HEADER LIGASE 11-FEB-21 7LP1 TITLE STRUCTURE OF NEDD4L WW3 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE NEDD4-LIKE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: WW 3 DOMAIN, RESIDUES 494-532; COMPND 5 SYNONYM: HECT-TYPE E3 UBIQUITIN TRANSFERASE NED4L,NEDD4.2,NEDD4-2; COMPND 6 EC: 2.3.2.26; COMPND 7 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: NEDD4L, KIAA0439, NEDL3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS PPXY BINDING, E3 UBIQUITIN LIGASE, NEDD4L, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR A.ALIAN,S.L.ALAM,T.THOMPSON,L.RHEINEMANN,W.I.SUNDQUIST REVDAT 3 18-OCT-23 7LP1 1 REMARK REVDAT 2 25-AUG-21 7LP1 1 JRNL REVDAT 1 28-JUL-21 7LP1 0 JRNL AUTH L.RHEINEMANN,T.THOMPSON,G.MERCENNE,E.L.PAINE,F.C.PETERSON, JRNL AUTH 2 B.F.VOLKMAN,S.L.ALAM,A.ALIAN,W.I.SUNDQUIST JRNL TITL INTERACTIONS BETWEEN AMOT PPXY MOTIFS AND NEDD4L WW DOMAINS JRNL TITL 2 FUNCTION IN HIV-1 RELEASE. JRNL REF J.BIOL.CHEM. V. 297 00975 2021 JRNL REFN ESSN 1083-351X JRNL PMID 34284061 JRNL DOI 10.1016/J.JBC.2021.100975 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 11771 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) : 0.184 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1185 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 29.4700 - 2.7000 1.00 1412 164 0.1793 0.2177 REMARK 3 2 2.7000 - 2.1400 1.00 1337 154 0.1847 0.2150 REMARK 3 3 2.1400 - 1.8700 1.00 1330 152 0.1729 0.1935 REMARK 3 4 1.8700 - 1.7000 1.00 1302 145 0.1912 0.2079 REMARK 3 5 1.7000 - 1.5800 1.00 1318 143 0.1752 0.2031 REMARK 3 6 1.5800 - 1.4900 1.00 1299 140 0.1952 0.2218 REMARK 3 7 1.4900 - 1.4100 1.00 1307 146 0.1991 0.2110 REMARK 3 8 1.4100 - 1.3500 0.98 1281 141 0.2231 0.2648 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) : 0.095 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.589 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.39 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 : 0.010 360 REMARK 3 ANGLE : 1.116 484 REMARK 3 CHIRALITY : 0.077 47 REMARK 3 PLANARITY : 0.008 63 REMARK 3 DIHEDRAL : 7.753 45 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 522 THROUGH 527 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.9623 10.0522 -3.1103 REMARK 3 T TENSOR REMARK 3 T11: 0.0790 T22: 0.1192 REMARK 3 T33: 0.0883 T12: -0.0136 REMARK 3 T13: 0.0027 T23: -0.0131 REMARK 3 L TENSOR REMARK 3 L11: 6.6719 L22: 7.0528 REMARK 3 L33: 2.1476 L12: -5.2743 REMARK 3 L13: -1.1994 L23: 0.4750 REMARK 3 S TENSOR REMARK 3 S11: -0.0706 S12: 0.0312 S13: -0.1360 REMARK 3 S21: 0.1338 S22: 0.0642 S23: 0.1506 REMARK 3 S31: 0.4885 S32: -0.1391 S33: -0.0316 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 528 THROUGH 532 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.2205 9.4586 6.6912 REMARK 3 T TENSOR REMARK 3 T11: 0.1848 T22: 0.2394 REMARK 3 T33: 0.2235 T12: 0.0750 REMARK 3 T13: 0.0103 T23: 0.0445 REMARK 3 L TENSOR REMARK 3 L11: 4.7646 L22: 2.7887 REMARK 3 L33: 7.7644 L12: 2.8713 REMARK 3 L13: 1.0125 L23: -2.2163 REMARK 3 S TENSOR REMARK 3 S11: 0.1503 S12: -0.6877 S13: -0.7197 REMARK 3 S21: 0.5320 S22: 0.0562 S23: 0.4878 REMARK 3 S31: 0.5527 S32: -0.3237 S33: -0.1026 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 494 THROUGH 502 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.5869 16.0865 11.8678 REMARK 3 T TENSOR REMARK 3 T11: 0.3238 T22: 0.2022 REMARK 3 T33: 0.1438 T12: 0.1488 REMARK 3 T13: -0.0272 T23: -0.0377 REMARK 3 L TENSOR REMARK 3 L11: 1.0055 L22: 2.6418 REMARK 3 L33: 0.3906 L12: 1.3146 REMARK 3 L13: 0.4354 L23: 1.0003 REMARK 3 S TENSOR REMARK 3 S11: -0.1412 S12: -0.1449 S13: 0.5282 REMARK 3 S21: 0.2620 S22: -0.0935 S23: 0.1950 REMARK 3 S31: -0.7633 S32: -0.4962 S33: 0.2503 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 503 THROUGH 507 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.0422 15.9915 0.7893 REMARK 3 T TENSOR REMARK 3 T11: 0.0963 T22: 0.1072 REMARK 3 T33: 0.0826 T12: 0.0117 REMARK 3 T13: -0.0179 T23: 0.0086 REMARK 3 L TENSOR REMARK 3 L11: 5.6859 L22: 4.4368 REMARK 3 L33: 4.8604 L12: -1.4013 REMARK 3 L13: 1.5903 L23: -2.6246 REMARK 3 S TENSOR REMARK 3 S11: -0.2419 S12: -0.0287 S13: 0.3507 REMARK 3 S21: 0.2035 S22: -0.0782 S23: -0.3699 REMARK 3 S31: -0.1916 S32: 0.1430 S33: 0.1962 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 508 THROUGH 521 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.7339 13.1776 -3.0971 REMARK 3 T TENSOR REMARK 3 T11: 0.0659 T22: 0.1230 REMARK 3 T33: 0.0609 T12: 0.0136 REMARK 3 T13: 0.0046 T23: -0.0087 REMARK 3 L TENSOR REMARK 3 L11: 2.6479 L22: 5.9800 REMARK 3 L33: 5.2302 L12: -2.2940 REMARK 3 L13: 0.8685 L23: -1.9120 REMARK 3 S TENSOR REMARK 3 S11: 0.0615 S12: 0.1781 S13: -0.0329 REMARK 3 S21: -0.1257 S22: -0.1779 S23: -0.0158 REMARK 3 S31: 0.2339 S32: 0.1661 S33: 0.1081 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 7LP1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1000252743. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11774 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 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 : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.2500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.16850 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.260 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: 2MPT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.6M AMMONIUM NITRATE, 5% GLYCEROL, REMARK 280 AND 0.1M SODIUM ACETATE AT PH 4.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K 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 18.28667 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 36.57333 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 36.57333 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 18.28667 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 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 605 DBREF 7LP1 A 494 532 UNP Q96PU5 NED4L_HUMAN 494 532 SEQRES 1 A 39 VAL THR GLN SER PHE LEU PRO PRO GLY TRP GLU MET ARG SEQRES 2 A 39 ILE ALA PRO ASN GLY ARG PRO PHE PHE ILE ASP HIS ASN SEQRES 3 A 39 THR LYS THR THR THR TRP GLU ASP PRO ARG LEU LYS PHE HET NO3 A 601 4 HET NO3 A 602 4 HET NO3 A 603 4 HET GOL A 604 14 HET GOL A 605 14 HETNAM NO3 NITRATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NO3 3(N O3 1-) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 7 HOH *43(H2 O) HELIX 1 AA1 ASP A 527 PHE A 532 5 6 SHEET 1 AA1 3 TRP A 503 ILE A 507 0 SHEET 2 AA1 3 PRO A 513 ASP A 517 -1 O PHE A 514 N ARG A 506 SHEET 3 AA1 3 THR A 522 THR A 524 -1 O THR A 522 N ASP A 517 SITE 1 AC1 9 PRO A 500 TRP A 503 ALA A 508 PRO A 509 SITE 2 AC1 9 ASN A 510 TRP A 525 GOL A 604 HOH A 701 SITE 3 AC1 9 HOH A 709 SITE 1 AC2 6 VAL A 494 THR A 495 GLN A 496 PHE A 498 SITE 2 AC2 6 HIS A 518 LYS A 521 SITE 1 AC3 3 ARG A 512 TRP A 525 HOH A 711 SITE 1 AC4 8 VAL A 494 THR A 495 ASP A 517 THR A 520 SITE 2 AC4 8 THR A 522 NO3 A 601 HOH A 701 HOH A 705 SITE 1 AC5 4 ARG A 506 ILE A 507 PHE A 532 HOH A 702 CRYST1 40.344 40.344 54.860 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 0.024787 0.014311 0.000000 0.00000 SCALE2 0.000000 0.028621 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018228 0.00000