HEADER SIGNALING PROTEIN, TRANSPORT PROTEIN 05-FEB-10 2KTR TITLE NMR STRUCTURE OF P62 PB1 DIMER DETERMINED BASED ON PCS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEQUESTOSOME-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PB1 DOMAIN, OPR DOMAIN, RESIDUES 3-100; COMPND 5 SYNONYM: P62, UBIQUITIN-BINDING PROTEIN P62, PROTEIN KINASE C-ZETA- COMPND 6 INTERACTING PROTEIN, PKC-ZETA-INTERACTING PROTEIN; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: SEQUESTOSOME-1; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: PB1 DOMAIN, OPR DOMAIN, RESIDUES 3-100; COMPND 13 SYNONYM: P62, UBIQUITIN-BINDING PROTEIN P62, PROTEIN KINASE C-ZETA- COMPND 14 INTERACTING PROTEIN, PKC-ZETA-INTERACTING PROTEIN; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET21; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 11 ORGANISM_COMMON: RAT; SOURCE 12 ORGANISM_TAXID: 10116; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 16 EXPRESSION_SYSTEM_VECTOR: PET21 KEYWDS AUTOPHAGY, NF-KB SIGNALING, HOMO-OLIGOMER, PB1 DIMER, SIGNALING KEYWDS 2 PROTEIN, TRANSPORT PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR T.SAIO,M.YOKOCHI,H.KUMETA,F.INAGAKI REVDAT 2 10-NOV-21 2KTR 1 REMARK DBREF SEQADV REVDAT 1 07-APR-10 2KTR 0 JRNL AUTH T.SAIO,M.YOKOCHI,H.KUMETA,F.INAGAKI JRNL TITL PCS-BASED STRUCTURE DETERMINATION OF PROTEIN-PROTEIN JRNL TITL 2 COMPLEXES JRNL REF J.BIOMOL.NMR V. 46 271 2010 JRNL REFN ISSN 0925-2738 JRNL PMID 20300805 JRNL DOI 10.1007/S10858-010-9401-4 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OLIVIA, X-PLOR NIH 2.9.20 REMARK 3 AUTHORS : MASASHI YOKOCHI (OLIVIA), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: IN THIS WORK, THE DIMER STRUCTURE OF REMARK 3 P62 PB1 WAS DETERMINED BY USING A RIGID-BODY DOCKING CALCULATION REMARK 3 BASED ON THE PSEUDO-CONTACT SHIFT. IN THE DOCKING CALCULATION, REMARK 3 THE COORDINATES OF CHAIN A WERE HELD FIXED, WHEREAS THE REMARK 3 COORDINATES OF CHAIN B WERE TREATED AS A RIGID BODY AND SET FREE REMARK 3 TO ROTATE AND TRANSLATE. THE DIFFERENCES AMONG THE MODELS ARE REMARK 3 RELATIVE ORIENTATIONS BETWEEN CHAIN A AND CHAIN B, NOT EACH REMARK 3 COORDINATES. IN THE CALCULATION, MONOMER STRUCTURES OF DR AND KE REMARK 3 WERE DOCKED EACH OTHER BASED ON THE INTER-SUBUNIT RESTRAINTS REMARK 3 FROM PSEUDO-CONTACT SHIFTS. THE COORDINATES OF DR AND KE WERE REMARK 3 GENERATED FROM THE MONOMER STRUCTURE OF DR (2KKC), USING PYMOL REMARK 3 SOFTWARE. FOR PSEUDO-CONTACT SHIFT RESTRAINTS, WE NEED A REMARK 3 PARAMAGNETIC LANTHANIDE ION FIXED IN THE TARGET PROTEIN. TO FIX REMARK 3 A LANTHANIDE IONS TO DR, WE UTILIZED THE LANTHANIDE BINDING REMARK 3 PEPTIDE TAG (LBT).THE CHAIN A REPRESENTS LBT-DR, AND CHAIN B REMARK 3 DOES KE. WE COLLECTED THE PSEUDO-CONTACT SHIFT RESTRAINS USING REMARK 3 LBT-DR/KE COMPLEX, WHILE THE DOCKING CALCULATIONS WERE PERFORMED REMARK 3 USING THE COORDINATES WITHOUT LBT. REMARK 4 REMARK 4 2KTR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000101562. