PDB Short entry for 2LB2 HEADER SIGNALING PROTEIN/TRANSCRIPTION 22-MAR-11 2LB2 TITLE STRUCTURE OF THE SECOND DOMAIN OF HUMAN NEDD4L IN COMPLEX WITH A TITLE 2 PHOSPHORYLATED PTPY MOTIF DERIVED FROM HUMAN SMAD3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE NEDD4-LIKE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 386-420; 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: RESIDUES 178-189; 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: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PETM11; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS NEDD4L, SMAD, CDK, SIGNAL TRANSDUCTION, SIGNALING PROTEIN- KEYWDS 2 TRANSCRIPTION COMPLEX EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR M.J.MACIAS,E.ARAGON,N.GOERNER,A.ZAROMYTIDOU,Q.XI,A.ESCOBEDO, AUTHOR 2 J.MASSAGUE REVDAT 1 06-JUL-11 2LB2 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 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE, REMARK 3 JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LB2 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-APR-11. REMARK 100 THE RCSB ID CODE IS RCSB102178. 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 : CNS 1.3, XEASY, TOPSPIN, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 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 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 HB3 PRO B 180 HD2 PRO B 181 1.17 REMARK 500 HG3 LYS A 375 HB THR A 381 1.36 REMARK 500 HG13 VAL A 384 HD1 TYR B 184 1.51 REMARK 500 HZ1 LYS A 378 O1P TPO B 179 1.51 REMARK 500 HB2 GLU A 372 HG3 GLU B 187 1.55 REMARK 500 HB3 TYR A 382 HZ3 TRP A 393 1.55 REMARK 500 HG11 VAL A 384 H LEU B 185 1.59 REMARK 500 HH TYR A 382 OE2 GLU B 187 1.60 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 24 PRO B 180 CA - CB - CG ANGL. DEV. = -11.4 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 ARG A 389 70.46 69.26 REMARK 500 1 PRO B 180 172.27 -47.65 REMARK 500 1 LEU B 185 70.16 49.17 REMARK 500 2 ARG A 389 70.49 69.92 REMARK 500 2 GLN A 399 -52.93 -120.00 REMARK 500 2 PRO B 180 170.96 -48.02 REMARK 500 3 ARG A 389 70.44 78.94 REMARK 500 3 PRO B 180 171.66 -47.76 REMARK 500 3 LEU B 185 70.13 66.57 REMARK 500 4 ARG A 389 70.29 72.85 REMARK 500 4 PRO B 180 173.67 -47.93 REMARK 500 4 LEU B 185 70.20 58.03 REMARK 500 5 ARG A 389 70.42 74.37 REMARK 500 5 PRO B 180 170.12 -47.89 REMARK 500 5 LEU B 185 68.34 63.65 REMARK 500 6 ARG A 389 70.48 80.43 REMARK 500 6 PRO B 180 171.20 -47.94 REMARK 500 7 ARG A 389 70.42 71.12 REMARK 500 7 PRO B 180 169.44 -48.39 REMARK 500 8 ARG A 389 70.39 69.14 REMARK 500 8 GLN A 399 -56.37 -120.45 REMARK 500 8 PRO B 180 172.83 -47.85 REMARK 500 9 ARG A 389 70.31 69.02 REMARK 500 9 PRO B 180 172.21 -47.43 REMARK 500 10 ARG A 389 70.28 71.23 REMARK 500 10 PRO B 180 172.46 -47.97 REMARK 500 10 LEU B 185 70.09 63.27 REMARK 500 11 ARG A 389 70.28 70.05 REMARK 500 11 PRO B 180 169.77 -48.13 REMARK 500 12 ARG A 389 70.16 72.15 REMARK 500 12 PRO B 180 172.14 -48.61 REMARK 500 12 LEU B 185 70.09 66.66 REMARK 500 13 ARG A 389 70.29 72.92 REMARK 500 13 PRO B 180 171.51 -48.06 REMARK 500 14 ARG A 389 70.48 69.07 REMARK 500 14 PRO B 180 169.42 -47.70 REMARK 500 15 ARG A 389 70.37 71.17 REMARK 500 15 PRO B 180 170.95 -48.18 REMARK 500 16 ARG A 389 70.20 69.45 REMARK 500 16 PRO B 180 171.00 -48.24 REMARK 500 17 ARG A 389 70.28 78.49 REMARK 500 17 PRO B 180 173.51 -48.01 REMARK 500 18 ARG A 389 70.44 69.54 REMARK 500 18 PRO B 180 171.89 -48.44 REMARK 500 19 ARG A 389 70.36 65.51 REMARK 500 19 GLN A 399 -70.01 -63.41 REMARK 500 19 PRO B 180 170.97 -48.39 REMARK 500 19 LEU B 185 70.30 56.44 REMARK 500 20 ARG A 389 70.32 75.24 REMARK 500 20 PRO B 180 171.40 -47.50 REMARK 500 REMARK 500 THIS ENTRY HAS 62 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17544 RELATED DB: BMRB REMARK 900 RELATED ID: 2LAW RELATED DB: PDB REMARK 900 RELATED ID: 2LAX RELATED DB: PDB REMARK 900 RELATED ID: 2LAY RELATED DB: PDB REMARK 900 RELATED ID: 2LAZ RELATED DB: PDB REMARK 900 RELATED ID: 2LB0 RELATED DB: PDB REMARK 900 RELATED ID: 2LB1 RELATED DB: PDB REMARK 900 RELATED ID: 2LB3 RELATED DB: PDB DBREF 2LB2 A 366 400 UNP Q96PU5 NED4L_HUMAN 386 420 DBREF 2LB2 B 178 189 UNP P84022 SMAD3_HUMAN 178 189 SEQRES 1 A 35 GLY LEU PRO SER GLY TRP GLU GLU ARG LYS ASP ALA LYS SEQRES 2 A 35 GLY ARG THR TYR TYR VAL ASN HIS ASN ASN ARG THR THR SEQRES 3 A 35 THR TRP THR ARG PRO ILE MET GLN LEU SEQRES 1 B 12 GLU TPO PRO PRO PRO GLY TYR LEU SER GLU ASP GLY MODRES 2LB2 TPO B 179 THR PHOSPHOTHREONINE HET TPO B 179 17 HETNAM TPO PHOSPHOTHREONINE HETSYN TPO PHOSPHONOTHREONINE FORMUL 2 TPO C4 H10 N O6 P HELIX 1 1 PRO A 396 LEU A 400 5 5 SHEET 1 A 3 TRP A 371 ASP A 376 0 SHEET 2 A 3 ARG A 380 ASN A 385 -1 O VAL A 384 N GLU A 372 SHEET 3 A 3 THR A 390 THR A 392 -1 O THR A 392 N TYR A 383 LINK C GLU B 178 N TPO B 179 1555 1555 1.33 LINK C TPO B 179 N PRO B 180 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