HEADER LIGASE/TRANSCRIPTION REGULATOR 16-MAR-11 2LAJ TITLE THIRD WW DOMAIN OF HUMAN NEDD4L IN COMPLEX WITH DOUBLY PHOSPHORYLATED TITLE 2 HUMAN SMAD3 DERIVED PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE NEDD4-LIKE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: WW 3 DOMAIN RESIDUES 496-535; 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: MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 3; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: SEQUENCE DATABASE RESIDUES 202-211; COMPND 12 SYNONYM: MAD HOMOLOG 3, MAD3, MOTHERS AGAINST DPP HOMOLOG 3, HMAD-3, COMPND 13 JV15-2, SMAD FAMILY MEMBER 3, SMAD 3, SMAD3, HSMAD3; 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: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PETM11; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS CDK, SIGNAL TRANSDUCTION, LIGASE-TRANSCRIPTION REGULATOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR M.J.MACIAS,E.ARAGON,N.GOERNER,A.ZAROMYTIDOU,Q.XI,A.ESCOBEDO, AUTHOR 2 J.MASSAGUE REVDAT 2 14-JUN-23 2LAJ 1 REMARK SEQADV LINK REVDAT 1 06-JUL-11 2LAJ 0 JRNL AUTH E.ARAGON,N.GOERNER,A.I.ZAROMYTIDOU,Q.XI,A.ESCOBEDO, JRNL AUTH 2 J.MASSAGUE,M.J.MACIAS JRNL TITL A SMAD ACTION TURNOVER SWITCH OPERATED BY WW DOMAIN READERS JRNL TITL 2 OF A PHOSPHOSERINE CODE. JRNL REF GENES DEV. V. 25 1275 2011 JRNL REFN ISSN 0890-9369 JRNL PMID 21685363 JRNL DOI 10.1101/GAD.2060811 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3, CNS 1.3 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LAJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000102161. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 285 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0.420 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM NEDD4LWW3, 3 MM SMAD3, 20 REMARK 210 MM SODIUM PHOSPHATE, 100 MM REMARK 210 SODIUM CHLORIDE, 2 MM SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O; 1 MM [U- REMARK 210 100% 15N] NEDD4LWW3, 3 MM SMAD3, REMARK 210 20 MM SODIUM PHOSPHATE, 100 MM REMARK 210 SODIUM CHLORIDE, 2 MM SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O; 1 MM [U- REMARK 210 100% 13C; U-100% 15N] NEDD4LWW3, REMARK 210 3 MM SMAD3, 20 MM SODIUM REMARK 210 PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 2 MM SODIUM AZIDE, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 2D 1H- REMARK 210 15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY, TOPSPIN, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY 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 1-15 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 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 HD11 LEU A 479 HG2 PRO A 508 1.