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5MM [U-99% 13C; U-99% 15N] REMARK 210 P62_1; 0.5MM P62_2; 20MM MES; REMARK 210 50MM SODIUM CHLORIDE; 0.5MM REMARK 210 TERBIUM(III) ION; 90% H2O/10% REMARK 210 D2O; 0.5 MM P62_1; 0.5MM [U-99% REMARK 210 13C; U-99% 15N] P62_2; 20MM MES; REMARK 210 50MM SODIUM CHLORIDE; 0.5MM REMARK 210 TERBIUM(III) ION; 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCA; 3D HN(CO)CA; 3D HNCACB; REMARK 210 3D HNCO REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : OLIVIA, X-PLOR NIH 2.9.20 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 758 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12301 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 5.2 KCAL/MOL 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 400 REMARK 400 COMPOUND REMARK 400 A67, R69, E207, AND A294 ARE MUTATIONS FOR THE PREVENTION OF HOMO- REMARK 400 OLIGOMERIZATION. S42, S226, AND S242 ARE FOR THE FIXATION OF REMARK 400 LANTHANIDE-BINDING PEPTIDE TAG(LBT). 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 1-10 REMARK 465 RES C SSSEQI REMARK 465 CYS A -16 REMARK 465 TYR A -15 REMARK 465 VAL A -14 REMARK 465 ASP A -13 REMARK 465 THR A -12 REMARK 465 ASN A -11 REMARK 465 ASN A -10 REMARK 465 ASP A -9 REMARK 465 GLY A -8 REMARK 465 ALA A -7 REMARK 465 TYR A -6 REMARK 465 GLU A -5 REMARK 465 GLY A -4 REMARK 465 ASP A -3 REMARK 465 GLU A -2 REMARK 465 LEU A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 HIS B 201 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 ALA A 17 107.84 -54.70 REMARK 500 1 PRO A 39 -171.82 -69.83 REMARK 500 1 PHE A 53 70.46 -116.62 REMARK 500 1 ALA A 74 105.59 -57.74 REMARK 500 1 SER A 76 30.68 -161.42 REMARK 500 1 ALA B 217 107.79 -54.69 REMARK 500 1 PRO B 239 -171.85 -69.87 REMARK 500 1 PHE B 253 70.43 -116.61 REMARK 500 1 ALA B 274 105.62 -57.76 REMARK 500 1 SER B 276 30.73 -161.41 REMARK 500 2 ALA A 17 107.84 -54.70 REMARK 500 2 PRO A 39 -171.82 -69.83 REMARK 500 2 PHE A 53 70.46 -116.62 REMARK 500 2 ALA A 74 105.59 -57.74 REMARK 500 2 SER A 76 30.68 -161.42 REMARK 500 2 ALA B 217 107.87 -54.76 REMARK 500 2 PRO B 239 -171.79 -69.78 REMARK 500 2 PHE B 253 70.46 -116.59 REMARK 500 2 ALA B 274 105.63 -57.82 REMARK 500 2 SER B 276 30.62 -161.46 REMARK 500 3 ALA A 17 107.84 -54.70 REMARK 500 3 PRO A 39 -171.82 -69.83 REMARK 500 3 PHE A 53 70.46 -116.62 REMARK 500 3 ALA A 74 105.59 -57.74 REMARK 500 3 SER A 76 30.68 -161.42 REMARK 500 3 ALA B 217 107.76 -54.57 REMARK 500 3 PRO B 239 -171.82 -69.90 REMARK 500 3 PHE B 253 70.46 -116.66 REMARK 500 3 ALA B 274 105.56 -57.72 REMARK 500 3 SER B 276 30.69 -161.39 REMARK 500 4 ALA A 17 107.84 -54.70 REMARK 500 4 PRO A 39 -171.82 -69.83 REMARK 500 4 PHE A 53 70.46 -116.62 REMARK 500 4 ALA A 74 105.59 -57.74 REMARK 500 4 SER A 76 30.68 -161.42 REMARK 500 4 ALA B 217 107.77 -54.75 REMARK 500 4 PRO B 239 -171.84 -69.79 REMARK 500 4 PHE B 253 70.42 -116.55 REMARK 500 4 ALA B 274 105.60 -57.73 REMARK 500 4 SER B 276 30.61 -161.42 REMARK 500 5 ALA A 17 107.84 -54.70 REMARK 500 5 PRO A 39 -171.82 -69.83 REMARK 500 5 PHE A 53 70.46 -116.62 REMARK 500 5 ALA A 74 105.59 -57.74 REMARK 500 5 SER A 76 30.68 -161.42 REMARK 500 5 ALA B 217 107.80 -54.65 REMARK 500 5 