HEADER SIGNALING PROTEIN 09-APR-19 6OIL TITLE CRYSTAL STRUCTURE OF HUMAN VISTA EXTRACELLULAR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: V-TYPE IMMUNOGLOBULIN DOMAIN-CONTAINING SUPPRESSOR OF T- COMPND 3 CELL ACTIVATION; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: PLATELET RECEPTOR GI24,STRESS-INDUCED SECRETED PROTEIN-1, COMPND 6 SISP-1,V-SET DOMAIN-CONTAINING IMMUNOREGULATORY RECEPTOR,V-SET COMPND 7 IMMUNOREGULATORY RECEPTOR; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: VSIR; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: EXPI293 SYSTEM KEYWDS T CELL ACTIVATION, TRANSMEMBRANE, SUPPRESSOR, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.MEHTA,J.R.COCHRAN,I.I.MATHEWS REVDAT 6 03-APR-24 6OIL 1 HETSYN REVDAT 5 29-JUL-20 6OIL 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 04-DEC-19 6OIL 1 REMARK REVDAT 3 13-NOV-19 6OIL 1 JRNL REVDAT 2 18-SEP-19 6OIL 1 TITLE REVDAT 1 11-SEP-19 6OIL 0 JRNL AUTH N.MEHTA,S.MADDINENI,I.I.MATHEWS,R.ANDRES PARRA SPERBERG, JRNL AUTH 2 P.S.HUANG,J.R.COCHRAN JRNL TITL STRUCTURE AND FUNCTIONAL BINDING EPITOPE OF V-DOMAIN IG JRNL TITL 2 SUPPRESSOR OF T CELL ACTIVATION. JRNL REF CELL REP V. 28 2509 2019 JRNL REFN ESSN 2211-1247 JRNL PMID 31484064 JRNL DOI 10.1016/J.CELREP.2019.07.073 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 11694 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 605 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 29.1594 - 2.9360 0.98 2800 138 0.1613 0.1998 REMARK 3 2 2.9360 - 2.3307 0.99 2778 172 0.2016 0.2393 REMARK 3 3 2.3307 - 2.0362 0.99 2767 149 0.1896 0.2505 REMARK 3 4 2.0362 - 1.8500 0.98 2744 146 0.2258 0.2637 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.26 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 1:151) REMARK 3 ORIGIN FOR THE GROUP (A): 16.8608 33.6278 30.9665 REMARK 3 T TENSOR REMARK 3 T11: 0.1694 T22: 0.1458 REMARK 3 T33: 0.1519 T12: 0.0030 REMARK 3 T13: 0.0082 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 1.6248 L22: 0.8509 REMARK 3 L33: 1.4671 L12: 0.2335 REMARK 3 L13: 0.4678 L23: -0.3127 REMARK 3 S TENSOR REMARK 3 S11: 0.0095 S12: -0.0895 S13: -0.0509 REMARK 3 S21: -0.0106 S22: 0.0006 S23: -0.0878 REMARK 3 S31: -0.2116 S32: -0.0507 S33: 0.0002 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6OIL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-APR-19. REMARK 100 THE DEPOSITION ID IS D_1000239767. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JAN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5-8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : SI(111) MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11704 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 29.156 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 9.222 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 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) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 8.44 REMARK 200 R MERGE FOR SHELL (I) : 1.46700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.460 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: ROSETTA GENERATED MODELS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG3350, 0.075M NABR, 0.05M HAT REMARK 280 BUFFER(COMBINATION OF HEPES (7.5), ADA (6.5), AND TRISHCL (8.0)), REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 32.04450 REMARK 290 SMTRY3 2 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 