HEADER TRANSCRIPTION 06-JUL-26 32DH TITLE CRYSTAL STRUCTURE OF YAP1(165-209) IN COMPLEX WITH LATS2(511- TITLE 2 522_C513S) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL COACTIVATOR YAP1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: YES-ASSOCIATED PROTEIN 1,PROTEIN YORKIE HOMOLOG,YES- COMPND 5 ASSOCIATED PROTEIN YAP65 HOMOLOG; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: SERINE/THREONINE-PROTEIN KINASE LATS2; COMPND 9 CHAIN: L; COMPND 10 SYNONYM: KINASE PHOSPHORYLATED DURING MITOSIS PROTEIN,LARGE TUMOR COMPND 11 SUPPRESSOR HOMOLOG 2,SERINE/THREONINE-PROTEIN KINASE KPM,WARTS-LIKE COMPND 12 KINASE; COMPND 13 EC: 2.7.11.1; COMPND 14 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: YAP1, YAP65; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; 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 YAP1, TRANSCRIPTIONAL CO-ACTIVATOR, YES-ASSOCIATED PROTEIN 1, PROTEIN KEYWDS 2 YORKIE HOMOLOG, YES-ASSOCIATED PROTEIN YAP65 HOMOLOG, LATS2, LARGE KEYWDS 3 TUMOR SUPPRESSOR HOMOLOG 2, PROTEIN COMPLEX, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR A.HINNIGER,S.GUTMANN REVDAT 1 07-OCT-26 32DH 0 JRNL AUTH C.MERLEN,Y.MESROUZE,S.CHAU,B.A.DIEHL,A.HINNIGER, JRNL AUTH 2 C.ZIMMERMANN,M.MEYERHOFER,P.FONTANA,S.GROEBKE,J.HINRICHS, JRNL AUTH 3 W.ABDUL RAHMAN,S.GUTMANN,C.FERNANDEZ,D.PETROVIC,P.CHENE JRNL TITL COMPARING YAP WW1 AND TAZ WW : SIMILAR BINDING SITES BUT JRNL TITL 2 DIFFERENT STABILITY AND CONFORMATIONAL DYNAMICS. JRNL REF BIOMOLECULES V. 16 2026 JRNL REFN ESSN 2218-273X JRNL PMID 42793187 JRNL DOI 10.3390/BIOM16091355 REMARK 2 REMARK 2 RESOLUTION. 1.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 1.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 76.7 REMARK 3 NUMBER OF REFLECTIONS : 23711 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1206 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 29.0900 - 2.1300 1.00 3413 180 0.1831 0.2029 REMARK 3 2 2.1300 - 1.6900 1.00 3291 180 0.1808 0.1660 REMARK 3 3 1.6900 - 1.4800 1.00 3241 179 0.1764 0.1838 REMARK 3 4 1.4800 - 1.3400 1.00 3269 160 0.1841 0.1835 REMARK 3 5 1.3400 - 1.2500 1.00 3243 163 0.2011 0.1776 REMARK 3 6 1.2500 - 1.1700 0.96 3080 171 0.2026 0.1984 REMARK 3 7 1.1700 - 1.1200 0.58 1879 101 0.2150 0.2514 REMARK 3 8 1.1200 - 1.0700 0.27 857 53 0.2794 0.2733 REMARK 3 9 1.0700 - 1.0300 0.07 232 19 0.3497 0.3278 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) : 0.102 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.627 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.88 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 : 0.010 472 REMARK 3 ANGLE : 1.169 647 REMARK 3 CHIRALITY : 0.086 65 REMARK 3 PLANARITY : 0.012 87 REMARK 3 DIHEDRAL : 10.909 184 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 16.6098 11.2242 5.7944 REMARK 3 T TENSOR REMARK 3 T11: 0.0892 T22: 0.1421 REMARK 3 T33: 0.1089 T12: -0.0138 REMARK 3 T13: 0.0032 T23: -0.0436 REMARK 3 L TENSOR REMARK 3 L11: 1.9329 L22: 0.9289 REMARK 3 L33: 2.0274 L12: -0.7244 REMARK 3 L13: -1.2983 L23: 0.2459 REMARK 3 S TENSOR REMARK 3 S11: -0.0535 S12: 0.3383 S13: -0.2806 REMARK 3 S21: -0.0653 S22: -0.1036 S23: 0.0968 REMARK 3 S31: 0.0905 S32: -0.3283 S33: 0.0563 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN L REMARK 3 ORIGIN FOR THE GROUP (A): 15.4563 18.2582 16.9609 REMARK 3 T TENSOR REMARK 