HEADER SIGNALING PROTEIN 31-JAN-08 2K0B TITLE NMR STRUCTURE OF THE UBA DOMAIN OF P62 (SQSTM1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEQUESTOSOME-1; COMPND 3 CHAIN: X; 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, ORCA, OSIL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-1 KEYWDS UBIQUITIN BINDING, HELICAL BUNDLE, THREE HELICES, ALTERNATIVE KEYWDS 2 SPLICING, APOPTOSIS, CYTOPLASM, DIFFERENTIATION, DISEASE MUTATION, KEYWDS 3 ENDOSOME, IMMUNE RESPONSE, METAL-BINDING, NUCLEUS, PHOSPHOPROTEIN, KEYWDS 4 POLYMORPHISM, ZINC, ZINC-FINGER, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR J.E.LONG,B.CIANI,T.R.A.GALLAGHER,J.R.CAVEY,P.W.SHEPPARD,R.LAYFIELD, AUTHOR 2 M.S.SEARLE REVDAT 4 16-MAR-22 2K0B 1 REMARK SEQADV REVDAT 3 24-FEB-09 2K0B 1 VERSN REVDAT 2 26-FEB-08 2K0B 1 JRNL REVDAT 1 19-FEB-08 2K0B 0 JRNL AUTH C.L.EVANS,J.E.LONG,T.R.GALLAGHER,J.D.HIRST,M.S.SEARLE JRNL TITL CONFORMATION AND DYNAMICS OF THE THREE-HELIX BUNDLE UBA JRNL TITL 2 DOMAIN OF P62 FROM EXPERIMENT AND SIMULATION. JRNL REF PROTEINS V. 71 227 2007 JRNL REFN ISSN 0887-3585 JRNL PMID 17932931 JRNL DOI 10.1002/PROT.21692 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: NULL REMARK 4 REMARK 4 2K0B COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000100514. 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 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 15N] SEQUESTOSOME REMARK 210 -1, 50 MM POTASSIUM PHOSPHATE, REMARK 210 50 MM SODIUM CHLORIDE, 90% H2O/ REMARK 210 10% D2O; 1 MM [U-100% 13C; U-100% REMARK 210 15N] SEQUESTOSOME-1, 50 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 2D 1H-13C HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCACB; 3D HNCO; 3D HN(CA)CO; REMARK 210 3D HCCH-TOCSY; 3D 1H-13C NOESY; REMARK 210 3D 1H-15N TOCSY 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 : TALOS, XWINNMR, CCPNMR 1.0.10 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 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: X 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 TRP X 28 H LEU X 32 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 PRO X 4 41.18 -75.08 REMARK 500 1 GLU X 5 12.59 -158.12 REMARK 500 1 ALA X 6 26.64 -173.19 REMARK 500 1 SER X 23 -148.71 -151.31 REMARK 500 1 GLU X 25 43.26 -82.90 REMARK 500 1 TYR X 38 76.62 63.18 REMARK 500 1 ILE X 47 45.44 -81.94 REMARK 500 1 GLN X 48 15.63 88.33 REMARK 500 1 SER X 50 20.96 -76.29 REMARK 500 1 LYS X 51 118.54 -167.91 REMARK 500 2 PRO X 4 33.87 -72.87 REMARK 500 2 ALA X 6 26.80 -173.58 REMARK 500 2 SER X 23 -134.86 -156.96 REMARK 500 2 GLU X 25 55.11 -97.61 REMARK 500 2 ARG X 31 -61.98 -94.99 REMARK 500 2 LEU X 32 -72.37 -47.16 REMARK 500 2 GLN X 48 -35.92 -159.80 REMARK 500 2 TYR X 49 34.96 -80.90 REMARK 500 3 ALA X 6 48.93 81.73 REMARK 500 3 GLN X 48 -41.56 -166.42 REMARK 500 3 TYR X 49 -158.48 -75.70 REMARK 500 3 SER X 50 21.83 -160.88 REMARK 500 4 PRO X 4 25.91 -75.25 REMARK 500 4 GLU X 25 65.17 -100.96 REMARK 500 4 GLN X 34 -71.27 -37.98 REMARK 500 4 LYS X 36 37.07 -88.01 REMARK 500 4 TYR X 38 73.90 68.57 REMARK 500 4 ILE X 47 44.33 -101.95 REMARK 500 4 SER X 50 47.65 -82.15 REMARK 500 4 LYS X 51 78.71 -165.38 REMARK 500 5 PRO X 4 37.50 -69.88 REMARK 500 5 GLU X 5 13.11 -146.93 REMARK 500 5 ALA X 6 41.62 -179.17 REMARK 500 5 ILE X 47 43.30 -88.05 REMARK 500 5 GLN X 48 38.13 85.88 REMARK 500 6 PRO X 4 40.77 -72.19 REMARK 500 6 GLU X 5 13.06 -151.73 REMARK 500 6 ALA X 6 21.38 -157.09 REMARK 500 6 GLU X 12 -60.74 -94.77 REMARK 500 6 LYS X 36 37.92 -78.30 REMARK 500 6 TYR X 38 77.86 59.78 REMARK 500 6 GLN X 48 -34.95 -166.89 REMARK 500 6 SER X 50 16.77 -153.06 REMARK 500 7 PRO X 4 37.77 -73.02 REMARK 500 7 ALA X 6 35.85 -177.09 REMARK 500 7 SER X 23 -149.28 -152.47 REMARK 500 7 GLU X 25 68.05 -115.69 REMARK 500 7 LYS X 36 37.14 -81.74 REMARK 500 7 TYR X 38 67.93 61.72 REMARK 500 7 GLN X 48 -48.84 -157.49 REMARK 500 REMARK 500 THIS ENTRY HAS 205 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15591 RELATED DB: BMRB REMARK 900 ASSIGNED NMR CHEMICAL SHIFTS DBREF 2K0B X 3 52 UNP Q13501 SQSTM_HUMAN 387 436 SEQADV 2K0B GLY X 1 UNP Q13501 EXPRESSION TAG SEQADV 2K0B SER X 2 UNP Q13501 EXPRESSION TAG SEQRES 1 X 52 GLY SER PRO PRO GLU ALA ASP PRO ARG LEU ILE GLU SER SEQRES 2 X 52 LEU SER GLN MET LEU SER MET GLY PHE SER ASP GLU GLY SEQRES 3 X 52 GLY TRP LEU THR ARG LEU LEU GLN THR LYS ASN TYR ASP SEQRES 4 X 52 ILE GLY ALA ALA LEU ASP THR ILE GLN TYR SER LYS HIS HELIX 1 1 ARG X 9 GLY X 21 1 13 HELIX 2 2 TRP X 28 LYS X 36 1 9 HELIX 3 3 ASP X 39 ILE X 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