HEADER CELL ADHESION 14-FEB-20 6LYC TITLE CRYSTAL STRUCTURE OF THE NOD SIRPA COMPLEX WITH D4-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIRPA OF THE NOD MOUSE STRAIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: D4-2; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630 KEYWDS COMPLEX, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR Y.MURATA,M.MATSUDA,A.NAKAGAWA,T.MATOZAKI REVDAT 5 29-NOV-23 6LYC 1 REMARK REVDAT 4 05-APR-23 6LYC 1 COMPND SOURCE REMARK DBREF REVDAT 4 2 1 SEQRES HET HETNAM FORMUL REVDAT 4 3 1 SHEET LINK SITE ATOM REVDAT 3 30-SEP-20 6LYC 1 JRNL REVDAT 2 29-JUL-20 6LYC 1 JRNL REMARK LINK REVDAT 1 01-JUL-20 6LYC 0 JRNL AUTH D.HAZAMA,Y.YIN,Y.MURATA,M.MATSUDA,T.OKAMOTO,D.TANAKA, JRNL AUTH 2 N.TERASAKA,J.ZHAO,M.SAKAMOTO,Y.KAKUCHI,Y.SAITO,T.KOTANI, JRNL AUTH 3 Y.NISHIMURA,A.NAKAGAWA,H.SUGA,T.MATOZAKI JRNL TITL MACROCYCLIC PEPTIDE-MEDIATED BLOCKADE OF THE CD47-SIRP ALPHA JRNL TITL 2 INTERACTION AS A POTENTIAL CANCER IMMUNOTHERAPY. JRNL REF CELL CHEM BIOL V. 27 1181 2020 JRNL REFN ESSN 2451-9456 JRNL PMID 32640189 JRNL DOI 10.1016/J.CHEMBIOL.2020.06.008 REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1-3660 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 22158 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 1068 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.7500 - 2.7200 0.95 2705 147 0.1747 0.1845 REMARK 3 2 2.7200 - 2.1600 0.96 2697 133 0.2208 0.2291 REMARK 3 3 2.1600 - 1.8900 0.92 2528 135 0.2168 0.2345 REMARK 3 4 1.8900 - 1.7200 0.92 2547 132 0.2497 0.2895 REMARK 3 5 1.7200 - 1.5900 0.95 2654 123 0.2649 0.2915 REMARK 3 6 1.5900 - 1.5000 0.96 2647 148 0.2629 0.3005 REMARK 3 7 1.5000 - 1.4200 0.97 2659 119 0.2850 0.3034 REMARK 3 8 1.4200 - 1.3600 0.96 2653 131 0.3122 0.3329 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.60 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 1074 REMARK 3 ANGLE : 1.119 1473 REMARK 3 CHIRALITY : 0.100 168 REMARK 3 PLANARITY : 0.009 189 REMARK 3 DIHEDRAL : 19.300 395 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 11.9643 -13.3855 -10.7054 REMARK 3 T TENSOR REMARK 3 T11: 0.1817 T22: 0.2229 REMARK 3 T33: 0.2794 T12: 0.0032 REMARK 3 T13: 0.0066 T23: 0.0622 REMARK 3 L TENSOR REMARK 3 L11: 3.0711 L22: 2.8527 REMARK 3 L33: 3.6714 L12: -0.6565 REMARK 3 L13: 0.1787 L23: 1.1780 REMARK 3 S TENSOR REMARK 3 S11: -0.0624 S12: -0.1153 S13: -0.0470 REMARK 3 S21: 0.0055 S22: 0.1102 S23: -0.0140 REMARK 3 S31: 0.0580 S32: 0.1977 S33: -0.0334 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SF FILE CONTAINS FRIEDEL PAIRS UNDER REMARK 3 I/F_MINUS AND I/F_PLUS COLUMNS. REMARK 4 REMARK 4 6LYC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1300015512. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : DOUBLE MIRRORS, SI(111) DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VERSION JAN 26, 2018 REMARK 200 BUILT=20180808 REMARK 200 DATA SCALING SOFTWARE : AUTOPROC SNAPSHOT_20181127 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22244 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 40.