HEADER SH3 DOMAIN/UBIQUITIN 07-JUL-08 2K6D TITLE CIN85 SH3-C DOMAIN IN COMPLEX WITH UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SH3 DOMAIN-CONTAINING KINASE-BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CIN85 SH3-C DOMAIN; COMPND 5 SYNONYM: CBL-INTERACTING PROTEIN OF 85 KDA, HUMAN SRC FAMILY KINASE- COMPND 6 BINDING PROTEIN 1, HSB-1, CD2-BINDING PROTEIN 3, CD2BP3; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: UBIQUITIN; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UBIQUITIN; COMPND 12 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: SH3KBP1, CIN85; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28-B; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PETM11 KEYWDS CIN85, SH3 DOMAIN, UBIQUITIN, ALTERNATIVE SPLICING, APOPTOSIS, CELL KEYWDS 2 JUNCTION, COILED COIL, CYTOPLASM, CYTOPLASMIC VESICLE, CYTOSKELETON, KEYWDS 3 ENDOCYTOSIS, MEMBRANE, PHOSPHOPROTEIN, POLYMORPHISM, SH3-BINDING, KEYWDS 4 SYNAPSE, SYNAPTOSOME, UBL CONJUGATION, NUCLEUS, SH3 DOMAIN-UBIQUITIN KEYWDS 5 COMPLEX EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR J.FORMAN-KAY,I.BEZSONOVA REVDAT 5 01-MAY-24 2K6D 1 SEQADV REVDAT 4 04-JUL-18 2K6D 1 REMARK SSBOND REVDAT 3 24-FEB-09 2K6D 1 VERSN REVDAT 2 02-SEP-08 2K6D 1 JRNL REVDAT 1 19-AUG-08 2K6D 0 JRNL AUTH I.BEZSONOVA,M.C.BRUCE,S.WIESNER,H.LIN,D.ROTIN,J.D.FORMAN-KAY JRNL TITL INTERACTIONS BETWEEN THE THREE CIN85 SH3 DOMAINS AND JRNL TITL 2 UBIQUITIN: IMPLICATIONS FOR CIN85 UBIQUITINATION. JRNL REF BIOCHEMISTRY V. 47 8937 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18680311 JRNL DOI 10.1021/BI800439T REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK, HADDOCK REMARK 3 AUTHORS : CYRIL DOMINGUEZ, ROLF BOELENS AND ALEXANDRE M.J.J. REMARK 3 BONVIN (HADDOCK), CYRIL DOMINGUEZ, ROLF BOELENS REMARK 3 AND ALEXANDRE M.J.J. BONVIN (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K6D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000100732. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.4 REMARK 210 IONIC STRENGTH : 0.150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.1 MM CIN85, 0.1 MM [U-100% REMARK 210 15N] UBIQUITIN, 50 MM SODIUM REMARK 210 PHOSPHATE, 2 MM DTT, 5 MM DSS, REMARK 210 150 MM SODIUM CHLORIDE, 90% H2O/ REMARK 210 10% D2O; 0.1 MM [U-100% 15N] REMARK 210 CIN85, 0.1 MM UBIQUITINY, 50 MM REMARK 210 SODIUM PHOSPHATE, 2 MM DTT, 5 MM REMARK 210 DSS, 150 MM SODIUM CHLORIDE, 90% REMARK 210 H2O/10% D2O; 1.0 MM [U-100% 13C; REMARK 210 U-100% 15N] CIN85, 50 MM SODIUM REMARK 210 PHOSPHATE, 2 MM DTT, 5 MM DSS, REMARK 210 150 MM SODIUM CHLORIDE, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; IPAP REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 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 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 278 -150.17 -101.74 REMARK 500 1 ALA A 280 97.46 -28.67 REMARK 500 1 CYS A 301 -133.51 -64.12 REMARK 500 1 PHE A 322 2.39 -63.42 REMARK 500 1 THR B 7 -149.95 -90.87 REMARK 500 1 LYS B 11 150.05 -43.62 REMARK 500 1 LEU B 71 -96.16 -78.46 REMARK 500 1 ARG B 72 64.04 156.69 REMARK 500 1 ARG B 74 -60.89 -131.37 REMARK 500 2 ILE A 275 -78.64 -78.38 REMARK 500 2 ALA A 280 104.24 -31.35 REMARK 500 2 CYS A 301 -144.72 -58.00 REMARK 500 2 THR B 7 -142.59 -91.30 REMARK 500 2 LYS B 11 153.45 -46.80 REMARK 500 2 LEU B 73 -62.67 -148.43 REMARK 500 3 ALA A 280 108.18 -30.05 REMARK 500 3 CYS A 301 -149.50 -61.93 REMARK 500 3 PHE A 322 -7.92 -56.87 REMARK 500 3 THR B 7 -146.35 -90.35 REMARK 500 3 LYS B 11 154.41 -46.96 REMARK 500 3 LEU B 71 -73.02 -125.17 REMARK 500 3 ARG B 72 -154.28 -167.18 REMARK 500 4 ALA A 280 104.73 -31.99 REMARK 500 4 CYS A 301 -158.79 -61.80 REMARK 500 4 PHE A 322 -1.38 -59.96 REMARK 500 4 THR B 7 -140.65 -78.97 REMARK 500 4 LEU B 71 -76.79 -108.40 REMARK 500 4 ARG B 72 -85.79 -173.38 REMARK 500 4 LEU B 73 -30.52 -135.45 REMARK 500 5 ALA A 280 114.43 -32.64 REMARK 500 5 CYS A 301 -155.95 -55.79 REMARK 500 5 THR B 7 -149.67 -84.91 REMARK 500 5 LYS B 11 157.20 -49.22 REMARK 500 5 LEU B 67 -165.89 -124.96 REMARK 500 5 LEU B 73 -34.60 -132.78 REMARK 500 6 ALA A 280 110.46 -34.34 REMARK 500 6 CYS A 301 -136.40 -59.79 REMARK 500 6 PHE A 322 -4.16 -56.76 REMARK 500 6 THR B 7 -155.05 -79.89 REMARK 500 6 LYS B 11 157.99 -49.76 REMARK 500 6 LEU B 71 -79.53 -135.68 REMARK 500 7 ALA A 280 104.26 -31.52 REMARK 500 7 CYS A 301 -147.65 -60.16 REMARK 500 7 THR B 7 -153.21 -81.21 REMARK 500 7 LYS B 11 157.36 -49.80 REMARK 500 7 LEU B 73 -157.70 -151.57 REMARK 500 8 ALA A 280 96.93 -30.59 REMARK 500 8 CYS A 301 -155.54 -60.77 REMARK 500 8 PHE A 322 0.08 -64.51 REMARK 500 8 THR B 7 -157.65 -77.61 REMARK 500 REMARK 500 THIS ENTRY HAS 51 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG B 54 0.16 SIDE CHAIN REMARK 500 2 ARG B 54 0.16 SIDE CHAIN REMARK 500 3 ARG B 54 0.16 SIDE CHAIN REMARK 500 4 ARG B 54 0.16 SIDE CHAIN REMARK 500 5 ARG B 54 0.16 SIDE CHAIN REMARK 500 6 ARG B 54 0.16 SIDE CHAIN REMARK 500 7 ARG B 54 0.16 SIDE CHAIN REMARK 500 8 ARG B 54 0.16 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2K6D A 267 328 UNP Q96B97 SH3K1_HUMAN 267 328 DBREF 2K6D B 1 75 UNP P62988 UBIQ_HUMAN 1 75 SEQADV 2K6D CYS B 76 UNP P62988 EXPRESSION TAG SEQRES 1 A 62 LYS SER LYS ASP TYR CYS LYS VAL ILE PHE PRO TYR GLU SEQRES 2 A 62 ALA GLN ASN ASP ASP GLU LEU THR ILE LYS GLU GLY ASP SEQRES 3 A 62 ILE VAL THR LEU ILE ASN LYS ASP CYS ILE ASP VAL GLY SEQRES 4 A 62 TRP TRP GLU GLY GLU LEU ASN GLY ARG ARG GLY VAL PHE SEQRES 5 A 62 PRO ASP ASN PHE VAL LYS LEU LEU PRO PRO 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 CYS HELIX 1 1 ASN A 321 VAL A 323 5 3 HELIX 2 2 THR B 22 GLY B 35 1 14 HELIX 3 3 PRO B 37 GLN B 41 5 5 HELIX 4 4 LEU B 56 ASN B 60 5 5 SHEET 1 A 5 ARG A 314 PRO A 319 0 SHEET 2 A 5 TRP A 306 LEU A 311 -1 N GLY A 309 O GLY A 316 SHEET 3 A 5 ILE A 293 ASN A 298 -1 N ILE A 297 O GLU A 308 SHEET 4 A 5 TYR A 271 LYS A 273 -1 N CYS A 272 O VAL A 294 SHEET 5 A 5 LYS A 324 LEU A 325 -1 O LYS A 324 N LYS A 273 SHEET 1 B 3 THR B 14 GLU B 16 0 SHEET 2 B 3 GLN B 2 LYS B 6 -1 N ILE B 3 O LEU B 15 SHEET 3 B 3 THR B 66 HIS B 68 1 O LEU B 67 N PHE B 4 SHEET 1 C 2 ILE B 44 PHE B 45 0 SHEET 2 C 2 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 MODEL 1