HEADER SIGNALING PROTEIN 27-JUN-21 7R8W TITLE CRYSTAL STRUCTURE OF THE LNK SH2 DOMAIN IN COMPLEX WITH A JAK2 PY813 TITLE 2 PHOSPHOPEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SH2B ADAPTER PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 325-437; COMPND 5 SYNONYM: LYMPHOCYTE ADAPTER PROTEIN,LYMPHOCYTE-SPECIFIC ADAPTER COMPND 6 PROTEIN LNK,SIGNAL TRANSDUCTION PROTEIN LNK; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: JAK2 PY813 PHOSPHOPEPTIDE; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: 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_TAXID: 9606 KEYWDS LNK, SH2B3, JAK/STAT, MPNS, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.MORRIS,N.J.KERSHAW,J.J.BABON REVDAT 5 23-OCT-24 7R8W 1 REMARK REVDAT 4 15-NOV-23 7R8W 1 REMARK REVDAT 3 18-OCT-23 7R8W 1 REMARK REVDAT 2 03-NOV-21 7R8W 1 JRNL REVDAT 1 06-OCT-21 7R8W 0 JRNL AUTH R.MORRIS,Y.ZHANG,J.I.ELLYARD,C.G.VINUESA,J.M.MURPHY, JRNL AUTH 2 A.LAKTYUSHIN,N.J.KERSHAW,J.J.BABON JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF TARGET RECOGNITION BY JRNL TITL 2 THE LYMPHOCYTE ADAPTOR PROTEIN LNK. JRNL REF NAT COMMUN V. 12 6110 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34671038 JRNL DOI 10.1038/S41467-021-26394-6 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 8091 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 811 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 38.5900 - 3.4500 1.00 1239 138 0.1696 0.2115 REMARK 3 2 3.4500 - 2.7400 0.99 1223 137 0.2060 0.2506 REMARK 3 3 2.7400 - 2.3900 1.00 1212 135 0.2404 0.3397 REMARK 3 4 2.3900 - 2.1800 1.00 1205 134 0.2031 0.2544 REMARK 3 5 2.1800 - 2.0200 1.00 1210 134 0.2098 0.3034 REMARK 3 6 2.0200 - 1.9000 0.99 1191 133 0.2277 0.2896 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.66 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 7R8W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000257799. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-17 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 : 8093 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 39.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.03577 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.39200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.840 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: PDB ENTRY 2HDX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CHLORIDE, 20% PEG3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 281.15K 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 18.93750 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6070 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 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 325 CD OE1 NE2 REMARK 470 LYS A 326 CG CD CE NZ REMARK 470 THR A 327 OG1 CG2 REMARK 470 ASP A 328 CG OD1 OD2 REMARK 470 ARG A 345 CD NE CZ NH1 NH2 REMARK 470 ARG A 370 NE CZ NH1 NH2 REMARK 470 ARG A 382 CD NE 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 GLN A 395 CG CD OE1 NE2 REMARK 470 ARG A 397 CD NE CZ NH1 NH2 REMARK 470 HIS A 402 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 411 CD NE CZ NH1 NH2 REMARK 470 ARG A 429 CZ NH1 NH2 REMARK 470 LEU A 437 CG CD1 CD2 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 PRO A 340 57.00 -91.74 REMARK 500 GLN A 399 -109.14 53.00 REMARK 500 CYS A 426 67.92 -104.73 REMARK 500 SER A 431 -105.88 -110.