PDB Short entry for 2K4D HEADER LIGASE 06-JUN-08 2K4D TITLE E2-C-CBL RECOGNITION IS NECESSARY BUT NOT SUFFICIENT FOR TITLE 2 UBIQUITINATION ACTIVITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE CBL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RING DOMAIN, RESIDUES 358-437; COMPND 5 SYNONYM: SIGNAL TRANSDUCTION PROTEIN CBL, PROTO-ONCOGENE C-CBL, COMPND 6 CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE, RING FINGER PROTEIN 55; COMPND 7 EC: 6.3.2.-; COMPND 8 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: CBL, CBL2, RNF55; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) ROSETTA 2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PLICHISGST KEYWDS PROTEIN, UBIQUITIN, C-CBL, UBCH5B, UBCH7, CALCIUM, CYTOPLASM, LIGASE, KEYWDS 2 METAL-BINDING, PHOSPHOPROTEIN, PROTO-ONCOGENE, SH2 DOMAIN, UBL KEYWDS 3 CONJUGATION PATHWAY, ZINC, ZINC-FINGER EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.HUANG,R.N.DE JONG,H.WIENK,S.G.WINKLER,H.T.M.TIMMERS,R.BOELENS REVDAT 3 14-JUN-23 2K4D 1 REMARK DBREF REVDAT 2 26-FEB-20 2K4D 1 REMARK SEQADV REVDAT 1 20-JAN-09 2K4D 0 JRNL AUTH A.HUANG,R.N.DE JONG,H.WIENK,G.S.WINKLER,H.T.M.TIMMERS, JRNL AUTH 2 R.BOELENS JRNL TITL E2-C-CBL RECOGNITION IS NECESSARY BUT NOT SUFFICIENT FOR JRNL TITL 2 UBIQUITINATION ACTIVITY JRNL REF J.MOL.BIOL. V. 385 507 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 18996392 JRNL DOI 10.1016/J.JMB.2008.10.044 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1.1, CYANA 2.1.1 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 GUNTERT, MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RECOORD APPROACH REMARK 4 REMARK 4 2K4D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000100660. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.3 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM [U-99% 15N] C-CBL; 50MM REMARK 210 POTASSIUM PHOSPHATE; 100MM REMARK 210 SODIUM CHLORIDE; 0.100MM ZINC REMARK 210 CHLORIDE; 0.2MM PMSF; 5MM DTT; REMARK 210 95% H2O/5% D2O; 1MM [U-99% 13C; REMARK 210 U-99% 15N] C-CBL; 50MM POTASSIUM REMARK 210 PHOSPHATE; 100MM SODIUM CHLORIDE; REMARK 210 0.100MM ZINC CHLORIDE; 0.2MM REMARK 210 PMSF; 5MM DTT; 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H NOESY; 3D CBCA(CO)NH; REMARK 210 3D C(CO)NH; 3D HNCO; 3D HNCA; 3D REMARK 210 HNCACB; 3D HBHA(CO)NH; 3D HN(CO) REMARK 210 CA; 3D HCCH-TOCSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-15N TOCSY; 3D 1H- REMARK 210 13C NOESY; 3D HNCACO; 3D CNH- REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 HZ3 LYS A 392 OE2 GLU A 394 1.59 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 GLU A 366 134.34 175.34 REMARK 500 1 LEU A 370 30.66 -76.19 REMARK 500 1 MET A 374 84.06 62.08 REMARK 500 1 LEU A 380 142.71 89.79 REMARK 500 1 ALA A 385 -7.94 71.66 REMARK 500 1 MET A 400 -176.86 -173.04 REMARK 500 1 GLU A 412 107.03 74.84 REMARK 500 1 GLN A 414 49.18 -78.11 REMARK 500 1 PHE A 418 -73.35 -80.29 REMARK 500 1 GLU A 422 116.43 -36.99 REMARK 500 1 ILE A 429 -86.99 -108.54 REMARK 500 1 VAL A 430 87.73 72.46 REMARK 500 1 PHE A 434 -78.83 64.69 REMARK 500 1 ASP A 435 89.19 -154.36 REMARK 500 2 GLN A 358 178.88 66.42 REMARK 500 2 ASP A 359 -78.40 -123.31 REMARK 500 2 HIS A 360 -53.37 66.57 REMARK 500 2 THR A 364 -100.37 -103.50 REMARK 500 2 CYS A 372 107.52 81.12 REMARK 