HEADER SIGNALING PROTEIN 24-MAY-22 8CZ9 TITLE CRYSTAL STRUCTURE OF THE E372K LNK SH2 DOMAIN MUTANT IN COMPLEX WITH A TITLE 2 JAK2 PY813 PHOSPHOPEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SH2B ADAPTER PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LYMPHOCYTE ADAPTER PROTEIN,LYMPHOCYTE-SPECIFIC ADAPTER COMPND 5 PROTEIN LNK,SIGNAL TRANSDUCTION PROTEIN LNK; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: JAK2 PY813 PHOSPHOPEPTIDE; COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: SH2B3, LNK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS LNK, SH2B3, JAK/STAT, MPNS, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.MORRIS,N.J.KERSHAW,J.J.BABON REVDAT 4 13-MAR-24 8CZ9 1 JRNL REVDAT 3 15-NOV-23 8CZ9 1 REMARK REVDAT 2 25-OCT-23 8CZ9 1 REMARK REVDAT 1 31-MAY-23 8CZ9 0 JRNL AUTH Y.ZHANG,R.MORRIS,G.J.BROWN,A.M.D.LORENZO,X.MENG,N.J.KERSHAW, JRNL AUTH 2 P.KIRIDENA,G.BURGIO,S.GROSS,J.Y.CAPPELLO,Q.SHEN,H.WANG, JRNL AUTH 3 C.TURNBULL,T.LEA-HENRY,M.STANLEY,Z.YU,F.D.BALLARD,A.CHUAH, JRNL AUTH 4 J.C.LEE,A.M.HATCH,A.ENDERS,S.L.MASTERS,A.P.HEADLEY,P.TRNKA, JRNL AUTH 5 D.MALLON,J.T.FLETCHER,G.D.WALTERS,M.SESTAN,M.JELUSIC, JRNL AUTH 6 M.C.COOK,V.ATHANASOPOULOS,D.A.FULCHER,J.J.BABON,C.G.VINUESA, JRNL AUTH 7 J.I.ELLYARD JRNL TITL RARE SH2B3 CODING VARIANTS IN LUPUS PATIENTS IMPAIR B CELL JRNL TITL 2 TOLERANCE AND PREDISPOSE TO AUTOIMMUNITY. JRNL REF J.EXP.MED. V. 221 2024 JRNL REFN ESSN 1540-9538 JRNL PMID 38417019 JRNL DOI 10.1084/JEM.20221080 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 16335 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1633 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 35.9000 - 3.7700 0.99 1277 141 0.1582 0.1931 REMARK 3 2 3.7700 - 2.9900 1.00 1249 139 0.1775 0.1939 REMARK 3 3 2.9900 - 2.6200 0.99 1242 138 0.1973 0.2252 REMARK 3 4 2.6100 - 2.3800 1.00 1234 137 0.2076 0.2253 REMARK 3 5 2.3800 - 2.2100 0.99 1213 135 0.1877 0.2248 REMARK 3 6 2.2100 - 2.0800 0.99 1229 136 0.1994 0.2135 REMARK 3 7 2.0800 - 1.9700 0.99 1226 136 0.1846 0.2146 REMARK 3 8 1.9700 - 1.8900 0.99 1214 136 0.1934 0.2981 REMARK 3 9 1.8900 - 1.8100 0.99 1222 136 0.2275 0.2756 REMARK 3 10 1.8100 - 1.7500 0.98 1191 131 0.2523 0.3286 REMARK 3 11 1.7500 - 1.7000 0.99 1198 133 0.2364 0.2685 REMARK 3 12 1.7000 - 1.6500 0.97 1207 135 0.2336 0.2727 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.73 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 : 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 8CZ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000265015. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95373 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 111266 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 35.