HEADER PROTEIN BINDING 04-SEP-09 2KNV TITLE NMR DIMER STRUCTURE OF THE UBA DOMAIN OF P62 (SQSTM1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEQUESTOSOME-1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UBA DOMAIN, UNP RESIDUES 387-436; COMPND 5 SYNONYM: PHOSPHOTYROSINE-INDEPENDENT LIGAND FOR THE LCK SH2 DOMAIN OF COMPND 6 62 KDA, UBIQUITIN-BINDING PROTEIN P62, EBI3-ASSOCIATED PROTEIN OF 60 COMPND 7 KDA, P60, EBIAP; 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: SQSTM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PGEX-4T-1 KEYWDS UBIQUITIN BINDING, UBIQUITIN-ASSOCIATED DOMAIN, PAGET S DISEASE OF KEYWDS 2 BONE, HELICAL BUNDLE, DIMER, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.E.LONG,M.S.SEARLE REVDAT 2 16-MAR-22 2KNV 1 REMARK SEQADV REVDAT 1 15-DEC-09 2KNV 0 JRNL AUTH J.LONG,T.P.GARNER,M.J.PANDYA,C.J.CRAVEN,P.CHEN,B.SHAW, JRNL AUTH 2 M.P.WILLIAMSON,R.LAYFIELD,M.S.SEARLE JRNL TITL DIMERISATION OF THE UBA DOMAIN OF P62 INHIBITS UBIQUITIN JRNL TITL 2 BINDING AND REGULATES NF-KAPPAB SIGNALLING JRNL REF J.MOL.BIOL. 2009 JRNL REFN ESSN 1089-8638 JRNL PMID 19931284 JRNL DOI 10.1016/J.JMB.2009.11.032 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1, HADDOCK 2.0 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), ALEXANDRE BONVIN REMARK 3 (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KNV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000101352. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3 MM [U-99% 13C; U-99% 15N] REMARK 210 UBA-1, 0.6 MM UBA-2, 50 MM REMARK 210 POTASSIUM PHOSPHATE-3, 50 MM REMARK 210 SODIUM CHLORIDE-4, 0.04 % SODIUM REMARK 210 AZIDE-5, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HALF-FILTER NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR 1.15, HADDOCK 2.0 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: 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 HZ2 LYS A 36 OE2 GLU B 25 1.56 REMARK 500 OE2 GLU A 25 HG1 THR B 35 1.60 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 ASN A 37 -178.05 66.62 REMARK 500 1 GLN A 48 -47.06 71.66 REMARK 500 1 TYR A 49 100.14 -53.78 REMARK 500 1 ASN B 37 171.39 69.99 REMARK 500 1 TYR B 38 38.39 -81.12 REMARK 500 1 GLN B 48 -14.17 68.77 REMARK 500 2 ASN A 37 168.11 69.00 REMARK 500 2 TYR A 38 36.51 -81.94 REMARK 500 2 GLN A 48 -38.58 69.50 REMARK 500 2 TYR A 49 79.21 -66.38 REMARK 500 2 GLU B 25 -60.78 -104.77 REMARK 500 2 ASN B 37 168.74 70.32 REMARK 500 2 TYR B 38 35.47 -87.31 REMARK 500 2 GLN B 48 -40.27 71.36 REMARK 500 2 TYR B 49 99.75 -60.28 REMARK 500 3 ASN A 37 177.53 67.26 