PRO B 239 -171.84 -69.85 REMARK 500 5 PHE B 253 70.50 -116.55 REMARK 500 5 ALA B 274 105.55 -57.64 REMARK 500 5 SER B 276 30.68 -161.44 REMARK 500 REMARK 500 THIS ENTRY HAS 100 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KKC RELATED DB: PDB REMARK 900 MONOMERIC STRUCTURE OF P62 PB1 REMARK 900 RELATED ID: 2RPV RELATED DB: PDB REMARK 900 STRUCTURE OF THE LBT ATTACHED TO GB1 REMARK 900 RELATED ID: 16736 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE CYVDTNNDGAYEGDELHMG OF CHAIN A IS FOR REMARK 999 LANTHANIDE-BINDING PEPTIDE SEQUENCE. DBREF 2KTR A -16 2 PDB 2KTR 2KTR -16 2 DBREF 2KTR A 3 100 UNP O08623 SQSTM_RAT 3 100 DBREF 2KTR B 203 300 UNP O08623 SQSTM_RAT 3 100 SEQADV 2KTR SER A 42 UNP O08623 CYS 42 ENGINEERED MUTATION SEQADV 2KTR ALA A 67 UNP O08623 ASP 67 ENGINEERED MUTATION SEQADV 2KTR ARG A 69 UNP O08623 ASP 69 ENGINEERED MUTATION SEQADV 2KTR HIS B 201 UNP O08623 EXPRESSION TAG SEQADV 2KTR MET B 202 UNP O08623 EXPRESSION TAG SEQADV 2KTR GLU B 207 UNP O08623 LYS 7 ENGINEERED MUTATION SEQADV 2KTR SER B 226 UNP O08623 CYS 26 ENGINEERED MUTATION SEQADV 2KTR SER B 242 UNP O08623 CYS 42 ENGINEERED MUTATION SEQADV 2KTR ALA B 294 UNP O08623 ARG 94 ENGINEERED MUTATION SEQRES 1 A 117 CYS TYR VAL ASP THR ASN ASN ASP GLY ALA TYR GLU GLY SEQRES 2 A 117 ASP GLU LEU HIS MET GLY SER LEU THR VAL LYS ALA TYR SEQRES 3 A 117 LEU LEU GLY LYS GLU GLU ALA ALA ARG GLU ILE ARG ARG SEQRES 4 A 117 PHE SER PHE CYS PHE SER PRO GLU PRO GLU ALA GLU ALA SEQRES 5 A 117 ALA ALA GLY PRO GLY PRO SER GLU ARG LEU LEU SER ARG SEQRES 6 A 117 VAL ALA VAL LEU PHE PRO ALA LEU ARG PRO GLY GLY PHE SEQRES 7 A 117 GLN ALA HIS TYR ARG ALA GLU ARG GLY ASP LEU VAL ALA SEQRES 8 A 117 PHE SER SER ASP GLU GLU LEU THR MET ALA MET SER TYR SEQRES 9 A 117 VAL LYS ASP ASP ILE PHE ARG ILE TYR ILE LYS GLU LYS SEQRES 1 B 100 HIS MET SER LEU THR VAL GLU ALA TYR LEU LEU GLY LYS SEQRES 2 B 100 GLU GLU ALA ALA ARG GLU ILE ARG ARG PHE SER PHE SER SEQRES 3 B 100 PHE SER PRO GLU PRO GLU ALA GLU ALA ALA ALA GLY PRO SEQRES 4 B 100 GLY PRO SER GLU ARG LEU LEU SER ARG VAL ALA VAL LEU SEQRES 5 B 100 PHE PRO ALA LEU ARG PRO GLY GLY PHE GLN ALA HIS TYR SEQRES 6 B 100 ARG ASP GLU ASP GLY ASP LEU VAL ALA PHE SER SER ASP SEQRES 7 B 100 GLU GLU LEU THR MET ALA MET SER TYR VAL LYS ASP ASP SEQRES 8 B 100 ILE PHE ALA ILE TYR ILE LYS GLU LYS HET TB A 400 1 HETNAM TB TERBIUM(III) ION FORMUL 3 TB TB 3+ HELIX 1 1 GLY A 40 PHE A 53 1 14 HELIX 2 2 SER A 77 VAL A 88 1 12 HELIX 3 3 GLY B 240 PHE B 253 1 14 HELIX 4 4 SER B 277 VAL B 288 1 12 SHEET 1 A 5 ALA A 17 PHE A 25 0 SHEET 2 A 5 LEU A 4 LEU A 11 -1 N LEU A 4 O PHE A 25 SHEET 3 A 5 ILE A 92 GLU A 99 1 O ILE A 97 N TYR A 9 SHEET 4 A 5 PHE A 61 ARG A 66 -1 N HIS A 64 O TYR A 96 SHEET 5 A 5 LEU A 72 PHE A 75 -1 O PHE A 75 N ALA A 63 SHEET 1 B 5 ALA B 217 SER B 226 0 SHEET 2 B 5 SER B 203 LEU B 211 -1 N LEU B 204 O PHE B 225 SHEET 3 B 5 ILE B 292 GLU B 299 1 O ILE B 297 N TYR B 209 SHEET 4 B 5 PHE B 261 ARG B 266 -1 N HIS B 264 O TYR B 296 SHEET 5 B 5 LEU B 272 PHE B 275 -1 O PHE B 275 N ALA B 263 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