HEADER PROTEIN BINDING 23-SEP-23 8WHJ TITLE CRYSTAL STRUCTURE OF CLASP2 TOG4 FUSED WITH LL5BETA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLIP-ASSOCIATING PROTEIN 2,PLECKSTRIN HOMOLOGY-LIKE DOMAIN COMPND 3 FAMILY B MEMBER 2; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: CYTOPLASMIC LINKER-ASSOCIATED PROTEIN 2,PROTEIN ORBIT COMPND 6 HOMOLOG 2,HORBIT2,PROTEIN LL5-BETA; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: AUTHOR STATED: A FRAGMENT OF LL5BETA HAS BEEN LINKED COMPND 9 TO THE C-TERMINAL DOMAIN OF CLASP2, WITH A THROMBIN CLEAVAGE SITE COMPND 10 (SLVPRGSG) SERVING AS THE CONNECTING SEQUENCE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CLASP2, KIAA0627, PHLDB2, LL5B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COMPLEX, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR X.JIA,Z.WEI REVDAT 1 28-AUG-24 8WHJ 0 JRNL AUTH X.JIA,L.LIN,S.GUO,L.ZHOU,G.JIN,J.DONG,J.XIAO,X.XIE,Y.LI, JRNL AUTH 2 S.HE,Z.WEI,C.YU JRNL TITL CLASP-MEDIATED COMPETITIVE BINDING IN PROTEIN CONDENSATES JRNL TITL 2 DIRECTS MICROTUBULE GROWTH. JRNL REF NAT COMMUN V. 15 6509 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 39095354 JRNL DOI 10.1038/S41467-024-50863-3 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 49212 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.129 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1993 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 25.5660 - 3.3717 1.00 3411 148 0.1368 0.1719 REMARK 3 2 3.3717 - 2.6772 1.00 3389 146 0.1430 0.1931 REMARK 3 3 2.6772 - 2.3390 1.00 3382 143 0.1360 0.1730 REMARK 3 4 2.3390 - 2.1253 1.00 3396 144 0.1241 0.1640 REMARK 3 5 2.1253 - 1.9730 1.00 3383 139 0.1182 0.1562 REMARK 3 6 1.9730 - 1.8567 1.00 3382 147 0.1209 0.1798 REMARK 3 7 1.8567 - 1.7637 1.00 3343 140 0.1159 0.1657 REMARK 3 8 1.7637 - 1.6870 1.00 3408 142 0.1078 0.1449 REMARK 3 9 1.6870 - 1.6221 1.00 3381 139 0.1052 0.1770 REMARK 3 10 1.6221 - 1.5661 0.99 3349 139 0.1067 0.1605 REMARK 3 11 1.5661 - 1.5171 1.00 3377 146 0.1104 0.1679 REMARK 3 12 1.5171 - 1.4738 1.00 3339 141 0.1155 0.1751 REMARK 3 13 1.4738 - 1.4350 1.00 3375 139 0.1376 0.1731 REMARK 3 14 1.4350 - 1.4000 0.99 3304 140 0.1648 0.2465 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 2043 REMARK 3 ANGLE : 1.172 2765 REMARK 3 CHIRALITY : 0.073 327 REMARK 3 PLANARITY : 0.006 350 REMARK 3 DIHEDRAL : 12.649 816 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 8WHJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 28-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1300041314. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-19 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49279 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : 0.82200 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 (%): 42.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 0.1 M BIS-TRIS REMARK 280 PH 5.5, AND 25% W/V PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 48.96750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.48375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 73.45125 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: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 GLY A 1245 REMARK 465 PRO A 1246 REMARK 465 GLY A 1247 REMARK 465 SER A 1248 REMARK 465 GLU A 1249 REMARK 465 PHE A 1250 REMARK 465 SER A 1251 REMARK 465 LEU A 1252 REMARK 465 ASP A 1253 REMARK 465 HIS A 1254 REMARK 465 SER A 1255 REMARK 465 SER A 1709 REMARK 465 GLY A 1710 REMARK 465 SER A 1711 REMARK 465 LEU A 1712 REMARK 465 VAL A 1713 REMARK 465 