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 PHE A 478 CB - CA - C ANGL. DEV. = -16.7 DEGREES REMARK 500 1 PHE A 478 CB - CG - CD2 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 PHE A 478 CB - CA - C ANGL. DEV. = -13.3 DEGREES REMARK 500 3 PHE A 478 CB - CA - C ANGL. DEV. = -14.6 DEGREES REMARK 500 3 PHE A 478 CB - CG - CD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 4 PHE A 478 CB - CA - C ANGL. DEV. = -14.9 DEGREES REMARK 500 4 PHE A 478 CB - CG - CD2 ANGL. DEV. = -5.2 DEGREES REMARK 500 5 PHE A 478 CB - CA - C ANGL. DEV. = -14.8 DEGREES REMARK 500 5 PHE A 478 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 6 PHE A 478 CB - CA - C ANGL. DEV. = -12.9 DEGREES REMARK 500 6 PHE A 478 CB - CG - CD2 ANGL. DEV. = -4.9 DEGREES REMARK 500 7 PHE A 478 CB - CA - C ANGL. DEV. = -16.5 DEGREES REMARK 500 7 PHE A 478 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 8 PHE A 478 CB - CA - C ANGL. DEV. = -13.8 DEGREES REMARK 500 8 PHE A 478 CB - CG - CD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 9 PHE A 478 CB - CA - C ANGL. DEV. = -14.0 DEGREES REMARK 500 9 PHE A 478 CB - CG - CD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 9 PRO A 513 C - N - CA ANGL. DEV. = 9.3 DEGREES REMARK 500 10 PHE A 478 CB - CA - C ANGL. DEV. = -14.6 DEGREES REMARK 500 11 PHE A 478 CB - CA - C ANGL. DEV. = -14.2 DEGREES REMARK 500 11 PHE A 478 CB - CG - CD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 12 PHE A 478 CB - CA - C ANGL. DEV. = -15.7 DEGREES REMARK 500 12 PHE A 478 CB - CG - CD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 12 PHE A 494 CB - CG - CD1 ANGL. DEV. = 4.4 DEGREES REMARK 500 13 PHE A 478 CB - CA - C ANGL. DEV. = -14.4 DEGREES REMARK 500 13 PHE A 478 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 14 PHE A 478 CB - CA - C ANGL. DEV. = -15.1 DEGREES REMARK 500 14 PHE A 478 CB - CG - CD2 ANGL. DEV. = -5.3 DEGREES REMARK 500 15 PHE A 478 CB - CA - C ANGL. DEV. = -14.5 DEGREES REMARK 500 15 PHE A 478 CB - CG - CD2 ANGL. DEV. = -5.4 DEGREES 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 480 174.05 -59.89 REMARK 500 1 PRO A 481 38.30 -79.30 REMARK 500 1 PRO A 489 1.86 -56.36 REMARK 500 1 PRO A 513 -9.63 -48.96 REMARK 500 1 PRO B 205 100.03 -59.62 REMARK 500 1 LEU B 207 99.24 -63.21 REMARK 500 2 PRO A 481 30.16 -88.59 REMARK 500 2 PRO A 489 2.78 -54.38 REMARK 500 2 PRO A 513 -9.51 -48.73 REMARK 500 2 VAL A 514 -9.67 -58.22 REMARK 500 2 PRO B 205 98.22 -59.53 REMARK 500 3 PRO A 481 29.15 -79.52 REMARK 500 3 PRO A 489 0.94 -55.95 REMARK 500 3 PRO A 513 -9.70 -50.86 REMARK 500 3 PRO B 205 98.48 -59.68 REMARK 500 4 PRO A 480 173.96 -59.82 REMARK 500 4 PRO A 481 36.00 -78.22 REMARK 500 4 PRO A 489 -3.78 -54.96 REMARK 500 4 PHE A 512 -39.69 -39.63 REMARK 500 4 PRO A 513 -9.61 -49.63 REMARK 500 4 VAL A 514 -9.50 -57.47 REMARK 500 4 PRO B 205 106.24 -59.58 REMARK 500 5 PRO A 480 171.54 -59.78 REMARK 500 5 PRO A 481 28.83 -74.79 REMARK 500 5 PRO A 489 -2.19 -57.67 REMARK 500 5 PRO A 513 -9.85 -50.40 REMARK 500 5 VAL A 514 -9.61 -59.96 REMARK 500 6 SER A 477 -75.24 -120.15 REMARK 500 6 PRO A 481 34.86 -80.17 REMARK 500 6 PRO A 489 -4.11 -52.68 REMARK 500 6 PRO A 513 -9.42 -48.06 REMARK 500 6 VAL A 514 -9.86 -57.35 REMARK 500 6 PRO B 205 106.25 -59.63 REMARK 500 6 LEU B 207 99.89 -61.47 REMARK 500 7 PRO A 481 36.74 -78.12 REMARK 500 7 PRO A 489 5.44 -57.83 REMARK 500 7 ASN A 499 -74.43 -164.60 REMARK 500 7 PHE A 512 -32.08 -39.96 REMARK 500 7 PRO A 513 -8.90 -46.95 