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 ASP A 29 REMARK 465 LYS A 30 REMARK 465 GLY A 31 REMARK 465 SER A 152 REMARK 465 SER A 153 REMARK 465 GLN A 154 REMARK 465 GLU A 155 REMARK 465 SER A 156 REMARK 465 GLU A 157 REMARK 465 GLN A 158 REMARK 465 ILE A 159 REMARK 465 THR A 160 REMARK 465 ALA A 161 REMARK 465 ALA A 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 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 GLN A 63 CD OE1 NE2 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 O HOH A 339 O HOH A 340 2.19 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 SER A 43 -149.87 -156.20 REMARK 500 REMARK 500 REMARK: NULL DBREF 6OIL A 1 162 UNP Q9H7M9 VISTA_HUMAN 33 194 SEQADV 6OIL GLN A 59 UNP Q9H7M9 ASN 91 ENGINEERED MUTATION SEQADV 6OIL GLN A 76 UNP Q9H7M9 ASN 108 ENGINEERED MUTATION SEQADV 6OIL GLU A 155 UNP Q9H7M9 ASP 187 ENGINEERED MUTATION SEQADV 6OIL GLN A 158 UNP Q9H7M9 ASN 190 ENGINEERED MUTATION SEQADV 6OIL HIS A 163 UNP Q9H7M9 EXPRESSION TAG SEQADV 6OIL HIS A 164 UNP Q9H7M9 EXPRESSION TAG SEQADV 6OIL HIS A 165 UNP Q9H7M9 EXPRESSION TAG SEQADV 6OIL HIS A 166 UNP Q9H7M9 EXPRESSION TAG SEQADV 6OIL HIS A 167 UNP Q9H7M9 EXPRESSION TAG SEQADV 6OIL HIS A 168 UNP Q9H7M9 EXPRESSION TAG SEQRES 1 A 168 PHE LYS VAL ALA THR PRO TYR SER LEU TYR VAL CYS PRO SEQRES 2 A 168 GLU GLY GLN ASN VAL THR LEU THR CYS ARG LEU LEU GLY SEQRES 3 A 168 PRO VAL ASP LYS GLY HIS ASP VAL THR PHE TYR LYS THR SEQRES 4 A 168 TRP TYR ARG SER SER ARG GLY GLU VAL GLN THR CYS SER SEQRES 5 A 168 GLU ARG ARG PRO ILE ARG GLN LEU THR PHE GLN ASP LEU SEQRES 6 A 168 HIS LEU HIS HIS GLY GLY HIS GLN ALA ALA GLN THR SER SEQRES 7 A 168 HIS ASP LEU ALA GLN ARG HIS GLY LEU GLU SER ALA SER SEQRES 8 A 168 ASP HIS HIS GLY ASN PHE SER ILE THR MET ARG ASN LEU SEQRES 9 A 168 THR LEU LEU ASP SER GLY LEU TYR CYS CYS LEU VAL VAL SEQRES 10 A 168 GLU ILE ARG HIS HIS HIS SER GLU HIS ARG VAL HIS GLY SEQRES 11 A 168 ALA MET GLU LEU GLN VAL GLN THR GLY LYS ASP ALA PRO SEQRES 12 A 168 SER ASN CYS VAL VAL TYR PRO SER SER SER GLN GLU SER SEQRES 13 A 168 GLU GLN ILE THR ALA ALA HIS HIS HIS HIS HIS HIS HET NAG A 201 14 HET NAG A 202 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 2 NAG 2(C8 H15 N O6) FORMUL 4 HOH *41(H2 O) HELIX 1 AA1 THR A 61 HIS A 66 1 6 HELIX 2 AA2 SER A 78 GLY A 86 1 9 HELIX 3 AA3 THR A 105 SER A 109 5 5 SHEET 1 AA1 5 LYS A 2 ALA A 4 0 SHEET 2 AA1 5 VAL A 18 LEU A 25 -1 O ARG A 23 N ALA A 4 SHEET 3 AA1 5 ASN A 96 MET A 101 -1 O MET A 101 N VAL A 18 SHEET 4 AA1 5 LEU A 87 SER A 91 -1 N GLU A 88 O THR A 100 SHEET 5 AA1 5 ALA A 75 GLN A 76 -1 N ALA A 75 O SER A 91 SHEET 1 AA2 6 LEU A 67 GLY A 70 0 SHEET 2 AA2 6 THR A 35 SER A 43 -1 N PHE A 36 O HIS A 69 SHEET 3 AA2 6 GLY A 110 ARG A 120 -1 O CYS A 113 N TYR A 41 SHEET 4 AA2 6 HIS A 123 GLN A 137 -1 O MET A 132 N TYR A 112 SHEET 5 AA2 6 TYR A 7 PRO A 13 1 N TYR A 10 O GLN A 135 SHEET 6 AA2 6 VAL A 147 PRO A 150 -1 O VAL A 147 N VAL A 11 SSBOND 1 CYS A 12 CYS A 146 1555 1555 2.06 SSBOND 2 CYS A 22 CYS A 114 1555 1555 2.03 SSBOND 3 CYS A 51 CYS A 113 1555 1555 2.04 LINK ND2 ASN A 17 C1 NAG A 201 1555 1555 1.44 LINK ND2 ASN A 103 C1 NAG A 202 1555 1555 1.44 CRYST1 29.169 64.089 37.695 90.00 91.73 90.00 P 1 21 1 2 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 0.034283 0.000000 0.001034 0.00000 SCALE2 0.000000 0.015603 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026541 0.00000