PDB Short entry for 2LI5 HEADER PROTEIN TRANSPORT 23-AUG-11 2LI5 TITLE NMR STRUCTURE OF ATG8-ATG7C30 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: AUTOPHAGY-RELATED PROTEIN 8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ATG8, AUTOPHAGY-RELATED UBIQUITIN-LIKE MODIFIER ATG8, COMPND 5 CYTOPLASM TO VACUOLE TARGETING PROTEIN 5; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: UBIQUITIN-LIKE MODIFIER-ACTIVATING ENZYME ATG7; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 601-630; COMPND 12 SYNONYM: ATG7C30, ATG12-ACTIVATING ENZYME E1 ATG7, AUTOPHAGY-RELATED COMPND 13 PROTEIN 7, CYTOPLASM TO VACUOLE TARGETING PROTEIN 2; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: ATG8, APG8, AUT7, CVT5, YBL078C, YBL0732; SOURCE 7 EXPRESSION_SYSTEM: ASPERGILLUS NIGER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 5061; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX6P; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 12 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 13 ORGANISM_TAXID: 559292; SOURCE 14 STRAIN: ATCC 204508 / S288C; SOURCE 15 GENE: ATG7, APG7, CVT2, YHR171W; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_VECTOR: PGEX6P KEYWDS ATG8, AUTOPHAGY, UBIQUITIN LIKE, PROTEIN TRANSPORT EXPDTA SOLUTION NMR NUMMDL 19 AUTHOR H.KUMETA,K.SATOO,N.N.NODA,Y.FUJIOKA,K.OGURA,H.NAKATOGAWA,Y.OHSUMI, AUTHOR 2 F.INAGAKI REVDAT 3 14-JUN-23 2LI5 1 REMARK SEQADV REVDAT 2 28-MAR-12 2LI5 1 JRNL REVDAT 1 16-NOV-11 2LI5 0 JRNL AUTH N.N.NODA,K.SATOO,Y.FUJIOKA,H.KUMETA,K.OGURA,H.NAKATOGAWA, JRNL AUTH 2 Y.OHSUMI,F.INAGAKI JRNL TITL STRUCTURAL BASIS OF ATG8 ACTIVATION BY A HOMODIMERIC E1, JRNL TITL 2 ATG7. JRNL REF MOL.CELL V. 44 462 2011 JRNL REFN ISSN 1097-2765 JRNL PMID 22055191 JRNL DOI 10.1016/J.MOLCEL.2011.08.035 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, SPARKY 3.113, 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 2LI5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000102413. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 170 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-99% 13C; U-99% 15N] REMARK 210 ATG8K26P-1, 2.0 MM ATG7C30-2, 20 REMARK 210 MM SODIUM PHOSPHATE-3, 150 MM REMARK 210 SODIUM CHLORIDE-4, 5 MM DTT-5, 5 REMARK 210 MM DSS-6, 0.02 % SODIUM AZIDE-7, REMARK 210 90% H2O/10% D2O; 0.5 MM [U-99% REMARK 210 13C; U-99% 15N] ATG7C30-8, 1.25 REMARK 210 MM ATG8K26P-9, 20 MM SODIUM REMARK 210 PHOSPHATE-10, 150 MM SODIUM REMARK 210 CHLORIDE-11, 5 MM DTT-12, 5 MM REMARK 210 DSS-13, 0.02 % SODIUM AZIDE-14, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D HCCH- REMARK 210 TOCSY ALIPHATIC; 2D HBCBCGCDHD; REMARK 210 2D 1H-13C HSQC AROMATIC; 3D HNCA; REMARK 210 3D HNCO; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 3D C(CO)NH; 3D HCCH- REMARK 210 TOCSY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 5.2, SPARKY 3.113, REMARK 210 TALOS+ 