PDB Short entry for 2MCN HEADER CELL CYCLE/SIGNALING PROTEIN 22-AUG-13 2MCN TITLE DISTINCT UBIQUITIN BINDING MODES EXHIBITED BY SH3 DOMAINS: MOLECULAR TITLE 2 DETERMINANTS AND FUNCTIONAL IMPLICATIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CD2-ASSOCIATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH3A DOMAIN (UNP RESIDUES 2-58); COMPND 5 SYNONYM: MESENCHYME-TO-EPITHELIUM TRANSITION PROTEIN WITH SH3 DOMAINS COMPND 6 1, METS-1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: UBIQUITIN; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 1-76; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: CD2AP, METS1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21A; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: UBC; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET29B KEYWDS CELL CYCLE-SIGNALING PROTEIN COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.ORTEGA-ROLDAN,L.SALMON,A.AZUAGA,M.BLACKLEDGE,N.VAN NULAND REVDAT 3 14-JUN-23 2MCN 1 REMARK REVDAT 2 27-APR-16 2MCN 1 DBREF REMARK SEQRES REVDAT 1 05-FEB-14 2MCN 0 JRNL AUTH J.L.ORTEGA ROLDAN,S.CASARES,M.RINGKJBING JENSEN,N.CARDENES, JRNL AUTH 2 J.BRAVO,M.BLACKLEDGE,A.I.AZUAGA,N.A.VAN NULAND JRNL TITL DISTINCT UBIQUITIN BINDING MODES EXHIBITED BY SH3 DOMAINS: JRNL TITL 2 MOLECULAR DETERMINANTS AND FUNCTIONAL IMPLICATIONS. JRNL REF PLOS ONE V. 8 73018 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 24039852 JRNL DOI 10.1371/JOURNAL.PONE.0073018 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK, CNS/SCULPTOR, HADDOCK REMARK 3 AUTHORS : DOMINGUEZ, BOELENS (HADDOCK), BRUNGER, ADAMS, REMARK 3 CLORE, GROS, NILGES AND READ (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MCN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000103478. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.2 MM [U-99% 15N] CD2AP SH3-A, REMARK 210 1 MM UBIQUITIN, 90% H2O/10% D2O; REMARK 210 0.25 MM [U-99% 15N] UBIQUITIN, REMARK 210 MM CD2AP SH3-A, 90% H2O/10% D2O; REMARK 210 0.9 MM [U-99% 13CU-99% 15N] REMARK 210 CD2AP SH3-A, 0.46 MM [U-99% 15N REMARK 210 UBIQUITIN; 0.8 MM [U-99% 13CU-99% REMARK 210 15N] CD2AP SH3-A, 1.37 MM [U-99% REMARK 210 15N] UBIQUITIN; 0.7 MM [U-99% REMARK 210 13CU-99% 15N] CD2AP SH3-A, 1.75 REMARK 210 MM [U-99% 15N] UBIQUITIN; 0.25 REMARK 210 MM [U-99% 13C; U-99% 15N] CD2AP REMARK 210 SH3-A, 1.75 MM [U-99% 15N] REMARK 210 UBIQUITIN REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO JNH, REMARK 210 JCC, JCH, JCAHA; 2D 1H-15N HSQC REMARK 210 FILTERED DIPSAP REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : UNIFORM NMR SYSTEM REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS/SCULPTOR, NMRVIEW, HADDOCK REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS, DOCKING, SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 1-10 REMARK 465 RES C SSSEQI REMARK 465 ARG A 59 REMARK 465 GLU A 60 REMARK 465 THR A 61 REMARK 465 GLU A 62 