HEADER SIGNALING PROTEIN 15-DEC-25 9TNG TITLE CRYSTAL STRUCTURE OF THE THIRD PDZ DOMAIN OF PSD-95 PROTEIN E401R TITLE 2 MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISKS LARGE HOMOLOG 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POSTSYNAPTIC DENSITY PROTEIN 95,PSD-95,SYNAPSE-ASSOCIATED COMPND 5 PROTEIN 90,SAP-90,SAP90; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: PDZ DOMAIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DLG4, PSD95; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBAT4 KEYWDS PDZ DOMAIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS REVDAT 1 13-MAY-26 9TNG 0 JRNL AUTH M.C.SALINAS-GARCIA,J.MURCIANO-CALLES,M.ANDUJAR-SANCHEZ, JRNL AUTH 2 E.ORTIZ-SALMERON,J.C.MARTINEZ,A.CAMARA-ARTIGAS JRNL TITL CONFORMATIONAL CHANGES ON THE THIRD PDZ DOMAIN OF PSD95 UPON JRNL TITL 2 PHOSPHORYLATION OF TYR397. JRNL REF J.STRUCT.BIOL. V. 218 08322 2026 JRNL REFN ESSN 1095-8657 JRNL PMID 42067080 JRNL DOI 10.1016/J.JSB.2026.108322 REMARK 2 REMARK 2 RESOLUTION. 0.95 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) : 0.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.180 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 45131 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.210 REMARK 3 FREE R VALUE TEST SET COUNT : 2351 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 19.3200 - 2.4400 0.97 2822 161 0.1498 0.1797 REMARK 3 2 2.4400 - 1.9400 0.99 2751 157 0.1319 0.1404 REMARK 3 3 1.9400 - 1.6900 0.99 2730 142 0.1314 0.1532 REMARK 3 4 1.6900 - 1.5400 1.00 2725 145 0.1257 0.1833 REMARK 3 5 1.5400 - 1.4300 0.99 2696 151 0.1264 0.1491 REMARK 3 6 1.4300 - 1.3400 0.99 2712 144 0.1281 0.1674 REMARK 3 7 1.3400 - 1.2800 1.00 2689 145 0.1268 0.1520 REMARK 3 8 1.2800 - 1.2200 0.99 2680 139 0.1256 0.1507 REMARK 3 9 1.2200 - 1.1700 0.99 2650 148 0.1247 0.1357 REMARK 3 10 1.1700 - 1.1300 0.99 2690 145 0.1297 0.1850 REMARK 3 11 1.1300 - 1.1000 0.98 2650 133 0.1399 0.1776 REMARK 3 12 1.1000 - 1.0700 0.98 2615 153 0.1563 0.1903 REMARK 3 13 1.0700 - 1.0400 0.98 2644 141 0.1654 0.1768 REMARK 3 14 1.0400 - 1.0100 0.95 2529 141 0.1871 0.2140 REMARK 3 15 1.0100 - 0.9900 0.84 2216 134 0.2366 0.2861 REMARK 3 16 0.9900 - 0.9700 0.65 1735 102 0.2871 0.3020 REMARK 3 17 0.9700 - 0.9500 0.46 1246 70 0.3114 0.3741 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) : 0.088 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.567 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.96 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 : 0.015 856 REMARK 3 ANGLE : 1.279 1157 REMARK 3 CHIRALITY : 0.105 122 REMARK 3 PLANARITY : 0.023 162 REMARK 3 DIHEDRAL : 11.489 330 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 9TNG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1292153016. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45187 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.950 REMARK 200 RESOLUTION RANGE LOW (A) : 19.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.02700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.97 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.89600 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 (%): 27.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULPHATE, 25% W/V PEG REMARK 280 4000, 0.1 M SODIUM ACETATE, PH 5.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K 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 16.45250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.41650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.35350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.41650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.45250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.35350 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 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 300 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 399 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 9TNG A 302 403 UNP P78352 DLG4_HUMAN 302 403 SEQADV 9TNG MET A 300 UNP P78352 INITIATING METHIONINE SEQADV 9TNG GLY A 301 UNP P78352 EXPRESSION TAG SEQADV 9TNG ARG A 401 UNP P78352 GLU 401 ENGINEERED MUTATION SEQRES 1 A 104 MET GLY LEU GLY GLU GLU ASP ILE PRO ARG GLU PRO ARG SEQRES 2 A 104 ARG ILE VAL ILE HIS ARG GLY SER THR GLY LEU GLY PHE SEQRES 3 A 104 ASN ILE VAL GLY GLY GLU ASP GLY GLU GLY ILE PHE ILE SEQRES 4 A 104 SER PHE ILE LEU ALA GLY GLY PRO ALA ASP LEU SER GLY SEQRES 5 A 104 GLU LEU ARG LYS GLY ASP GLN ILE LEU SER VAL ASN GLY SEQRES 6 A 104 VAL ASP LEU ARG ASN ALA SER HIS GLU GLN ALA ALA ILE SEQRES 7 A 104 ALA LEU LYS ASN ALA GLY GLN THR VAL THR ILE ILE ALA SEQRES 8 A 104 GLN TYR LYS PRO GLU GLU TYR SER ARG PHE ARG ALA LYS HET ACT A 501 7 HET ACT A 502 7 HETNAM ACT ACETATE ION FORMUL 2 ACT 2(C2 H3 O2 1-) FORMUL 4 HOH *120(H2 O) HELIX 1 AA1 GLY A 345 GLY A 351 1 7 HELIX 2 AA2 SER A 371 ALA A 382 1 12 HELIX 3 AA3 LYS A 393 ALA A 402 1 10 SHEET 1 AA1 4 ARG A 312 HIS A 317 0 SHEET 2 AA1 4 THR A 385 TYR A 392 -1 O ILE A 388 N ILE A 314 SHEET 3 AA1 4 ASP A 357 VAL A 362 -1 N GLN A 358 O GLN A 391 SHEET 4 AA1 4 VAL A 365 ASP A 366 -1 O VAL A 365 N VAL A 362 SHEET 1 AA2 2 PHE A 325 GLU A 331 0 SHEET 2 AA2 2 GLU A 334 ILE A 341 -1 O PHE A 337 N VAL A 328 CRYST1 32.905 36.707 62.833 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 0.030391 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027243 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015915 0.00000 CONECT 1672 1673 1674 1675 CONECT 1673 1672 CONECT 1674 1672 CONECT 1675 1672 1676 1677 1678 CONECT 1676 1675 CONECT 1677 1675 CONECT 1678 1675 CONECT 1679 1680 1681 1682 CONECT 1680 1679 CONECT 1681 1679 CONECT 1682 1679 1683 1684 1685 CONECT 1683 1682 CONECT 1684 1682 CONECT 1685 1682 MASTER 228 0 2 3 6 0 0 6 907 1 14 8 END