PDB Short entry for 2K6Q HEADER APOPTOSIS INHIBITOR/APOPTOSIS 17-JUL-08 2K6Q TITLE LC3 P62 COMPLEX STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LC3, MICROTUBULE-ASSOCIATED PROTEIN 1 LIGHT CHAIN 3 BETA, COMPND 5 MAP1A/1B LIGHT CHAIN 3 B, MAP1A/MAP1B LC3 B, MAP1 LIGHT CHAIN 3-LIKE COMPND 6 PROTEIN 2, AUTOPHAGY-RELATED PROTEIN LC3 B, AUTOPHAGY-RELATED COMPND 7 UBIQUITIN-LIKE MODIFIER LC3 B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: P62_PEPTIDE FROM SEQUESTOSOME-1; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: UBIQUITIN-BINDING PROTEIN P62, PROTEIN KINASE C-ZETA- COMPND 13 INTERACTING PROTEIN, PKC-ZETA-INTERACTING PROTEIN; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: MAP1LC3B, MAP1ALC3, MAP1LC3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGEX6P; 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: PGEX6P KEYWDS LC3, P62, ALTERNATIVE SPLICING, AUTOPHAGY, CYTOPLASM, CYTOPLASMIC KEYWDS 2 VESICLE, LIPOPROTEIN, MEMBRANE, MICROTUBULE, UBL CONJUGATION KEYWDS 3 PATHWAY, APOPTOSIS, DIFFERENTIATION, ENDOSOME, IMMUNE RESPONSE, KEYWDS 4 METAL-BINDING, NUCLEUS, PHOSPHOPROTEIN, ZINC, ZINC-FINGER, APOPTOSIS KEYWDS 5 INHIBITOR-APOPTOSIS COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.NODA,H.KUMETA,H.NAKATOGAWA,K.SATOO,W.ADACHI,J.ISHII,Y.FUJIOKA, AUTHOR 2 Y.OHSUMI,F.INAGAKI REVDAT 4 14-JUN-23 2K6Q 1 REMARK REVDAT 3 26-FEB-20 2K6Q 1 REMARK SEQADV REVDAT 2 24-FEB-09 2K6Q 1 VERSN REVDAT 1 02-SEP-08 2K6Q 0 JRNL AUTH N.NODA,H.KUMETA,H.NAKATOGAWA,K.ADACHI,W.ADACHI,J.ISHII, JRNL AUTH 2 Y.FUJIOKA,Y.OHSUMI,F.INAGAKI JRNL TITL STRUCTURAL BASIS OF TARGET RECOGNITION BY ATG8/LC3 DURING JRNL TITL 2 SELECTIVE AUTOPHAGY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, SPARKY 3.110, CYANA 2.1 REMARK 3 AUTHORS : VARIAN (VNMR), GODDARD (SPARKY), GUNTERT, REMARK 3 MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K6Q COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000100745. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.125 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-99% 13C; U-99% 15N] REMARK 210 LC3, 1.2 MM P62 PEPTIDE, 25 MM REMARK 210 SODIUM PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O; 0.8 REMARK 210 MM [U-99% 13C; U-99% 15N] P62 REMARK 210 PEPTIDE, 1.2 MM LC3, 25 MM REMARK 210 SODIUM PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HCCH-TOCSY; 3D 1H-13C NOESY; REMARK 210 3D 1H-15N NOESY; 3D HNCA; 3D REMARK 210 HN(CA)HA; 3D HBHA(CO)NH; 3D C(CO) REMARK 210 NH; 3D HNCO; 3D CCH-TOCSY; 2D REMARK 210 HBCBCGCDHD; 2D HBCBHCCDCEHE; 3D REMARK 210 CBCA(CO)NH 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 : NMRPIPE, TALOS, SPARKY 3.110, REMARK 210 CYANA 2.1 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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: 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 MET A 1 99.45 -39.04 REMARK 500 1 ARG A 10 -79.89 -38.50 REMARK 500 1 LYS A 39 94.05 -55.26 REMARK 500 1 GLN A 43 -86.89 -74.13 REMARK 500 1 LEU A 47 150.36 -40.36 REMARK 500 1 ASP A 56 46.01 -87.11 REMARK 500 1 HIS A 57 21.50 -151.17 REMARK 