HEADER SIGNALING PROTEIN 03-APR-23 8IXV TITLE CRYSTAL STRUCTURE OF INTRACELLULAR B30.2 DOMAIN OF BTN3A IN COMPLEX TITLE 2 WITH 2CL-HMBPP COMPND MOL_ID: 1; COMPND 2 MOLECULE: BUTYROPHILIN SUBFAMILY 3 MEMBER A1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 328-513; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BTN3A1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BUTYROPHILIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.Y.YANG,S.M.YI,J.W.HUANG,C.C.CHEN,R.T.GUO REVDAT 4 18-OCT-23 8IXV 1 JRNL REVDAT 3 11-OCT-23 8IXV 1 JRNL REVDAT 2 20-SEP-23 8IXV 1 JRNL REVDAT 1 13-SEP-23 8IXV 0 JRNL AUTH L.YUAN,X.MA,Y.YANG,Y.QU,X.LI,X.ZHU,W.MA,J.DUAN,J.XUE,H.YANG, JRNL AUTH 2 J.W.HUANG,S.YI,M.ZHANG,N.CAI,L.ZHANG,Q.DING,K.LAI,C.LIU, JRNL AUTH 3 L.ZHANG,X.LIU,Y.YAO,S.ZHOU,X.LI,P.SHEN,Q.CHANG,S.R.MALWAL, JRNL AUTH 4 Y.HE,W.LI,C.CHEN,C.C.CHEN,E.OLDFIELD,R.T.GUO,Y.ZHANG JRNL TITL PHOSPHOANTIGENS GLUE BUTYROPHILIN 3A1 AND 2A1 TO ACTIVATE V JRNL TITL 2 GAMMA 9V DELTA 2 T CELLS. JRNL REF NATURE V. 621 840 2023 JRNL REFN ESSN 1476-4687 JRNL PMID 37674084 JRNL DOI 10.1038/S41586-023-06525-3 REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 23139 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1144 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 32.2100 - 3.4400 0.91 2711 116 0.1860 0.2302 REMARK 3 2 3.4400 - 2.7300 1.00 2800 156 0.1850 0.2150 REMARK 3 3 2.7300 - 2.3900 1.00 2761 152 0.2087 0.2605 REMARK 3 4 2.3800 - 2.1700 1.00 2779 135 0.2039 0.2587 REMARK 3 5 2.1700 - 2.0100 1.00 2733 163 0.2108 0.2646 REMARK 3 6 2.0100 - 1.8900 1.00 2749 143 0.2074 0.2324 REMARK 3 7 1.8900 - 1.8000 1.00 2722 152 0.2327 0.2694 REMARK 3 8 1.8000 - 1.7200 1.00 2740 127 0.2726 0.3440 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.211 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.235 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.12 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 : 0.007 1585 REMARK 3 ANGLE : 1.101 2155 REMARK 3 CHIRALITY : 0.069 228 REMARK 3 PLANARITY : 0.008 274 REMARK 3 DIHEDRAL : 10.418 213 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 8IXV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-APR-23. REMARK 100 THE DEPOSITION ID IS D_1300036735. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : LIQUID ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER METALJET REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.34 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON III REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23485 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 45.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 8.460 REMARK 200 R MERGE (I) : 0.04820 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.9600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.21790 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CALCIUM ACETATE HYDRATE, REMARK 280 PEG8000,SODIUM CITRATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K 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 22.88700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.70250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.97200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.70250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.88700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.97200 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL 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 MET A 296 REMARK 465 LEU A 484 REMARK 465 GLU A 485 REMARK 465 HIS A 486 REMARK 465 HIS A 487 REMARK 465 HIS A 488 REMARK 465 HIS A 489 REMARK 465 HIS A 490 REMARK 465 HIS A 491 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 