PRO A 1714 REMARK 465 ARG A 1715 REMARK 465 GLY A 1716 REMARK 465 ASP A 1737 REMARK 465 GLU A 1738 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 GLU A1289 -57.60 74.21 REMARK 500 ASP A1451 0.63 -69.26 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 A2200 DISTANCE = 6.15 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8WHH RELATED DB: PDB REMARK 900 FOR THE SAME CITATION DBREF 8WHJ A 1251 1710 UNP O75122 CLAP2_HUMAN 1053 1282 DBREF 8WHJ A 1719 1738 UNP Q86SQ0 PHLB2_HUMAN 719 738 SEQADV 8WHJ GLY A 1245 UNP O75122 EXPRESSION TAG SEQADV 8WHJ PRO A 1246 UNP O75122 EXPRESSION TAG SEQADV 8WHJ GLY A 1247 UNP O75122 EXPRESSION TAG SEQADV 8WHJ SER A 1248 UNP O75122 EXPRESSION TAG SEQADV 8WHJ GLU A 1249 UNP O75122 EXPRESSION TAG SEQADV 8WHJ PHE A 1250 UNP O75122 EXPRESSION TAG SEQADV 8WHJ SER A 1711 UNP O75122 LINKER SEQADV 8WHJ LEU A 1712 UNP O75122 LINKER SEQADV 8WHJ VAL A 1713 UNP O75122 LINKER SEQADV 8WHJ PRO A 1714 UNP O75122 LINKER SEQADV 8WHJ ARG A 1715 UNP O75122 LINKER SEQADV 8WHJ GLY A 1716 UNP O75122 LINKER SEQADV 8WHJ SER A 1717 UNP O75122 LINKER SEQADV 8WHJ GLY A 1718 UNP O75122 LINKER SEQRES 1 A 264 GLY PRO GLY SER GLU PHE SER LEU ASP HIS SER ASP LEU SEQRES 2 A 264 VAL ALA GLU LEU LEU LYS GLU LEU SER ASN HIS ASN GLU SEQRES 3 A 264 ARG VAL GLU GLU ARG LYS ILE ALA LEU TYR GLU LEU MET SEQRES 4 A 264 LYS LEU THR GLN GLU GLU SER PHE SER VAL TRP ASP GLU SEQRES 5 A 264 HIS PHE LYS THR ILE LEU LEU LEU LEU LEU GLU THR LEU SEQRES 6 A 264 GLY ASP LYS GLU PRO THR ILE ARG ALA LEU ALA LEU LYS SEQRES 7 A 264 VAL LEU ARG GLU ILE LEU ARG HIS GLN PRO ALA ARG PHE SEQRES 8 A 264 LYS ASN TYR ALA GLU LEU THR VAL MET LYS THR LEU GLU SEQRES 9 A 264 ALA HIS LYS ASP PRO HIS LYS GLU VAL VAL ARG SER ALA SEQRES 10 A 264 GLU GLU ALA ALA SER VAL LEU ALA THR SER ILE SER PRO SEQRES 11 A 264 GLU GLN CYS ILE LYS VAL LEU CYS PRO ILE ILE GLN THR SEQRES 12 A 264 ALA ASP TYR PRO ILE ASN LEU ALA ALA ILE LYS MET GLN SEQRES 13 A 264 THR LYS VAL ILE GLU ARG VAL SER LYS GLU THR LEU ASN SEQRES 14 A 264 LEU LEU LEU PRO GLU ILE MET PRO GLY LEU ILE GLN GLY SEQRES 15 A 264 TYR ASP ASN SER GLU SER SER VAL ARG LYS ALA CYS VAL SEQRES 16 A 264 PHE CYS LEU VAL ALA VAL HIS ALA VAL ILE GLY ASP GLU SEQRES 17 A 264 LEU LYS PRO HIS LEU SER GLN LEU THR GLY SER LYS MET SEQRES 18 A 264 LYS LEU LEU ASN LEU TYR ILE LYS ARG ALA GLN THR GLY SEQRES 19 A 264 SER GLY SER LEU VAL PRO ARG GLY SER GLY SER LYS HIS SEQRES 20 A 264 PHE GLU ASP LEU GLU PHE GLN GLN LEU GLU HIS GLU SER SEQRES 21 A 264 ARG LEU ASP GLU HET CL A1801 1 HET PEG A1802 7 HETNAM CL CHLORIDE ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 CL CL 1- FORMUL 3 PEG C4 H10 O3 FORMUL 4 HOH *300(H2 O) HELIX 1 AA1 ASP A 1256 SER A 1266 1 11 HELIX 2 AA2 ARG A 1271 GLU A 1288 1 18 HELIX 3 AA3 SER A 1290 LEU A 1309 1 20 HELIX 4 AA4 GLU A 1313 GLN A 1331 1 19 HELIX 5 AA5 PRO A 1332 ASN A 1337 5 6 HELIX 6 AA6 TYR A 1338 ALA A 1349 1 12 HELIX 7 AA7 HIS A 1350 ASP A 1352 5 3 HELIX 8 AA8 HIS A 1354 ILE A 1372 1 19 HELIX 9 AA9 SER A 1373 ALA A 1388 1 16 HELIX 10 AB1 PRO A 1391 GLU A 1405 1 15 HELIX 11 AB2 SER A 1408 TYR A 1427 1 20 HELIX 12 AB3 GLU A 1431 GLY A 1450 1 20 HELIX 13 AB4 ASP A 1451 SER A 1458 5 8 HELIX 14 AB5 THR A 1461 GLY A 1478 1 18 HELIX 15 AB6 GLY A 1718 ARG A 1735 1 18 CISPEP 1 TYR A 1390 PRO A 1391 0 3.29 CRYST1 51.132 51.132 97.935 90.00 90.00 90.00 P 41 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 0.019557 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019557 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010211 0.00000