REMARK 500 3 TYR A 38 36.86 -87.16 REMARK 500 3 GLN A 48 -44.41 69.43 REMARK 500 3 SER A 50 -30.92 -143.63 REMARK 500 3 ASN B 37 166.91 67.65 REMARK 500 3 GLN B 48 -7.22 65.57 REMARK 500 3 LYS B 51 -70.89 -118.99 REMARK 500 4 ASN A 37 163.53 73.49 REMARK 500 4 TYR A 38 36.21 -81.72 REMARK 500 4 GLN A 48 -51.20 70.50 REMARK 500 4 ASN B 37 179.74 67.64 REMARK 500 4 TYR B 38 30.34 -96.16 REMARK 500 5 ASN A 37 169.32 69.53 REMARK 500 5 TYR A 38 41.85 -85.89 REMARK 500 5 GLN A 48 -43.37 71.95 REMARK 500 5 TYR A 49 90.21 -69.09 REMARK 500 5 SER B 23 126.41 -172.92 REMARK 500 5 ASN B 37 -177.92 69.28 REMARK 500 5 TYR B 38 34.28 -94.62 REMARK 500 5 GLN B 48 -42.16 73.49 REMARK 500 5 TYR B 49 97.89 -57.32 REMARK 500 5 SER B 50 -39.99 -136.59 REMARK 500 6 ASN A 37 175.26 68.69 REMARK 500 6 GLN A 48 -30.31 69.49 REMARK 500 6 LYS A 51 -62.36 -122.20 REMARK 500 6 ASN B 37 178.67 69.45 REMARK 500 6 TYR B 38 35.37 -92.27 REMARK 500 6 GLN B 48 -51.25 71.34 REMARK 500 6 TYR B 49 100.02 -54.21 REMARK 500 6 LYS B 51 -69.14 -94.34 REMARK 500 7 ASN A 37 171.83 69.03 REMARK 500 7 TYR A 38 33.28 -83.73 REMARK 500 7 GLN A 48 -39.02 71.94 REMARK 500 7 TYR A 49 97.79 -57.15 REMARK 500 7 LYS A 51 -64.92 -121.53 REMARK 500 REMARK 500 THIS ENTRY HAS 78 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K0B RELATED DB: PDB REMARK 900 MONOMERIC UNIT REMARK 900 RELATED ID: 2JY7 RELATED DB: PDB REMARK 900 MONOMERIC UNIT RDC REFINED REMARK 900 RELATED ID: 15591 RELATED DB: BMRB REMARK 900 ORIGINAL ASSIGNMENT DBREF 2KNV A 3 52 UNP Q13501 SQSTM_HUMAN 387 436 DBREF 2KNV B 3 52 UNP Q13501 SQSTM_HUMAN 387 436 SEQADV 2KNV GLY A 1 UNP Q13501 EXPRESSION TAG SEQADV 2KNV SER A 2 UNP Q13501 EXPRESSION TAG SEQADV 2KNV GLY B 1 UNP Q13501 EXPRESSION TAG SEQADV 2KNV SER B 2 UNP Q13501 EXPRESSION TAG SEQRES 1 A 52 GLY SER PRO PRO GLU ALA ASP PRO ARG LEU ILE GLU SER SEQRES 2 A 52 LEU SER GLN MET LEU SER MET GLY PHE SER ASP GLU GLY SEQRES 3 A 52 GLY TRP LEU THR ARG LEU LEU GLN THR LYS ASN TYR ASP SEQRES 4 A 52 ILE GLY ALA ALA LEU ASP THR ILE GLN TYR SER LYS HIS SEQRES 1 B 52 GLY SER PRO PRO GLU ALA ASP PRO ARG LEU ILE GLU SER SEQRES 2 B 52 LEU SER GLN MET LEU SER MET GLY PHE SER ASP GLU GLY SEQRES 3 B 52 GLY TRP LEU THR ARG LEU LEU GLN THR LYS ASN TYR ASP SEQRES 4 B 52 ILE GLY ALA ALA LEU ASP THR ILE GLN TYR SER LYS HIS HELIX 1 1 ASP A 7 GLY A 21 1 15 HELIX 2 2 GLY A 27 LYS A 36 1 10 HELIX 3 3 ASP A 39 ILE A 47 1 9 HELIX 4 4 ILE B 11 MET B 20 1 10 HELIX 5 5 TRP B 28 LYS B 36 1 9 HELIX 6 6 ASP B 39 ILE B 47 1 9 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