500 1 GLN A 72 56.11 38.57 REMARK 500 1 SER A 87 172.16 -57.73 REMARK 500 1 VAL A 89 -30.57 -39.41 REMARK 500 1 GLU A 102 -59.45 -134.32 REMARK 500 1 ARG A 103 157.07 -38.33 REMARK 500 1 TRP B 338 -151.78 -69.64 REMARK 500 2 LYS A 5 176.94 -52.07 REMARK 500 2 GLN A 9 -66.75 -92.99 REMARK 500 2 ARG A 10 -75.43 -40.35 REMARK 500 2 LYS A 39 96.06 -57.32 REMARK 500 2 GLN A 43 -79.30 -39.17 REMARK 500 2 HIS A 57 21.25 -151.57 REMARK 500 2 GLN A 72 50.25 38.85 REMARK 500 2 VAL A 89 135.22 -39.96 REMARK 500 2 SER A 90 21.31 86.44 REMARK 500 2 VAL A 91 99.27 -38.72 REMARK 500 2 GLU A 102 -51.22 -135.49 REMARK 500 2 ARG A 103 153.20 -36.22 REMARK 500 2 TRP B 338 -153.58 -78.74 REMARK 500 3 SER A 3 134.47 -171.78 REMARK 500 3 LYS A 5 177.43 -53.50 REMARK 500 3 GLN A 9 -65.16 -95.41 REMARK 500 3 ARG A 10 -77.99 -37.91 REMARK 500 3 ARG A 11 108.57 -47.32 REMARK 500 3 LYS A 39 100.04 -56.72 REMARK 500 3 GLN A 43 -78.31 -38.88 REMARK 500 3 ASP A 56 46.58 -87.54 REMARK 500 3 HIS A 57 22.71 -149.20 REMARK 500 3 GLN A 72 44.98 38.70 REMARK 500 3 SER A 87 172.04 -57.48 REMARK 500 3 VAL A 89 -31.03 -38.57 REMARK 500 3 GLU A 102 -57.54 -121.09 REMARK 500 3 ARG A 103 152.45 -37.55 REMARK 500 3 SER A 115 32.33 -90.63 REMARK 500 3 ASP B 335 40.84 -95.93 REMARK 500 3 TRP B 338 -154.43 -69.01 REMARK 500 4 LYS A 5 -170.35 -54.75 REMARK 500 4 ARG A 10 -72.61 -50.66 REMARK 500 4 LYS A 39 93.16 -69.60 REMARK 500 4 GLN A 43 -81.55 -42.65 REMARK 500 4 ASP A 56 46.00 -86.71 REMARK 500 4 HIS A 57 19.40 -148.80 REMARK 500 4 GLN A 72 47.97 38.60 REMARK 500 REMARK 500 THIS ENTRY HAS 308 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UGM RELATED DB: PDB REMARK 900 RELATED ID: 2ZJD RELATED DB: PDB REMARK 900 RELATED ID: 15877 RELATED DB: BMRB DBREF 2K6Q A 1 120 UNP Q62625 MLP3B_RAT 1 120 DBREF 2K6Q B 332 347 UNP O08623 SQSTM_RAT 331 346 SEQADV 2K6Q SER A 0 UNP Q62625 EXPRESSION TAG SEQADV 2K6Q MET B 331 UNP O08623 EXPRESSION TAG SEQRES 1 A 121 SER MET PRO SER GLU LYS THR PHE LYS GLN ARG ARG SER SEQRES 2 A 121 PHE GLU GLN ARG VAL GLU ASP VAL ARG LEU ILE ARG GLU SEQRES 3 A 121 GLN HIS PRO THR LYS ILE PRO VAL ILE ILE GLU ARG TYR SEQRES 4 A 121 LYS GLY GLU LYS GLN LEU PRO VAL LEU ASP LYS THR LYS SEQRES 5 A 121 PHE LEU VAL PRO ASP HIS VAL ASN MET SER GLU LEU ILE SEQRES 6 A 121 LYS ILE ILE ARG ARG ARG LEU GLN LEU ASN ALA ASN GLN SEQRES 7 A 121 ALA PHE PHE LEU LEU VAL ASN GLY HIS SER MET VAL SER SEQRES 8 A 121 VAL SER THR PRO ILE SER GLU VAL TYR GLU SER GLU ARG SEQRES 9 A 121 ASP GLU ASP GLY PHE LEU TYR MET VAL TYR ALA SER GLN SEQRES 10 A 121 GLU THR PHE GLY SEQRES 1 B 17 MET SER GLY GLY ASP ASP ASP TRP THR HIS LEU SER SER SEQRES 2 B 17 LYS GLU VAL ASP HELIX 1 1 SER A 12 HIS A 27 1 16 HELIX 2 2 ASN A 59 GLN A 72 1 14 HELIX 3 3 PRO A 94 SER A 101 1 8 SHEET 1 A 5 PHE A 80 VAL A 83 0 SHEET 2 A 5 LEU A 109 ALA A 114 -1 O VAL A 112 N LEU A 82 SHEET 3 A 5 LYS A 30 ARG A 37 1 N ILE A 34 O MET A 111 SHEET 4 A 5 LYS A 51 PRO A 55 -1 O VAL A 54 N ILE A 31 SHEET 5 A 5 THR B 339 HIS B 340 1 O THR B 339 N LEU A 53 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