601 O HOH A 787 2.01 REMARK 500 NZ LYS A 375 O HOH A 601 2.09 REMARK 500 O HOH A 658 O HOH A 711 2.13 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 ASP A 343 54.21 -98.26 REMARK 500 TRP A 350 -60.25 -126.05 REMARK 500 TRP A 377 148.11 -176.85 REMARK 500 ASN A 409 12.63 -145.83 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 A 864 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A 865 DISTANCE = 6.64 ANGSTROMS DBREF 8IXV A 298 483 UNP O00481 BT3A1_HUMAN 328 513 SEQADV 8IXV MET A 296 UNP O00481 EXPRESSION TAG SEQADV 8IXV GLY A 297 UNP O00481 EXPRESSION TAG SEQADV 8IXV LEU A 484 UNP O00481 EXPRESSION TAG SEQADV 8IXV GLU A 485 UNP O00481 EXPRESSION TAG SEQADV 8IXV HIS A 486 UNP O00481 EXPRESSION TAG SEQADV 8IXV HIS A 487 UNP O00481 EXPRESSION TAG SEQADV 8IXV HIS A 488 UNP O00481 EXPRESSION TAG SEQADV 8IXV HIS A 489 UNP O00481 EXPRESSION TAG SEQADV 8IXV HIS A 490 UNP O00481 EXPRESSION TAG SEQADV 8IXV HIS A 491 UNP O00481 EXPRESSION TAG SEQRES 1 A 196 MET GLY ALA TYR ASN GLU TRP LYS LYS ALA LEU PHE LYS SEQRES 2 A 196 PRO ALA ASP VAL ILE LEU ASP PRO LYS THR ALA ASN PRO SEQRES 3 A 196 ILE LEU LEU VAL SER GLU ASP GLN ARG SER VAL GLN ARG SEQRES 4 A 196 ALA LYS GLU PRO GLN ASP LEU PRO ASP ASN PRO GLU ARG SEQRES 5 A 196 PHE ASN TRP HIS TYR CYS VAL LEU GLY CYS GLU SER PHE SEQRES 6 A 196 ILE SER GLY ARG HIS TYR TRP GLU VAL GLU VAL GLY ASP SEQRES 7 A 196 ARG LYS GLU TRP HIS ILE GLY VAL CYS SER LYS ASN VAL SEQRES 8 A 196 GLN ARG LYS GLY TRP VAL LYS MET THR PRO GLU ASN GLY SEQRES 9 A 196 PHE TRP THR MET GLY LEU THR ASP GLY ASN LYS TYR ARG SEQRES 10 A 196 THR LEU THR GLU PRO ARG THR ASN LEU LYS LEU PRO LYS SEQRES 11 A 196 PRO PRO LYS LYS VAL GLY VAL PHE LEU ASP TYR GLU THR SEQRES 12 A 196 GLY ASP ILE SER PHE TYR ASN ALA VAL ASP GLY SER HIS SEQRES 13 A 196 ILE HIS THR PHE LEU ASP VAL SER PHE SER GLU ALA LEU SEQRES 14 A 196 TYR PRO VAL PHE ARG ILE LEU THR LEU GLU PRO THR ALA SEQRES 15 A 196 LEU THR ILE CYS PRO ALA LEU GLU HIS HIS HIS HIS HIS SEQRES 16 A 196 HIS HET PEG A 501 7 HET EDO A 502 4 HET RZO A 503 17 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM EDO 1,2-ETHANEDIOL HETNAM RZO [BIS(CHLORANYL)-[[(E)-3-METHYL-4-OXIDANYL-BUT-2-ENOXY]- HETNAM 2 RZO OXIDANYL-PHOSPHORYL]METHYL]PHOSPHONIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 2 PEG C4 H10 O3 FORMUL 3 EDO C2 H6 O2 FORMUL 4 RZO C6 H12 CL2 O7 P2 FORMUL 5 HOH *265(H2 O) HELIX 1 AA1 GLY A 297 PHE A 307 1 11 HELIX 2 AA2 ASP A 315 ALA A 319 5 5 HELIX 3 AA3 THR A 395 ASN A 398 5 4 SHEET 1 AA1 5 LYS A 308 PRO A 309 0 SHEET 2 AA1 5 ARG A 364 GLU A 370 1 O ARG A 364 N LYS A 308 SHEET 3 AA1 5 LEU A 478 ILE A 480 -1 O THR A 479 N GLU A 370 SHEET 4 AA1 5 SER A 331 ARG A 334 -1 N VAL A 332 O LEU A 478 SHEET 5 AA1 5 LEU A 323 VAL A 325 -1 N LEU A 324 O GLN A 333 SHEET 1 AA2 5 LYS A 308 PRO A 309 0 SHEET 2 AA2 5 ARG A 364 GLU A 370 1 O ARG A 364 N LYS A 308 SHEET 3 AA2 5 LYS A 429 ASP A 435 -1 O LEU A 434 N HIS A 365 SHEET 4 AA2 5 ASP A 440 ASN A 445 -1 O TYR A 444 N GLY A 431 SHEET 5 AA2 5 HIS A 451 PHE A 455 -1 O PHE A 455 N ILE A 441 SHEET 1 AA3 6 CYS A 353 LEU A 355 0 SHEET 2 AA3 6 LEU A 464 ARG A 469 -1 O PHE A 468 N VAL A 354 SHEET 3 AA3 6 TRP A 377 SER A 383 -1 N CYS A 382 O TYR A 465 SHEET 4 AA3 6 PHE A 400 THR A 406 -1 O TRP A 401 N VAL A 381 SHEET 5 AA3 6 LYS A 410 THR A 413 -1 O ARG A 412 N GLY A 404 SHEET 6 AA3 6 THR A 419 ASN A 420 -1 O THR A 419 N THR A 413 CISPEP 1 GLU A 416 PRO A 417 0 -7.25 CRYST1 45.774 61.944 75.405 90.00 90.00 90.00 P 21 21 21 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 0.021846 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016144 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013262 0.00000