VAL B 13 SHEET 3 BC 4 GLY B 87 ARG B 95 -1 O GLY B 87 N LEU B 111 SHEET 4 BC 4 THR B 101 SER B 105 -1 O THR B 101 N ARG B 95 SHEET 1 BD 3 ALA B 21 LEU B 23 0 SHEET 2 BD 3 ILE B 76 ILE B 78 -1 O ILE B 76 N LEU B 23 SHEET 3 BD 3 VAL B 60 THR B 62 -1 O THR B 61 N SER B 77 SHEET 1 CA 6 SER C 9 PHE C 12 0 SHEET 2 CA 6 ARG C 103 TYR C 113 1 O GLU C 110 N VAL C 10 SHEET 3 CA 6 GLY C 92 GLU C 100 -1 O GLY C 92 N LEU C 111 SHEET 4 CA 6 VAL C 36 PHE C 42 -1 O TYR C 37 N THR C 99 SHEET 5 CA 6 ARG C 45 ASP C 51 -1 O ARG C 45 N PHE C 42 SHEET 6 CA 6 LYS C 56 THR C 58 -1 O LYS C 56 N ASP C 51 SHEET 1 CB 2 THR C 18 ILE C 21 0 SHEET 2 CB 2 LEU C 80 ASP C 83 -1 O LEU C 80 N ILE C 21 SHEET 1 DA 6 SER D 9 PHE D 12 0 SHEET 2 DA 6 ARG D 103 TYR D 113 1 O GLU D 110 N VAL D 10 SHEET 3 DA 6 GLY D 92 GLU D 100 -1 O GLY D 92 N LEU D 111 SHEET 4 DA 6 VAL D 36 PHE D 42 -1 O TYR D 37 N THR D 99 SHEET 5 DA 6 ARG D 45 ASP D 51 -1 O ARG D 45 N PHE D 42 SHEET 6 DA 6 LYS D 56 THR D 58 -1 O LYS D 56 N ASP D 51 SHEET 1 DB 3 THR D 18 ILE D 21 0 SHEET 2 DB 3 LEU D 80 ASP D 83 -1 O LEU D 80 N ILE D 21 SHEET 3 DB 3 LYS D 67 ILE D 68 -1 O LYS D 67 N LYS D 81 SSBOND 1 CYS A 25 CYS A 91 1555 1555 2.06 SSBOND 2 CYS B 25 CYS B 91 1555 1555 2.07 SSBOND 3 CYS C 23 CYS C 96 1555 1555 2.05 SSBOND 4 CYS D 23 CYS D 96 1555 1555 2.05 LINK C1 NAG A1117 ND2 ASN D 93 1555 1555 1.46 LINK C1 NAG B1120 ND2 ASN C 93 1555 1555 1.45 LINK C PCA C 1 N LEU C 2 1555 1555 1.33 LINK ND2 ASN C 16 C1 NAG C1117 1555 1555 1.45 LINK ND2 ASN C 32 C1 NAG C1118 1555 1555 1.46 LINK C PCA D 1 N LEU D 2 1555 1555 1.33 LINK ND2 ASN D 16 C1 NAG D1117 1555 1555 1.45 LINK ND2 ASN D 32 C1 NAG D1118 1555 1555 1.45 CISPEP 1 ILE A 31 PRO A 32 0 4.52 CISPEP 2 SER A 98 PRO A 99 0 3.54 CISPEP 3 ILE B 31 PRO B 32 0 5.29 CISPEP 4 SER B 98 PRO B 99 0 3.33 CRYST1 42.477 72.410 89.826 90.00 95.01 90.00 P 1 21 1 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 0.023542 0.000000 0.002064 0.00000 SCALE2 0.000000 0.013810 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011175 0.00000