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 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 TYR A 8 -171.45 -178.14 REMARK 500 1 ASN A 28 70.66 35.71 REMARK 500 1 ASP B 52 -6.62 -57.35 REMARK 500 1 SER B 65 -161.41 -70.91 REMARK 500 1 ARG B 72 107.40 -57.60 REMARK 500 1 LEU B 73 91.24 62.77 REMARK 500 2 ASN A 52 4.84 -68.24 REMARK 500 2 LEU B 56 8.07 -66.40 REMARK 500 2 ARG B 74 91.02 55.76 REMARK 500 3 ASP B 52 -5.28 -58.34 REMARK 500 3 ARG B 72 -0.54 -142.93 REMARK 500 3 LEU B 73 92.85 63.41 REMARK 500 4 TYR A 8 -177.87 -178.03 REMARK 500 4 ASN A 28 69.18 39.31 REMARK 500 4 LEU B 71 -82.14 -93.78 REMARK 500 4 ARG B 72 -63.90 -168.81 REMARK 500 5 PHE B 45 116.71 176.25 REMARK 500 5 ASP B 52 -5.81 -58.49 REMARK 500 5 ARG B 74 -83.75 62.00 REMARK 500 6 ASP B 52 -7.67 -57.65 REMARK 500 6 SER B 65 -159.58 -70.59 REMARK 500 6 THR B 66 88.17 -160.04 REMARK 500 6 ARG B 72 -76.84 -56.09 REMARK 500 7 ARG A 27 157.32 -47.98 REMARK 500 7 ASN A 28 104.20 -20.61 REMARK 500 7 ILE B 13 87.61 38.61 REMARK 500 7 ASP B 52 -5.39 -57.91 REMARK 500 7 LEU B 56 12.58 -67.11 REMARK 500 7 LEU B 71 -132.61 -116.47 REMARK 500 7 LEU B 73 4.45 -162.75 REMARK 500 8 ILE B 3 -160.15 -120.02 REMARK 500 8 ASP B 52 -19.63 -46.09 REMARK 500 8 ASN B 60 35.07 39.60 REMARK 500 8 LEU B 71 -69.93 -128.97 REMARK 500 8 ARG B 72 -73.31 -158.59 REMARK 500 8 LEU B 73 86.43 -162.86 REMARK 500 9 LEU B 71 -168.70 -121.56 REMARK 500 9 ARG B 72 -161.35 -72.01 REMARK 500 10 SER B 65 -161.35 -71.94 REMARK 500 10 ARG B 72 106.48 -51.01 REMARK 500 10 LEU B 73 91.84 54.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19447 RELATED DB: BMRB REMARK 900 RELATED ID: 2LZ6 RELATED DB: PDB DBREF 2MCN A 2 62 UNP Q9JLQ0 CD2AP_MOUSE 2 62 DBREF 2MCN B 1 76 UNP P0CG48 UBC_HUMAN 1 76 SEQRES 1 A 61 VAL ASP TYR ILE VAL GLU TYR ASP TYR ASP ALA VAL HIS SEQRES 2 A 61 ASP ASP GLU LEU THR ILE ARG VAL GLY GLU ILE ILE ARG SEQRES 3 A 61 ASN VAL LYS LYS LEU GLN GLU GLU GLY TRP LEU GLU GLY SEQRES 4 A 61 GLU LEU ASN GLY ARG ARG GLY MET PHE PRO ASP ASN PHE SEQRES 5 A 61 VAL LYS GLU ILE LYS ARG GLU THR GLU SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HELIX 1 1 PRO A 50 VAL A 54 5 5 HELIX 2 2 THR B 22 ASP B 32 1 11 HELIX 3 3 PRO B 37 GLN B 41 5 5 HELIX 4 4 THR B 55 ASN B 60 5 6 SHEET 1 A 5 ARG A 45 PHE A 49 0 SHEET 2 A 5 LEU A 38 LEU A 42 -1 N LEU A 42 O ARG A 45 SHEET 3 A 5 GLU A 24 LYS A 31 -1 N LYS A 30 O GLU A 39 SHEET 4 A 5 TYR A 4 VAL A 6 -1 N VAL A 6 O GLU A 24 SHEET 5 A 5 LYS A 55 GLU A 56 -1 O LYS A 55 N ILE A 5 SHEET 1 B 2 ASP A 9 TYR A 10 0 SHEET 2 B 2 ILE A 20 ARG A 21 -1 O ILE A 20 N TYR A 10 SHEET 1 C 5 LEU B 15 GLU B 16 0 SHEET 2 C 5 GLN B 2 THR B 7 -1 N ILE B 3 O LEU B 15 SHEET 3 C 5 THR B 66 VAL B 70 1 O LEU B 67 N LYS B 6 SHEET 4 C 5 ARG B 42 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 C 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 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