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.490 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: 7R8W 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: 18% PEG 8000, 0.05 M MGAC , 0.1 M TRIS REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281.15K 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 37.91450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.80900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 37.91450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.80900 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: 1410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 616 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 651 LIES ON A SPECIAL POSITION. 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 328 REMARK 465 HIS A 329 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 PHE A 330 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 370 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 382 NE CZ NH1 NH2 REMARK 470 ARG A 387 CZ NH1 NH2 REMARK 470 GLU A 392 CG CD OE1 OE2 REMARK 470 ARG A 393 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 411 CZ NH1 NH2 REMARK 470 ARG A 415 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 421 CD OE1 OE2 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 OE1 GLU A 367 O HOH A 601 2.04 REMARK 500 O HOH C 906 O HOH C 911 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 GLN A 399 -113.74 56.19 REMARK 500 SER A 431 -106.48 -116.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7R8X RELATED DB: PDB REMARK 900 RELATED ID: 7R8W RELATED DB: PDB DBREF 8CZ9 A 328 437 UNP P50745 SH2B3_RAT 111 220 DBREF 8CZ9 C 811 818 PDB 8CZ9 8CZ9 811 818 SEQADV 8CZ9 LYS A 372 UNP P50745 GLU 155 ENGINEERED MUTATION SEQRES 1 A 110 ASP HIS PHE LEU SER CYS TYR PRO TRP PHE HIS GLY PRO SEQRES 2 A 110 ILE SER ARG VAL ARG ALA ALA GLN LEU VAL GLN LEU GLN SEQRES 3 A 110 GLY PRO ASP ALA HIS GLY VAL PHE LEU VAL ARG GLN SER SEQRES 4 A 110 GLU SER ARG ARG GLY LYS TYR VAL LEU THR PHE ASN LEU SEQRES 5 A 110 GLN GLY ARG ALA LYS HIS LEU ARG LEU VAL LEU THR GLU SEQRES 6 A 110 ARG GLY GLN CYS ARG VAL GLN HIS LEU HIS PHE PRO SER SEQRES 7 A 110 VAL VAL ASP MET LEU ARG HIS PHE GLN ARG SER PRO ILE SEQRES 8 A 110 PRO LEU GLU CYS GLY ALA ALA CYS ASP VAL ARG LEU SER SEQRES 9 A 110 GLY TYR VAL VAL VAL VAL SEQRES 1 C 8 PRO ASP PTR GLU LEU LEU THR GLU HET PTR C 813 16 HET CL A 501 1 HETNAM PTR O-PHOSPHOTYROSINE HETNAM CL CHLORIDE ION HETSYN PTR PHOSPHONOTYROSINE FORMUL 2 PTR C9 H12 N O6 P FORMUL 3 CL CL 1- FORMUL 4 HOH *76(H2 O) HELIX 1 AA1 PHE A 330 TYR A 334 5 5 HELIX 2 AA2 SER A 342 LEU A 352 1 11 HELIX 3 AA3 GLN A 353 HIS A 358 5 6 HELIX 4 AA4 SER A 405 SER A 416 1 12 HELIX 5 AA5 CYS A 422 ASP A 427 5 6 SHEET 1 AA1 5 PHE A 361 GLN A 365 0 SHEET 2 AA1 5 TYR A 373 LEU A 379 -1 O VAL A 374 N ARG A 364 SHEET 3 AA1 5 ARG A 382 LEU A 390 -1 O ARG A 382 N LEU A 379 SHEET 4 AA1 5 CYS A 396 VAL A 398 -1 O ARG A 397 N VAL A 389 SHEET 5 AA1 5 LEU A 401 PHE A 403 -1 O LEU A 401 N VAL A 398 SSBOND 1 CYS A 422 CYS A 426 1555 1555 2.03 LINK C ASP C 812 N PTR C 813 1555 1555 1.32 LINK C PTR C 813 N GLU C 814 1555 1555 1.32 CRYST1 75.829 37.618 50.497 90.00 108.76 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 0.013188 0.000000 0.004480 0.00000 SCALE2 0.000000 0.026583 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020915 0.00000