500 2 GLU A 386 -54.00 -126.20 REMARK 500 2 GLU A 412 78.28 63.04 REMARK 500 2 PHE A 418 -67.67 -90.67 REMARK 500 2 GLU A 422 109.68 -44.55 REMARK 500 3 LYS A 362 -177.96 66.27 REMARK 500 3 VAL A 363 74.94 -100.73 REMARK 500 3 MET A 374 -52.24 72.31 REMARK 500 3 GLU A 412 89.44 66.31 REMARK 500 3 ARG A 420 72.37 57.95 REMARK 500 3 CYS A 421 -158.91 -126.56 REMARK 500 3 LYS A 424 -57.40 -123.65 REMARK 500 3 ILE A 429 149.68 61.07 REMARK 500 3 ASP A 435 71.46 52.10 REMARK 500 4 SER A 356 -74.96 -102.51 REMARK 500 4 GLN A 358 -175.12 60.97 REMARK 500 4 ASP A 359 -70.51 -94.66 REMARK 500 4 GLU A 412 89.21 74.50 REMARK 500 4 PHE A 418 -72.44 -93.38 REMARK 500 4 GLU A 422 115.53 -38.34 REMARK 500 4 LYS A 424 -39.80 -134.99 REMARK 500 4 PRO A 433 92.04 -61.62 REMARK 500 5 ASP A 359 80.04 59.60 REMARK 500 5 GLN A 367 31.24 -72.57 REMARK 500 5 MET A 374 91.72 -177.31 REMARK 500 5 ALA A 385 -37.00 70.87 REMARK 500 5 GLU A 412 92.93 72.72 REMARK 500 5 PHE A 418 -72.45 -91.91 REMARK 500 5 GLU A 422 124.30 -35.73 REMARK 500 5 PHE A 434 -63.21 -92.14 REMARK 500 6 SER A 356 95.76 63.66 REMARK 500 6 ILE A 361 126.98 75.34 REMARK 500 REMARK 500 THIS ENTRY HAS 173 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 13 ARG A 420 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FBV RELATED DB: PDB REMARK 900 C-CBL UBCH7 CRYSTAL STRUCTURE REMARK 900 RELATED ID: 15796 RELATED DB: BMRB DBREF 2K4D A 358 437 UNP P22681 CBL_HUMAN 358 437 SEQADV 2K4D GLY A 355 UNP P22681 EXPRESSION TAG SEQADV 2K4D SER A 356 UNP P22681 EXPRESSION TAG SEQADV 2K4D LEU A 357 UNP P22681 EXPRESSION TAG SEQRES 1 A 83 GLY SER LEU GLN ASP HIS ILE LYS VAL THR GLN GLU GLN SEQRES 2 A 83 TYR GLU LEU TYR CYS GLU MET GLY SER THR PHE GLN LEU SEQRES 3 A 83 CYS LYS ILE CYS ALA GLU ASN ASP LYS ASP VAL LYS ILE SEQRES 4 A 83 GLU PRO CYS GLY HIS LEU MET CYS THR SER CYS LEU THR SEQRES 5 A 83 SER TRP GLN GLU SER GLU GLY GLN GLY CYS PRO PHE CYS SEQRES 6 A 83 ARG CYS GLU ILE LYS GLY THR GLU PRO ILE VAL VAL ASP SEQRES 7 A 83 PRO PHE ASP PRO ARG HET ZN A 500 1 HET ZN A 600 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 CYS A 401 GLU A 410 1 10 SHEET 1 A 3 HIS A 398 MET A 400 0 SHEET 2 A 3 VAL A 391 PRO A 395 -1 N VAL A 391 O MET A 400 SHEET 3 A 3 ILE A 423 PRO A 428 -1 O GLU A 427 N LYS A 392 SSBOND 1 CYS A 401 CYS A 404 1555 1555 2.95 LINK SG CYS A 381 ZN ZN A 500 1555 1555 1.91 CISPEP 1 GLU A 394 PRO A 395 1 0.44 CISPEP 2 GLU A 394 PRO A 395 2 -1.57 CISPEP 3 GLU A 394 PRO A 395 3 0.29 CISPEP 4 GLU A 394 PRO A 395 4 -0.05 CISPEP 5 GLU A 394 PRO A 395 5 1.72 CISPEP 6 GLU A 394 PRO A 395 6 -0.20 CISPEP 7 GLU A 394 PRO A 395 7 2.15 CISPEP 8 GLU A 394 PRO A 395 8 0.96 CISPEP 9 GLU A 394 PRO A 395 9 -2.28 CISPEP 10 GLU A 394 PRO A 395 10 -0.66 CISPEP 11 GLU A 394 PRO A 395 11 -2.47 CISPEP 12 GLU A 394 PRO A 395 12 -1.33 CISPEP 13 GLU A 394 PRO A 395 13 1.99 CISPEP 14 GLU A 394 PRO A 395 14 -1.60 CISPEP 15 GLU A 394 PRO A 395 15 1.26 CISPEP 16 GLU A 394 PRO A 395 16 0.64 CISPEP 17 GLU A 394 PRO A 395 17 -1.40 CISPEP 18 GLU A 394 PRO A 395 18 1.95 CISPEP 19 GLU A 394 PRO A 395 19 -0.96 CISPEP 20 GLU A 394 PRO A 395 20 0.98 SITE 1 AC1 5 CYS A 381 ILE A 383 CYS A 384 ASN A 387 SITE 2 AC1 5 ASP A 388 SITE 1 AC2 4 ILE A 393 CYS A 396 HIS A 398 CYS A 421 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