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.39300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.6.04 REMARK 200 STARTING MODEL: 2YZ1 REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS REMARK 200 COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M IMIDAZOLE, 0.1 M MES (PH 6.5), REMARK 280 0.09 M NAF, 0.09 M NABR, 0.09 M NAI, 12.5% MPD (2-METHYL-2,4- REMARK 280 PENTANEDIOL), 12.5% PEG1000, AND 12.5% PEG3350, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 41.48350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.36050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.48350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.36050 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL 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 GLY A 0 REMARK 465 PRO A 1 REMARK 465 LEU A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 ARG A 5 REMARK 465 GLY A 47 REMARK 465 GLN A 48 REMARK 465 SER A 68 REMARK 465 ASP A 69 REMARK 465 ALA A 120 REMARK 465 ALA A 121 REMARK 465 ALA A 122 REMARK 465 SER A 123 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 CH3 ACE B 101 SG CYS B 115 1.77 REMARK 500 OE1 GLU A 14 O HOH A 301 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 215 DISTANCE = 6.82 ANGSTROMS DBREF 6LYC A 0 123 PDB 6LYC 6LYC 0 123 DBREF 6LYC B 101 117 PDB 6LYC 6LYC 101 117 SEQRES 1 A 124 GLY PRO LEU GLY SER ARG THR GLU VAL LYS VAL ILE GLN SEQRES 2 A 124 PRO GLU LYS SER VAL SER VAL ALA ALA GLY ASP SER THR SEQRES 3 A 124 VAL LEU ASN CYS THR LEU THR SER LEU LEU PRO VAL GLY SEQRES 4 A 124 PRO ILE ARG TRP TYR ARG GLY VAL GLY GLN SER ARG GLN SEQRES 5 A 124 LEU ILE TYR SER PHE THR THR GLU HIS PHE PRO ARG VAL SEQRES 6 A 124 THR ASN VAL SER ASP ALA THR LYS ARG SER ASN LEU ASP SEQRES 7 A 124 PHE SER ILE ARG ILE SER ASN VAL THR PRO GLU ASP ALA SEQRES 8 A 124 GLY THR TYR TYR CYS VAL LYS PHE GLN ARG GLY SER PRO SEQRES 9 A 124 ASP THR GLU ILE GLN SER GLY GLY GLY THR GLU VAL TYR SEQRES 10 A 124 VAL LEU ALA ALA ALA ALA SER SEQRES 1 B 17 ACE DTY ARG TYR SER ALA VAL TYR SER ILE HIS PRO SER SEQRES 2 B 17 TRP CYS GLY NH2 HET ACE B 101 3 HET DTY B 102 12 HET NH2 B 117 1 HET ACY A 201 4 HETNAM ACE ACETYL GROUP HETNAM DTY D-TYROSINE HETNAM NH2 AMINO GROUP HETNAM ACY ACETIC ACID FORMUL 2 ACE C2 H4 O FORMUL 2 DTY C9 H11 N O3 FORMUL 2 NH2 H2 N FORMUL 3 ACY C2 H4 O2 FORMUL 4 HOH *70(H2 O) HELIX 1 AA1 PRO A 62 ASN A 66 5 5 HELIX 2 AA2 ARG A 73 ASP A 77 5 5 HELIX 3 AA3 THR A 86 ALA A 90 5 5 SHEET 1 AA1 2 VAL A 10 ILE A 11 0 SHEET 2 AA1 2 THR A 30 LEU A 31 -1 O THR A 30 N ILE A 11 SHEET 1 AA2 4 SER A 16 ALA A 20 0 SHEET 2 AA2 4 THR A 113 LEU A 118 1 O TYR A 116 N VAL A 17 SHEET 3 AA2 4 GLY A 91 GLN A 99 -1 N GLY A 91 O VAL A 115 SHEET 4 AA2 4 THR A 105 SER A 109 -1 O GLN A 108 N LYS A 97 SHEET 1 AA3 6 SER A 16 ALA A 20 0 SHEET 2 AA3 6 THR A 113 LEU A 118 1 O TYR A 116 N VAL A 17 SHEET 3 AA3 6 GLY A 91 GLN A 99 -1 N GLY A 91 O VAL A 115 SHEET 4 AA3 6 ILE A 40 ARG A 44 -1 N ARG A 41 O VAL A 96 SHEET 5 AA3 6 GLN A 51 PHE A 56 -1 O ILE A 53 N TRP A 42 SHEET 6 AA3 6 SER B 113 CYS B 115 -1 O TRP B 114 N SER A 55 SHEET 1 AA4 3 THR A 25 LEU A 27 0 SHEET 2 AA4 3 ILE A 80 ILE A 82 -1 O ILE A 80 N LEU A 27 SHEET 3 AA4 3 TYR B 104 ALA B 106 -1 O SER B 105 N ARG A 81 SSBOND 1 CYS A 29 CYS A 95 1555 1555 1.99 LINK C ACE B 101 N DTY B 102 1555 1555 1.43 LINK C DTY B 102 N ARG B 103 1555 1555 1.33 LINK C GLY B 116 N NH2 B 117 1555 1555 1.34 CISPEP 1 LEU A 35 PRO A 36 0 -3.75 CISPEP 2 SER A 102 PRO A 103 0 -1.23 CRYST1 82.967 30.721 43.482 90.00 100.26 90.00 C 1 2 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 0.012053 0.000000 0.002181 0.00000 SCALE2 0.000000 0.032551 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023371 0.00000