HEADER PROTEIN BINDING 20-AUG-09 2KNB TITLE SOLUTION NMR STRUCTURE OF THE PARKIN UBL DOMAIN IN COMPLEX WITH THE TITLE 2 ENDOPHILIN-A1 SH3 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE PARKIN; COMPND 3 CHAIN: A; COMPND 4 EC: 6.3.2.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ENDOPHILIN-A1; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: ENDOPHILIN-1, SH3 DOMAIN-CONTAINING GRB2-LIKE PROTEIN 2, SH3 COMPND 10 DOMAIN PROTEIN 2A, SH3P4; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: BROWN RAT,RAT,RATS; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: PARK2, PRKN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: K12; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: BL21 DE3; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PGEX-6P1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 13 ORGANISM_COMMON: BROWN RAT,RAT,RATS; SOURCE 14 ORGANISM_TAXID: 10116; SOURCE 15 GENE: SH3GL2, SH3D2A, SH3P4; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: K12; SOURCE 19 EXPRESSION_SYSTEM_VARIANT: BL21 DE3; SOURCE 20 EXPRESSION_SYSTEM_VECTOR: PGEX-2TK KEYWDS UBL, SH3, PARKIN, ENDOPHILIN, CELL JUNCTION, CELL MEMBRANE, CELL KEYWDS 2 PROJECTION, ENDOPLASMIC RETICULUM, LIGASE, MEMBRANE, METAL-BINDING, KEYWDS 3 NUCLEUS, POSTSYNAPTIC CELL MEMBRANE, S-NITROSYLATION, SYNAPSE, UBL KEYWDS 4 CONJUGATION PATHWAY, ZINC-FINGER, ENDOCYTOSIS, LIPID-BINDING, KEYWDS 5 PHOSPHOPROTEIN, SH3 DOMAIN, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.TREMPE,K.GUENNADI,C.M.EDNA,G.KALLE REVDAT 3 01-MAY-24 2KNB 1 REMARK SEQADV REVDAT 2 19-JUN-13 2KNB 1 JRNL VERSN REVDAT 1 22-DEC-09 2KNB 0 JRNL AUTH J.F.TREMPE,C.X.CHEN,K.GRENIER,E.M.CAMACHO,G.KOZLOV, JRNL AUTH 2 P.S.MCPHERSON,K.GEHRING,E.A.FON JRNL TITL SH3 DOMAINS FROM A SUBSET OF BAR PROTEINS DEFINE A JRNL TITL 2 UBL-BINDING DOMAIN AND IMPLICATE PARKIN IN SYNAPTIC JRNL TITL 3 UBIQUITINATION. JRNL REF MOL.CELL V. 36 1034 2009 JRNL REFN ISSN 1097-2765 JRNL PMID 20064468 JRNL DOI 10.1016/J.MOLCEL.2009.11.021 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.5, CNS 1.2 REMARK 3 AUTHORS : DELAGLIO, F. ET AL. (NMRPIPE), BRUNGER, A. ET AL. REMARK 3 (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HADDOCK USED TO DOCK UBL AND SH3 REMARK 3 CRYSTAL STRUCTURES USING INTERMOLECULAR NOES AND RDCS REMARK 4 REMARK 4 2KNB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000101333. