PDB Short entry for 2MPT HEADER LIGASE 02-JUN-14 2MPT TITLE WW3 DOMAIN OF NEDD4L IN COMPLEX WITH ITS HECT DOMAIN PY MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE NEDD4-LIKE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: WW3 DOMAIN, UNP RESIDUES 496-539; COMPND 5 SYNONYM: NEDD4.2, NEDD4-2; COMPND 6 EC: 6.3.2.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE NEDD4-LIKE; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: HECT DOMAIN PY MOTIF, UNP RESIDUES 945-957; COMPND 12 SYNONYM: NEDD4.2, NEDD4-2; COMPND 13 EC: 6.3.2.-; 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: NEDD4L, KIAA0439, NEDL3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PETM11; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS WW, NEDD4L, NEDD4.2, HECT, PY, WW3, AUTO-UBIQUITINATION, PROTEASOMAL KEYWDS 2 DEGRADATION, UBIQUITIN LIGASE, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.ESCOBEDO,M.J.MACIAS,T.GOMES,E.ARAGON,P.MARTIN-MALPARTIDA,L.RUIZ REVDAT 1 22-OCT-14 2MPT 0 JRNL AUTH A.ESCOBEDO,T.GOMES,E.ARAGON,P.MARTIN-MALPARTIDA,L.RUIZ, JRNL AUTH 2 M.J.MACIAS JRNL TITL STRUCTURAL BASIS OF THE ACTIVATION AND DEGRADATION JRNL TITL 2 MECHANISMS OF THE E3 UBIQUITIN LIGASE NEDD4L. JRNL REF STRUCTURE V. 22 1446 2014 JRNL REFN ISSN 0969-2126 JRNL PMID 25295397 JRNL DOI 10.1016/J.STR.2014.08.016 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNSSOLVE REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MPT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUN-14. REMARK 100 THE RCSB ID CODE IS RCSB103905. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7 MM WW3-1, 1.4 MM HECT_PY-2, REMARK 210 150 MM SODIUM CHLORIDE-3, 20 MM REMARK 210 SODIUM PHOSPHATE-4, 90% H2O/10% REMARK 210 D2O; 1 MM [U-100% 15N] WW3-5, 2 REMARK 210 MM HECT_PY-6, 150 MM SODIUM REMARK 210 CHLORIDE-7, 20 MM SODIUM REMARK 210 PHOSPHATE-8, 90% H2O/10% D2O; 0.8 REMARK 210 MM [U-100% 13C; U-100% 15N] WW3- REMARK 210 9, 1.6 MM HECT_PY-10, 150 MM REMARK 210 SODIUM CHLORIDE-11, 20 MM SODIUM REMARK 210 PHOSPHATE-12, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 3D 1H-15N NOESY; 3D 1H-15N TOCSY; REMARK 210 3D HNCACB; 3D CBCA(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNSSOLVE, CARA, NMRPIPE, REMARK 210 TOPSPIN, TALOS REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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, 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 472 REMARK 465 ALA A 473 REMARK 465 MET A 474 REMARK 465 GLU A 475 REMARK 465 GLN A 476 REMARK 465 SER A 477 REMARK 465 LEU A 510 REMARK 465 LYS A 511 REMARK 465 PHE A 512 REMARK 465 PRO A 513 REMARK 465 VAL A 514 REMARK 465 HIS A 515 REMARK 465 MET A 516 REMARK 465 ARG A 517 REMARK 465 SER A 518 REMARK 465 LYS A 519 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP A 497 HG1 THR A 500 1.53 REMARK 500 REMARK 500 REMARK: NULL 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 1 PRO A 489 -3.10 -58.42 REMARK 500 2 PRO A 480 140.63 -39.54 REMARK 500 2 PRO A 481 108.13 -51.80 REMARK 500 2 PRO A 489 -5.70 -57.44 REMARK 500 2 PRO A 508 38.06 -74.91 REMARK 500 3 PRO A 480 158.02 -43.96 REMARK 500 3 PRO A 489 -6.71 -55.41 REMARK 500 3 LYS A 501 37.81 72.27 REMARK 500 4 PRO A 480 157.69 -37.14 REMARK 500 4 PRO A 489 -69.88 -16.95 REMARK 500 4 LYS A 501 50.20 70.39 REMARK 500 4 PRO A 508 21.60 -73.79 REMARK 500 5 PRO A 480 140.18 -38.11 REMARK 500 5 PRO A 489 -3.49 -58.15 REMARK 500 6 PRO A 508 23.07 -77.92 REMARK 500 7 PRO A 489 -7.41 -43.65 REMARK 500 8 PRO A 480 130.77 -28.68 REMARK 500 8 LYS A 501 31.40 78.94 REMARK 500 9 PRO A 489 -3.40 -57.60 REMARK 500 9 PRO A 508 -78.38 -70.04 REMARK 500 10 PRO A 480 138.55 -29.33 REMARK 500 10 LYS A 501 41.72 73.45 REMARK 500 10 GLU B 935 178.97 -49.04 REMARK 500 11 PRO A 481 -82.93 -27.19 REMARK 500 11 PRO A 489 -4.04 -59.97 REMARK 500 11 LEU B 926 -179.66 -68.59 REMARK 500 11 GLU B 935 150.29 -48.58 REMARK 500 12 PRO A 480 152.98 -44.89 REMARK 500 12 PRO A 489 -3.38 -47.21 REMARK 500 12 LYS A 501 50.41 75.74 REMARK 500 12 PRO A 508 -79.19 -72.52 REMARK 500 12 GLU B 935 169.34 -48.32 REMARK 500 13 PRO A 480 138.51 -36.62 REMARK 500 13 PRO A 489 -4.04 -58.64 REMARK 500 13 GLU B 935 166.59 -48.38 REMARK 500 14 PRO A 480 160.14 -44.13 REMARK 500 14 PRO A 489 -7.21 -56.86 REMARK 500 14 LYS A 501 44.46 71.73 REMARK 500 15 PRO A 480 157.86 -43.20 REMARK 500 16 PRO A 489 2.59 -56.61 REMARK 500 17 PRO A 480 144.93 -37.85 REMARK 500 17 PRO A 489 -5.70 -53.68 REMARK 500 17 LYS A 501 50.01 72.60 REMARK 500 17 TRP A 505 -76.41 -78.92 REMARK 500 17 PRO A 508 -15.35 -38.44 REMARK 500 18 PRO A 480 149.76 -39.05 REMARK 500 18 PRO A 481 -8.54 -59.11 REMARK 500 19 PRO A 489 1.83 -56.83 REMARK 500 19 LYS A 501 40.62 75.05 REMARK 500 20 PRO A 480 142.03 -31.02 REMARK 500 REMARK 500 THIS ENTRY HAS 53 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25000 RELATED DB: BMRB DBREF 2MPT A 476 519 UNP Q96PU5 NED4L_HUMAN 496 539 DBREF 2MPT B 925 937 UNP Q96PU5 NED4L_HUMAN 945 957 SEQADV 2MPT GLY A 472 UNP Q96PU5 EXPRESSION TAG SEQADV 2MPT ALA A 473 UNP Q96PU5 EXPRESSION TAG SEQADV 2MPT MET A 474 UNP Q96PU5 EXPRESSION TAG SEQADV 2MPT GLU A 475 UNP Q96PU5 EXPRESSION TAG SEQADV 2MPT NH2 B 938 UNP Q96PU5 AMIDATION SEQRES 1 A 48 GLY ALA MET GLU GLN SER PHE LEU PRO PRO GLY TRP GLU SEQRES 2 A 48 MET ARG ILE ALA PRO ASN GLY ARG PRO PHE PHE ILE ASP SEQRES 3 A 48 HIS ASN THR LYS THR THR THR TRP GLU ASP PRO ARG LEU SEQRES 4 A 48 LYS PHE PRO VAL HIS MET ARG SER LYS SEQRES 1 B 14 ARG LEU ASP LEU PRO PRO TYR GLU THR PHE GLU ASP LEU SEQRES 2 B 14 NH2 HET NH2 B 938 3 HETNAM NH2 AMINO GROUP FORMUL 2 NH2 H2 N SHEET 1 A 3 TRP A 483 ILE A 487 0 SHEET 2 A 3 PRO A 493 ASP A 497 -1 O PHE A 494 N ARG A 486 SHEET 3 A 3 THR A 502 THR A 504 -1 O THR A 504 N PHE A 495 LINK C LEU B 937 N NH2 B 938 1555 1555 1.32 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000