3 T11: 0.1002 T22: 0.0980 REMARK 3 T33: 0.0783 T12: -0.0001 REMARK 3 T13: 0.0021 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 1.9871 L22: 0.9519 REMARK 3 L33: 0.5315 L12: -0.9217 REMARK 3 L13: -0.6141 L23: 0.2257 REMARK 3 S TENSOR REMARK 3 S11: 0.0970 S12: 0.1111 S13: -0.1656 REMARK 3 S21: 0.0060 S22: -0.1057 S23: 0.0325 REMARK 3 S31: -0.0579 S32: -0.0022 S33: 0.0842 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 32DH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JUL-26. REMARK 100 THE DEPOSITION ID IS D_1292158596. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8856033 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VERSION JUN 30, 2023 REMARK 200 BUILT=20230630 REMARK 200 DATA SCALING SOFTWARE : AIMLESS V1.12.12 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23712 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.030 REMARK 200 RESOLUTION RANGE LOW (A) : 45.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 13.80 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.63100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.17 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 AMMONIUM ACETATE, 0.1 M BIS-TRIS REMARK 280 PH 6.5, AND 25 % (W/V) PEG3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 12.53100 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.06200 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.06200 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 12.53100 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 APPLY THE FOLLOWING TO CHAINS: A, L 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 L 204 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 GLY A 161 REMARK 465 ALA A 162 REMARK 465 MET A 163 REMARK 465 GLY A 164 REMARK 465 PHE A 165 REMARK 465 GLU A 166 REMARK 465 GLN A 209 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 L 225 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH L 226 DISTANCE = 6.20 ANGSTROMS DBREF 32DH A 165 209 UNP P46937 YAP1_HUMAN 165 209 DBREF 32DH L 2 13 UNP Q9NRM7 LATS2_HUMAN 511 522 SEQADV 32DH GLY A 161 UNP P46937 EXPRESSION TAG SEQADV 32DH ALA A 162 UNP P46937 EXPRESSION TAG SEQADV 32DH MET A 163 UNP P46937 EXPRESSION TAG SEQADV 32DH GLY A 164 UNP P46937 EXPRESSION TAG SEQADV 32DH ACE L 1 UNP Q9NRM7 ACETYLATION SEQADV 32DH SER L 4 UNP Q9NRM7 CYS 513 ENGINEERED MUTATION SEQRES 1 A 49 GLY ALA MET GLY PHE GLU ILE PRO ASP ASP VAL PRO LEU SEQRES 2 A 49 PRO ALA GLY TRP GLU MET ALA LYS THR SER SER GLY GLN SEQRES 3 A 49 ARG TYR PHE LEU ASN HIS ILE ASP GLN THR THR THR TRP SEQRES 4 A 49 GLN ASP PRO ARG LYS ALA MET LEU SER GLN SEQRES 1 L 13 ACE ARG ARG SER PRO PRO PRO PRO TYR PRO LYS HIS LEU HET ACE L 1 3 HETNAM ACE ACETYL GROUP FORMUL 2 ACE C2 H4 O FORMUL 3 HOH *69(H2 O) HELIX 1 AA1 PRO A 202 SER A 208 1 7 SHEET 1 AA1 3 TRP A 177 LYS A 181 0 SHEET 2 AA1 3 ARG A 187 ASN A 191 -1 O LEU A 190 N GLU A 178 SHEET 3 AA1 3 THR A 196 THR A 198 -1 O THR A 196 N ASN A 191 LINK C ACE L 1 N ARG L 2 1555 1555 1.33 CRYST1 53.036 53.036 37.593 90.00 90.00 120.00 P 31 2 1 6 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 0.018855 0.010886 0.000000 0.00000 SCALE2 0.000000 0.021772 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026601 0.00000 CONECT 345 346 347 348 CONECT 346 345 CONECT 347 345 CONECT 348 345 MASTER 271 0 1 1 3 0 0 6 512 2 4 5 END