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2 MM [U-99% 13C; U-99% 15N] REMARK 210 UBL, 1.2 MM SH3, 100% D2O; 1.2 REMARK 210 MM [U-99% 13C; U-99% 15N] SH3, REMARK 210 1.2 MM UBL, 100% D2O; 0.8 MM [U- REMARK 210 99% 13C; U-99% 15N] UBL, 1.6 MM REMARK 210 SH3, 95% H2O/5% D2O; 0.8 MM [U- REMARK 210 99% 13C; U-99% 15N] SH3, 1.6 MM REMARK 210 UBL, 95% H2O/5% D2O; 0.8 MM [U- REMARK 210 99% 15N] UBL, 1.6 MM SH3, 95% REMARK 210 H2O/5% D2O; 0.8 MM [U-99% 15N] REMARK 210 SH3, 1.6 MM UBL, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D CBCA(CO)NH; 3D HNCACB; 2D 1H REMARK 210 -15N HSQC; 3D HCCH-COSY; 3D 1H- REMARK 210 13C NOESY; 2D 1H-13C HSQC; 2D 1H- REMARK 210 15N IPAP-HSQC; 3D 1H-13C NOESY REMARK 210 COUPLED REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.115, CNS 1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 GLY B 282 REMARK 465 SER B 283 REMARK 465 ARG B 284 REMARK 465 ARG B 285 REMARK 465 ALA B 286 REMARK 465 SER B 287 REMARK 465 VAL B 288 REMARK 465 GLY B 289 REMARK 465 SER B 290 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 ASP A 60 33.01 -86.70 REMARK 500 1 ASP B 324 -156.85 -151.88 REMARK 500 2 ASP A 60 41.56 -83.45 REMARK 500 2 ILE B 323 -67.70 -95.73 REMARK 500 2 ASP B 324 -155.17 -126.45 REMARK 500 3 SER A 9 -167.29 -120.86 REMARK 500 3 TYR A 11 -168.30 -100.53 REMARK 500 3 ASN A 58 21.65 -141.55 REMARK 500 3 ASP B 324 -154.66 -144.38 REMARK 500 4 ASN A 8 29.61 49.19 REMARK 500 4 TYR A 11 -161.56 -102.36 REMARK 500 4 ASP A 60 26.00 -77.35 REMARK 500 4 ASP B 324 -149.56 -130.12 REMARK 500 4 ASN B 342 30.60 -78.29 REMARK 500 4 LEU B 347 -61.72 -93.24 REMARK 500 5 CYS A 59 -149.50 -147.91 REMARK 500 5 ILE B 323 -66.81 -90.01 REMARK 500 5 ASP B 324 -159.52 -127.56 REMARK 500 5 ASN B 342 29.04 -77.79 REMARK 500 6 ASP A 60 35.63 -81.81 REMARK 500 6 ASN B 321 -177.05 -171.17 REMARK 500 6 ILE B 323 -72.22 -76.94 REMARK 500 6 ASP B 324 -146.77 -120.06 REMARK 500 6 ASN B 326 -26.22 -140.50 REMARK 500 6 LEU B 347 -63.35 -96.59 REMARK 500 7 GLN A 64 66.08 70.75 REMARK 500 7 ASP B 324 -156.22 -151.04 REMARK 500 7 ASN B 326 -26.95 -141.15 REMARK 500 7 ASN B 342 33.83 -80.51 REMARK 500 8 CYS A 59 -158.42 -145.75 REMARK 500 8 ASP B 324 -151.48 -147.94 REMARK 500 8 ASN B 342 23.57 -79.20 REMARK 500 9 ILE B 323 -75.17 -82.93 REMARK 500 9 ASP B 324 -157.06 -123.78 REMARK 500 9 ASN B 326 -37.61 -130.03 REMARK 500 10 ILE B 323 -70.23 -87.82 REMARK 500 10 ASP B 324 -155.97 -125.70 REMARK 500 11 ASP A 60 31.63 -79.45 REMARK 500 11 ASP B 324 -139.09 -140.58 REMARK 500 12 GLN A 64 60.67 65.33 REMARK 500 12 ASP B 324 -155.50 -143.60 REMARK 500 12 ASN B 342 35.18 -79.44 REMARK 500 12 LEU B 347 -65.55 -91.07 REMARK 500 13 TYR A 11 -165.36 -100.91 REMARK 500 13 ASP A 60 32.91 -85.45 REMARK 500 13 ASP B 324 -146.75 -157.07 REMARK 500 14 PRO B 351 103.79 -50.00 REMARK 500 15 ASP A 60 39.13 -83.05 REMARK 500 15 ARG A 75 90.81 -69.66 REMARK 500 15 ASP B 324 -155.60 -138.76 REMARK 500 REMARK 500 THIS ENTRY HAS 72 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2KNB A 1 76 UNP Q9JK66 PRKN2_RAT 1 76 DBREF 2KNB B 291 352 UNP O35179 SH3G2_RAT 291 352 SEQADV 2KNB GLY A -4 UNP Q9JK66 EXPRESSION TAG SEQADV 2KNB PRO A -3 UNP Q9JK66 EXPRESSION TAG SEQADV 2KNB LEU A -2 UNP Q9JK66 EXPRESSION TAG SEQADV 2KNB GLY A -1 UNP Q9JK66 EXPRESSION TAG SEQADV 2KNB SER A 0 UNP Q9JK66 EXPRESSION TAG SEQADV 2KNB GLY B 282 UNP O35179 EXPRESSION TAG SEQADV 2KNB SER B 283 UNP O35179 EXPRESSION TAG SEQADV 2KNB ARG B 284 UNP O35179 EXPRESSION TAG SEQADV 2KNB ARG B 285 UNP O35179 EXPRESSION TAG SEQADV 2KNB ALA B 286 UNP O35179 EXPRESSION TAG SEQADV 2KNB SER B 287 UNP O35179 EXPRESSION TAG SEQADV 2KNB VAL B 288 UNP O35179 EXPRESSION TAG SEQADV 2KNB GLY B 289 UNP O35179 EXPRESSION TAG SEQADV 2KNB SER B 290 UNP O35179 EXPRESSION TAG SEQRES 1 A 81 GLY PRO LEU GLY SER MET ILE VAL PHE VAL ARG PHE ASN SEQRES 2 A 81 SER SER TYR GLY PHE PRO VAL GLU VAL ASP SER ASP THR SEQRES 3 A 81 SER ILE PHE GLN LEU LYS GLU VAL VAL ALA LYS ARG GLN SEQRES 4 A 81 GLY VAL PRO ALA ASP GLN LEU ARG VAL ILE PHE ALA GLY SEQRES 5 A 81 LYS GLU LEU GLN ASN HIS LEU THR VAL GLN ASN CYS ASP SEQRES 6 A 81 LEU GLU GLN GLN SER ILE VAL HIS ILE VAL GLN ARG PRO SEQRES 7 A 81 GLN ARG LYS SEQRES 1 B 71 GLY SER ARG ARG ALA SER VAL GLY SER ASP GLN PRO CYS SEQRES 2 B 71 CYS ARG ALA LEU TYR ASP PHE GLU PRO GLU ASN GLU GLY SEQRES 3 B 71 GLU LEU GLY PHE LYS GLU GLY ASP ILE ILE THR LEU THR SEQRES 4 B 71 ASN GLN ILE ASP GLU ASN TRP TYR GLU GLY MET LEU HIS SEQRES 5 B 71 GLY GLN SER GLY PHE PHE PRO ILE ASN TYR VAL GLU ILE SEQRES 6 B 71 LEU VAL ALA LEU PRO HIS HELIX 1 1 SER A 22 GLY A 35 1 14 HELIX 2 2 PRO A 37 ASP A 39 5 3 HELIX 3 3 THR A 55 CYS A 59 5 5 SHEET 1 A 5 PHE A 13 GLU A 16 0 SHEET 2 A 5 ILE A 2 ARG A 6 -1 N VAL A 3 O VAL A 15 SHEET 3 A 5 SER A 65 GLN A 71 1 O VAL A 67 N PHE A 4 SHEET 4 A 5 LEU A 41 PHE A 45 -1 N ILE A 44 O HIS A 68 SHEET 5 A 5 LYS A 48 LEU A 50 -1 O LYS A 48 N PHE A 45 SHEET 1 B 5 GLN B 335 PRO B 340 0 SHEET 2 B 5 TRP B 327 LEU B 332 -1 N TYR B 328 O PHE B 339 SHEET 3 B 5 ILE B 316 GLN B 322 -1 N ASN B 321 O GLU B 329 SHEET 4 B 5 CYS B 295 ALA B 297 -1 N CYS B 295 O ILE B 317 SHEET 5 B 5 VAL B 344 ILE B 346 -1 O GLU B 345 N ARG B 296 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