PDB Short entry for 2LZ6 HEADER SIGNALING PROTEIN 24-SEP-12 2LZ6 TITLE DISTINCT UBIQUITIN BINDING MODES EXHIBITED BY SH3 DOMAINS: MOLECULAR TITLE 2 DETERMINANTS AND FUNCTIONAL IMPLICATIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: CD2-ASSOCIATED PROTEIN; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: SH3 3 DOMAIN RESIDUES 270-329; COMPND 9 SYNONYM: MESENCHYME-TO-EPITHELIUM TRANSITION PROTEIN WITH SH3 DOMAINS COMPND 10 1, METS-1; COMPND 11 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: UBC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET29B; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 11 ORGANISM_COMMON: MOUSE; SOURCE 12 ORGANISM_TAXID: 10090; SOURCE 13 GENE: CD2AP, METS1; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_VECTOR: PETM-11 KEYWDS SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.ORTEGA-ROLDAN,A.AZUAGA,M.BLACKLEDGE,N.VAN NULAND REVDAT 3 14-JUN-23 2LZ6 1 REMARK SEQADV REVDAT 2 27-APR-16 2LZ6 1 ATOM REMARK SEQADV SEQRES REVDAT 1 02-OCT-13 2LZ6 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 REMARK 3 AUTHORS : ALEXANDRE BONVIN (HADDOCK), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNS/SCULPTOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DOCKING REMARK 4 REMARK 4 2LZ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000103009. 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-C, REMARK 210 1 MM UBIQUITIN, 90% H2O/10% D2O; REMARK 210 0.25 MM [U-99% 15N] UBIQUITIN, 1 REMARK 210 MM CD2AP SH3-C, 90% H2O/10% D2O; REMARK 210 0.9 MM [U-99% 13C; U-99% 15N] REMARK 210 CD2AP SH3-C, 0.46 MM [U-99% 15N] REMARK 210 UBIQUITIN, 90% H2O/10% D2O; REMARK 210 0.828 MM [U-99% 13C; U-99% 15N] REMARK 210 CD2AP SH3-C, 1.37 MM [U-99% 15N] REMARK 210 UBIQUITIN, 90% H2O/10% D2O; 0.78 REMARK 210 MM [U-99% 13C; U-99% 15N] CD2AP REMARK 210 SH3-C, 1.75 MM [U-99% 15N] REMARK 210 UBIQUITIN, 90% H2O/10% D2O; 0.25 REMARK 210 MM [U-99% 13C; U-99% 15N] CD2AP REMARK 210 SH3-C, 1.75 MM [U-99% 15N] REMARK 210 UBIQUITIN, 90% H2O/10% D2O 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 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 GLY B 1 REMARK 465 ALA B 2 REMARK 465 MET B 3 REMARK 465 GLY B 4 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 72 87.44 53.95 REMARK 500 1 LYS B 6 116.98 -165.69 REMARK 500 1 SER B 35 113.62 -167.06 REMARK 500 1 LYS B 36 5.11 -69.32 REMARK 500 1 ASN B 49 64.74 -17.69 REMARK 500 1 ASN B 58 92.92 60.00 REMARK 500 1 GLN B 62 105.62 -54.47 REMARK 500 2 SER A 20 31.18 -77.87 REMARK 500 2 LYS A 33 -62.04 -93.11 REMARK 500 2 ARG A 42 38.04 -142.77 REMARK 500 2 LEU A 43 127.59 -20.83 REMARK 500 2 ALA A 46 13.71 51.81 REMARK 500 2 LYS A 48 -154.21 -70.27 REMARK 500 2 ARG A 54 163.20 -34.24 REMARK 500 2 GLN A 62 -165.42 -105.47 REMARK 500 2 LEU A 69 -172.13 -63.94 REMARK 500 2 VAL A 70 106.81 -162.94 REMARK 500 2 LEU A 71 76.42 -112.41 REMARK 500 2 LYS B 6 117.18 -169.37 REMARK 500 2 LYS B 36 -72.20 -65.18 REMARK 500 2 GLU B 37 100.16 -44.80 REMARK 500 2 ASN B 49 65.69 -18.30 REMARK 500 2 ASP B 57 -13.55 79.57 REMARK 500 2 ASN B 58 76.60 56.22 REMARK 500 3 LYS A 33 -63.04 -90.23 REMARK 500 3 ARG A 72 95.14 61.37 REMARK 500 3 LYS B 36 -72.26 -58.32 REMARK 500 3 GLU B 37 96.05 -45.04 REMARK 500 3 ASN B 49 65.19 -17.88 REMARK 500 3 ASP B 57 -14.14 79.75 REMARK 500 3 ASN B 58 76.94 57.30 REMARK 500 4 ARG A 54 152.53 -26.77 REMARK 500 4 ARG A 72 100.33 50.31 REMARK 500 4 LYS B 36 6.22 -69.52 REMARK 500 4 ASN B 49 64.45 -17.92 REMARK 500 4 ASP B 57 -10.68 78.78 REMARK 500 4 PHE B 59 3.97 -56.64 REMARK 500 5 SER A 20 32.92 -80.95 REMARK 500 5 ARG A 54 156.34 -28.55 REMARK 500 5 ARG A 74 147.82 -176.43 REMARK 500 5 GLU B 22 146.69 -32.35 REMARK 500 5 ASN B 49 80.96 -22.03 REMARK 500 5 ASP B 57 -12.45 77.34 REMARK 500 5 ASN B 58 75.66 58.19 REMARK 500 6 LYS A 48 -163.04 -71.07 REMARK 500 6 LEU A 50 106.51 58.50 REMARK 500 6 ARG A 54 155.17 -27.53 REMARK 500 6 GLN A 62 -168.68 -109.35 REMARK 500 6 LEU A 73 -150.07 -144.94 REMARK 500 6 ARG A 74 92.06 -55.14 REMARK 500 REMARK 500 THIS ENTRY HAS 83 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18737 RELATED DB: BMRB REMARK 900 RELATED ID: 2LZ7 RELATED DB: PDB DBREF 2LZ6 A 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 2LZ6 B 5 64 UNP Q9JLQ0 CD2AP_MOUSE 270 329 SEQADV 2LZ6 GLY B 1 UNP Q9JLQ0 EXPRESSION TAG SEQADV 2LZ6 ALA B 2 UNP Q9JLQ0 EXPRESSION TAG SEQADV 2LZ6 MET B 3 UNP Q9JLQ0 EXPRESSION TAG SEQADV 2LZ6 GLY B 4 UNP Q9JLQ0 EXPRESSION TAG SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 B 64 GLY ALA MET GLY ALA LYS GLU TYR CYS ARG THR LEU PHE SEQRES 2 B 64 PRO TYR THR GLY THR ASN GLU ASP GLU LEU THR PHE ARG SEQRES 3 B 64 GLU GLY GLU ILE ILE HIS LEU ILE SER LYS GLU THR GLY SEQRES 4 B 64 GLU ALA GLY TRP TRP LYS GLY GLU LEU ASN GLY LYS GLU SEQRES 5 B 64 GLY VAL PHE PRO ASP ASN PHE ALA VAL GLN ILE SER HELIX 1 1 THR A 22 GLY A 35 1 14 SHEET 1 A 5 ILE A 13 GLU A 16 0 SHEET 2 A 5 GLN A 2 THR A 7 -1 N VAL A 5 O ILE A 13 SHEET 3 A 5 SER A 65 VAL A 70 1 O SER A 65 N PHE A 4 SHEET 4 A 5 ARG A 42 PHE A 45 -1 N ARG A 42 O VAL A 70 SHEET 5 A 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 SHEET 1 B 5 LYS B 51 PRO B 56 0 SHEET 2 B 5 TRP B 43 LEU B 48 -1 N LEU B 48 O LYS B 51 SHEET 3 B 5 ILE B 30 SER B 35 -1 N ILE B 34 O LYS B 45 SHEET 4 B 5 TYR B 8 THR B 11 -1 N CYS B 9 O ILE B 31 SHEET 5 B 5 ALA B 60 GLN B 62 -1 O VAL B 61 N ARG B 10 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