PDB Short entry for 2JY8 HEADER PROTEIN BINDING 07-DEC-07 2JY8 TITLE NMR STRUCTURE OF THE UBIQUITIN ASSOCIATED (UBA) DOMAIN OF P62 (SQSTM1) TITLE 2 IN COMPLEX WITH UBIQUITIN. RDC REFINED COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-BINDING PROTEIN P62; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UBA DOMAIN; COMPND 5 SYNONYM: SEQUESTOSOME-1, PHOSPHOTYROSINE-INDEPENDENT LIGAND FOR THE COMPND 6 LCK SH2 DOMAIN OF 62 KDA, EBI3-ASSOCIATED PROTEIN OF 60 KDA, P60, COMPND 7 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, ORCA, OSIL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; 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, HELICAL BUNDLE, THREE KEYWDS 2 HELICES, ALTERNATIVE SPLICING, APOPTOSIS, CYTOPLASM, KEYWDS 3 DIFFERENTIATION, DISEASE MUTATION, ENDOSOME, IMMUNE RESPONSE, METAL- KEYWDS 4 BINDING, NUCLEUS, PHOSPHOPROTEIN, POLYMORPHISM, ZINC, ZINC-FINGER, KEYWDS 5 PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 21 AUTHOR J.E.LONG,R.LAYFIELD,M.S.SEARLE REVDAT 4 19-FEB-20 2JY8 1 REMARK SEQADV REVDAT 3 24-FEB-09 2JY8 1 VERSN REVDAT 2 11-MAR-08 2JY8 1 JRNL REVDAT 1 18-DEC-07 2JY8 0 JRNL AUTH J.LONG,T.R.GALLAGHER,J.R.CAVEY,P.W.SHEPPARD,S.H.RALSTON, JRNL AUTH 2 R.LAYFIELD,M.S.SEARLE JRNL TITL UBIQUITIN RECOGNITION BY THE UBIQUITIN-ASSOCIATED DOMAIN OF JRNL TITL 2 P62 INVOLVES A NOVEL CONFORMATIONAL SWITCH JRNL REF J.BIOL.CHEM. V. 283 5427 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18083707 JRNL DOI 10.1074/JBC.M704973200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.14, X-PLOR NIH 2.14 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: IN THE FIRST STAGE, HIGH TEMPERATURE REMARK 3 CARTESIAN DYNAMICS WAS PERFORMED AT 1000 K WITH A TIME STEP OF REMARK 3 0.005 PS, FOR 20,000 STEPS, USING THE VERLET INTEGRATOR. DURING REMARK 3 THE SECOND COOLING PHASE OF THE PROTOCOL, THE TEMPERATURE WAS REMARK 3 REDUCED FROM 1000 K TO 100 K IN STEPS OF 50 K, WITH A TIME STEP REMARK 3 OF 5 FS, OVER 40,000 STEPS DURING WHICH THE RELATIVE WEIGHTING REMARK 3 OF NON-BONDED ENERGY TERMS WERE INCREASED FROM 10% OF THEIR REMARK 3 DEFAULT VALUES TO THEIR FORCE FIELD DEFAULT. THESE INITIAL REMARK 3 STRUCTURES WERE THEN REFINED WITH ANOTHER 10000 COOLING STEP REMARK 4 REMARK 4 2JY8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000100439. 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 : 1 MM [U-100% 15N] PROTEIN, 50 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 0.04 % SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O; 1 MM [U- REMARK 210 100% 13C; U-100% 15N] PROTEIN, REMARK 210 50 MM POTASSIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 0.04 % SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O; 1 MM [U- REMARK 210 100% 15N] PROTEIN, 50 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 0.04 % SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N TOCSY; REMARK 210 3D 1H-15N NOESY; 2D 