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7R8X RELATED DB: PDB DBREF 7R8W A 325 437 UNP O09039 SH2B3_MOUSE 325 437 DBREF 7R8W B 5 9 PDB 7R8W 7R8W 5 9 SEQRES 1 A 113 GLN LYS THR ASP HIS PHE LEU SER CYS TYR PRO TRP PHE SEQRES 2 A 113 HIS GLY PRO ILE SER ARG VAL ARG ALA ALA GLN LEU VAL SEQRES 3 A 113 GLN LEU GLN GLY PRO ASP ALA HIS GLY VAL PHE LEU VAL SEQRES 4 A 113 ARG GLN SER GLU SER ARG ARG GLY GLU TYR VAL LEU THR SEQRES 5 A 113 PHE ASN LEU GLN GLY ARG ALA LYS HIS LEU ARG LEU VAL SEQRES 6 A 113 LEU THR GLU ARG GLY GLN CYS ARG VAL GLN HIS LEU HIS SEQRES 7 A 113 PHE PRO SER VAL VAL ASP MET LEU ARG HIS PHE GLN ARG SEQRES 8 A 113 SER PRO ILE PRO LEU GLU CYS GLY ALA ALA CYS ASP VAL SEQRES 9 A 113 ARG LEU SER GLY TYR VAL VAL VAL LEU SEQRES 1 B 5 PTR GLU LEU LEU THR HET PTR B 5 16 HETNAM PTR O-PHOSPHOTYROSINE HETSYN PTR PHOSPHONOTYROSINE FORMUL 2 PTR C9 H12 N O6 P FORMUL 3 HOH *25(H2 O) HELIX 1 AA1 LYS A 326 SER A 332 1 7 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 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 PHE A 403 N CYS A 396 SSBOND 1 CYS A 422 CYS A 426 1555 1555 2.04 LINK C PTR B 5 N GLU B 6 1555 1555 1.32 CRYST1 35.060 37.875 38.883 90.00 97.02 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 0.028523 0.000000 0.003514 0.00000 SCALE2 0.000000 0.026403 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025913 0.00000 TER 851 LEU A 437 HETATM 852 N PTR B 5 43.393 9.495 1.844 1.00 52.92 N HETATM 853 CA PTR B 5 43.265 8.043 2.127 1.00 45.81 C HETATM 854 C PTR B 5 44.180 7.283 1.181 1.00 48.44 C HETATM 855 O PTR B 5 44.084 7.492 -0.029 1.00 56.78 O HETATM 856 CB PTR B 5 41.821 7.573 2.037 1.00 43.70 C HETATM 857 CG PTR B 5 40.991 7.833 3.263 1.00 43.90 C HETATM 858 CD1 PTR B 5 39.753 8.444 3.159 1.00 49.78 C HETATM 859 CD2 PTR B 5 41.431 7.445 4.514 1.00 35.18 C HETATM 860 CE1 PTR B 5 38.974 8.691 4.274 1.00 48.18 C HETATM 861 CE2 PTR B 5 40.674 7.672 5.647 1.00 35.79 C HETATM 862 CZ PTR B 5 39.445 8.289 5.508 1.00 44.03 C HETATM 863 OH PTR B 5 38.678 8.546 6.637 1.00 43.15 O HETATM 864 P PTR B 5 38.903 9.812 7.541 1.00 40.99 P HETATM 865 O1P PTR B 5 38.341 11.030 6.892 1.00 42.32 O HETATM 866 O2P PTR B 5 40.367 10.006 7.740 1.00 36.58 O HETATM 867 O3P PTR B 5 38.248 9.585 8.857 1.00 35.91 O TER 900 THR B 9 HETATM 901 O HOH A 501 42.792 6.423 24.330 1.00 46.76 O HETATM 902 O HOH A 502 54.943 -1.179 1.894 1.00 46.53 O HETATM 903 O HOH A 503 29.502 2.728 5.390 1.00 44.21 O HETATM 904 O HOH A 504 45.374 14.551 6.537 1.00 52.28 O HETATM 905 O HOH A 505 58.716 0.507 15.250 1.00 38.59 O HETATM 906 O HOH A 506 62.221 3.750 11.796 1.00 38.82 O HETATM 907 O HOH A 507 41.875 7.294 21.728 1.00 35.01 O HETATM 908 O HOH A 508 55.693 -6.899 12.274 1.00 36.03 O HETATM 909 O HOH A 509 38.733 -0.726 22.202 1.00 39.38 O HETATM 910 O HOH A 510 47.012 8.656 4.296 1.00 36.31 O HETATM 911 O HOH A 511 51.162 7.269 21.223 1.00 40.96 O HETATM 912 O HOH A 512 53.951 6.848 18.222 1.00 27.35 O HETATM 913 O HOH A 513 32.248 -0.880 7.013 1.00 41.44 O HETATM 914 O HOH A 514 47.276 12.732 8.654 1.00 35.68 O HETATM 915 O HOH A 515 39.150 12.941 18.222 1.00 38.71 O HETATM 916 O HOH A 516 45.704 15.259 18.621 1.00 34.07 O HETATM 917 O HOH A 517 40.517 15.541 11.648 1.00 41.96 O HETATM 918 O HOH A 518 50.258 16.343 13.474 1.00 38.52 O HETATM 919 O HOH A 519 49.459 12.352 20.394 1.00 40.03 O HETATM 920 O HOH A 520 36.239 -8.331 12.065 1.00 42.27 O HETATM 921 O HOH A 521 56.773 9.003 5.329 1.00 43.74 O HETATM 922 O HOH A 522 50.127 2.819 23.617 1.00 33.86 O HETATM 923 O HOH A 523 46.486 12.896 19.681 1.00 38.73 O HETATM 924 O HOH A 524 41.454 16.346 9.320 1.00 46.74 O HETATM 925 O HOH B 101 42.217 3.869 1.510 1.00 40.32 O CONECT 751 771 CONECT 771 751 CONECT 852 853 CONECT 853 852 854 856 CONECT 854 853 855 868 CONECT 855 854 CONECT 856 853 857 CONECT 857 856 858 859 CONECT 858 857 860 CONECT 859 857 861 CONECT 860 858 862 CONECT 861 859 862 CONECT 862 860 861 863 CONECT 863 862 864 CONECT 864 863 865 866 867 CONECT 865 864 CONECT 866 864 CONECT 867 864 CONECT 868 854 MASTER 234 0 1 4 5 0 0 6 923 2 19 10 END