REMARK 500 7 VAL A 514 -9.86 -46.43 REMARK 500 7 PRO B 205 105.68 -59.65 REMARK 500 8 PRO A 480 171.82 -59.80 REMARK 500 8 PRO A 481 24.48 -77.51 REMARK 500 8 PRO A 489 -4.16 -57.61 REMARK 500 8 PHE A 512 -39.31 -39.67 REMARK 500 8 PRO A 513 -9.62 -50.98 REMARK 500 8 PRO B 205 102.76 -59.62 REMARK 500 9 PRO A 480 174.38 -59.91 REMARK 500 9 PRO A 481 24.62 -74.43 REMARK 500 9 PRO A 489 -3.19 -52.78 REMARK 500 REMARK 500 THIS ENTRY HAS 82 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE A 478 LEU A 479 1 -132.73 REMARK 500 GLY A 482 TRP A 483 1 -141.84 REMARK 500 PHE A 478 LEU A 479 2 -134.07 REMARK 500 GLY A 482 TRP A 483 2 -138.68 REMARK 500 PHE A 478 LEU A 479 3 -131.71 REMARK 500 GLY A 482 TRP A 483 3 -143.28 REMARK 500 PHE A 478 LEU A 479 4 -132.27 REMARK 500 GLY A 482 TRP A 483 4 -142.03 REMARK 500 PHE A 478 LEU A 479 5 -131.29 REMARK 500 GLY A 482 TRP A 483 5 -141.46 REMARK 500 PHE A 478 LEU A 479 6 -130.29 REMARK 500 GLY A 482 TRP A 483 6 -140.10 REMARK 500 PHE A 478 LEU A 479 7 -133.21 REMARK 500 GLY A 482 TRP A 483 7 -142.54 REMARK 500 PHE A 478 LEU A 479 8 -130.67 REMARK 500 GLY A 482 TRP A 483 8 -141.96 REMARK 500 PHE A 478 LEU A 479 9 -129.79 REMARK 500 GLY A 482 TRP A 483 9 -142.35 REMARK 500 PHE A 478 LEU A 479 10 -130.01 REMARK 500 GLY A 482 TRP A 483 10 -141.88 REMARK 500 PHE A 478 LEU A 479 11 -130.78 REMARK 500 GLY A 482 TRP A 483 11 -141.90 REMARK 500 PHE A 478 LEU A 479 12 -131.45 REMARK 500 GLY A 482 TRP A 483 12 -141.61 REMARK 500 PHE A 478 LEU A 479 13 -130.39 REMARK 500 GLY A 482 TRP A 483 13 -141.03 REMARK 500 PHE A 478 LEU A 479 14 -131.70 REMARK 500 GLY A 482 TRP A 483 14 -141.74 REMARK 500 PHE A 478 LEU A 479 15 -134.57 REMARK 500 GLY A 482 TRP A 483 15 -144.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17529 RELATED DB: BMRB DBREF 2LAJ A 476 515 UNP Q96PU5 NED4L_HUMAN 496 535 DBREF 2LAJ B 202 211 UNP P84022 SMAD3_HUMAN 202 211 SEQADV 2LAJ GLY A 472 UNP Q96PU5 EXPRESSION TAG SEQADV 2LAJ ALA A 473 UNP Q96PU5 EXPRESSION TAG SEQADV 2LAJ MET A 474 UNP Q96PU5 EXPRESSION TAG SEQADV 2LAJ GLU A 475 UNP Q96PU5 EXPRESSION TAG SEQADV 2LAJ TYR A 496 UNP Q96PU5 ILE 516 ENGINEERED MUTATION SEQRES 1 A 44 GLY ALA MET GLU GLN SER PHE LEU PRO PRO GLY TRP GLU SEQRES 2 A 44 MET ARG ILE ALA PRO ASN GLY ARG PRO PHE PHE TYR ASP SEQRES 3 A 44 HIS ASN THR LYS THR THR THR TRP GLU ASP PRO ARG LEU SEQRES 4 A 44 LYS PHE PRO VAL HIS SEQRES 1 B 10 ALA GLY SEP PRO ASN LEU SEP PRO ASN PRO MODRES 2LAJ SEP B 204 SER PHOSPHOSERINE MODRES 2LAJ SEP B 208 SER PHOSPHOSERINE HET SEP B 204 14 HET SEP B 208 14 HETNAM SEP PHOSPHOSERINE HETSYN SEP PHOSPHONOSERINE FORMUL 2 SEP 2(C3 H8 N O6 P) HELIX 1 1 ASP A 507 HIS A 515 5 9 SHEET 1 A 3 TRP A 483 ALA A 488 0 SHEET 2 A 3 ARG A 492 ASP A 497 -1 O ARG A 492 N ALA A 488 SHEET 3 A 3 THR A 502 THR A 504 -1 O THR A 504 N PHE A 495 LINK C GLY B 203 N SEP B 204 1555 1555 1.32 LINK C SEP B 204 N PRO B 205 1555 1555 1.34 LINK C LEU B 207 N SEP B 208 1555 1555 1.33 LINK C SEP B 208 N PRO B 209 1555 1555 1.34 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 MODEL 1