1H-13C HSQC; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D 1H-13C NOESY; 3D REMARK 210 HNCO; 3D HN(CA)CO; 2D 1H-15N REMARK 210 HSQC-IPAP 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 : XWINNMR 3.5, CCPNMR 1.0.10, REMARK 210 TALOS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 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: 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 O LEU A 32 H THR A 35 1.51 REMARK 500 O ASP A 7 H ILE A 11 1.53 REMARK 500 O GLU A 12 H SER A 15 1.57 REMARK 500 OD2 ASP A 24 H THR A 30 1.58 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 5 -11.86 87.88 REMARK 500 1 ASP A 7 -59.96 -152.85 REMARK 500 1 PRO A 8 -71.29 -62.14 REMARK 500 1 LEU A 18 -14.41 -46.91 REMARK 500 1 SER A 19 -8.61 -55.97 REMARK 500 1 LEU A 32 -70.54 -58.38 REMARK 500 1 ASN A 37 -4.87 101.94 REMARK 500 1 TYR A 38 -121.41 -123.15 REMARK 500 1 GLN A 48 -100.74 -163.30 REMARK 500 1 TYR A 49 71.47 -2.12 REMARK 500 1 SER A 50 -108.73 167.91 REMARK 500 2 GLU A 5 -12.33 84.63 REMARK 500 2 ASP A 7 -72.84 -150.70 REMARK 500 2 PRO A 8 -70.40 -57.63 REMARK 500 2 SER A 13 -32.64 -38.33 REMARK 500 2 SER A 15 -25.92 -37.11 REMARK 500 2 SER A 19 -28.95 -35.23 REMARK 500 2 PHE A 22 148.84 176.76 REMARK 500 2 TRP A 28 -37.86 -156.77 REMARK 500 2 THR A 30 -70.22 -47.55 REMARK 500 2 THR A 35 -25.44 -31.52 REMARK 500 2 ASN A 37 55.79 105.08 REMARK 500 2 TYR A 38 -177.73 172.45 REMARK 500 2 ILE A 40 -34.34 -27.12 REMARK 500 2 ILE A 47 0.51 -67.87 REMARK 500 2 TYR A 49 45.27 -161.70 REMARK 500 3 GLU A 5 -56.89 172.82 REMARK 500 3 SER A 13 -27.45 -39.52 REMARK 500 3 SER A 15 -29.36 -37.97 REMARK 500 3 LEU A 18 -27.42 -34.06 REMARK 500 3 SER A 19 -17.17 -47.24 REMARK 500 3 THR A 30 -32.30 -30.82 REMARK 500 3 GLN A 34 -7.57 -47.24 REMARK 500 3 THR A 35 -31.00 -33.19 REMARK 500 3 ASN A 37 15.87 100.45 REMARK 500 3 ILE A 40 -68.70 95.28 REMARK 500 3 ALA A 43 -72.54 -64.03 REMARK 500 3 LEU A 44 -28.08 -37.60 REMARK 500 3 GLN A 48 -40.41 -136.75 REMARK 500 3 TYR A 49 97.66 33.85 REMARK 500 3 LYS A 51 -169.87 -68.23 REMARK 500 4 ALA A 6 59.82 -156.59 REMARK 500 4 TRP A 28 -39.28 -149.83 REMARK 500 4 ASN A 37 64.80 100.53 REMARK 500 4 TYR A 38 -172.02 169.50 REMARK 500 4 ILE A 40 -28.23 -36.38 REMARK 500 4 LEU A 44 -33.45 -38.44 REMARK 500 4 ILE A 47 24.57 -69.61 REMARK 500 4 TYR A 49 -30.92 179.05 REMARK 500 5 PRO A 4 34.53 -82.19 REMARK 500 REMARK 500 THIS ENTRY HAS 266 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JY7 RELATED DB: PDB REMARK 900 RELATED ID: 15592 RELATED DB: BMRB DBREF 2JY8 A 3 52 UNP Q13501 SQSTM_HUMAN 387 436 SEQADV 2JY8 GLY A 1 UNP Q13501 EXPRESSION TAG SEQADV 2JY8 SER A 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 HELIX 1 1 ASP A 7 LEU A 14 1 8 HELIX 2 2 SER A 15 MET A 17 5 3 HELIX 3 3 GLY A 27 GLN A 34 1 8 HELIX 4 4 THR A 35 ASN A 37 5 3 HELIX 5 5 ASP A 39 GLN A 48 1 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