1.01, 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 : 19 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: 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 HG CYS A 33 HD13 ILE A 64 1.12 REMARK 500 HD12 ILE A 44 HH TYR A 49 1.14 REMARK 500 HE2 GLU A 8 H LEU B 614 1.25 REMARK 500 HB1 ALA A 89 HD12 ILE A 94 1.30 REMARK 500 HB3 GLU A 34 HG21 THR A 108 1.34 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 MET A 1 -168.99 -70.19 REMARK 500 1 LYS A 2 -54.89 -125.92 REMARK 500 1 THR A 4 -80.23 -129.65 REMARK 500 1 ASN A 27 41.27 -93.53 REMARK 500 1 SER A 39 161.80 -41.18 REMARK 500 1 LYS A 48 105.92 -165.44 REMARK 500 1 LEU A 50 77.88 -104.08 REMARK 500 1 ASP A 82 21.88 81.92 REMARK 500 1 PRO A 86 -168.21 -74.98 REMARK 500 1 LEU A 90 123.31 -23.86 REMARK 500 1 ASN A 113 42.23 -93.96 REMARK 500 1 ILE B 601 -104.24 -108.49 REMARK 500 1 ARG B 613 -45.51 -143.82 REMARK 500 1 PHE B 619 130.59 -172.33 REMARK 500 1 GLU B 620 69.92 -157.20 REMARK 500 1 TRP B 621 -166.30 -164.99 REMARK 500 1 GLU B 622 -75.64 -29.76 REMARK 500 1 ASP B 623 118.40 175.88 REMARK 500 1 SER B 626 135.20 -34.21 REMARK 500 2 MET A 1 -169.63 -104.96 REMARK 500 2 THR A 4 -73.66 -126.22 REMARK 500 2 GLU A 8 -64.10 -90.49 REMARK 500 2 ARG A 24 -60.73 -95.34 REMARK 500 2 ASN A 27 39.07 -91.28 REMARK 500 2 LYS A 48 108.48 -165.93 REMARK 500 2 LEU A 50 78.05 -111.61 REMARK 500 2 VAL A 61 -36.13 -39.24 REMARK 500 2 MET A 69 36.15 33.89 REMARK 500 2 ILE A 76 114.32 -163.12 REMARK 500 2 ASP A 82 24.08 82.04 REMARK 500 2 LEU A 90 120.46 -31.12 REMARK 500 2 MET A 91 -36.82 -34.70 REMARK 500 2 ASN A 113 48.83 -96.74 REMARK 500 2 GLU B 612 -53.51 -123.39 REMARK 500 2 ARG B 613 -43.28 -137.18 REMARK 500 2 ASN B 616 -35.00 -39.85 REMARK 500 2 GLU B 620 -72.48 -136.24 REMARK 500 2 GLU B 622 -172.90 -52.24 REMARK 500 2 SER B 626 144.47 -38.55 REMARK 500 3 MET A 1 -179.88 -55.55 REMARK 500 3 LYS A 2 -74.56 -134.91 REMARK 500 3 THR A 4 -81.73 -130.92 REMARK 500 3 GLU A 12 -29.58 -39.42 REMARK 500 3 PHE A 25 86.45 -153.19 REMARK 500 3 ASN A 27 49.85 -109.91 REMARK 500 3 LYS A 48 108.72 -167.31 REMARK 500 3 LEU A 50 78.15 -100.62 REMARK 500 3 ASN A 81 34.32 73.31 REMARK 500 3 PRO A 86 -165.29 -75.02 REMARK 500 3 LEU A 90 117.09 -23.73 REMARK 500 REMARK 500 THIS ENTRY HAS 358 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KWC RELATED DB: PDB REMARK 900 RELATED ID: 17879 RELATED DB: BMRB DBREF 2LI5 A 1 116 UNP P38182 ATG8_YEAST 1 116 DBREF 2LI5 B 601 630 UNP P38862 ATG7_YEAST 601 630 SEQADV 2LI5 HIS A 0 UNP P38182 EXPRESSION TAG SEQADV 2LI5 PRO A 26 UNP P38182 LYS 26 ENGINEERED MUTATION SEQADV 2LI5 GLY B 597 UNP P38862 EXPRESSION TAG SEQADV 2LI5 PRO B 598 UNP P38862 EXPRESSION TAG SEQADV 2LI5 HIS B 599 UNP P38862 EXPRESSION TAG SEQADV 2LI5 MET B 600 UNP P38862 EXPRESSION TAG SEQRES 1 A 117 HIS MET LYS SER THR PHE LYS SER GLU TYR PRO PHE GLU SEQRES 2 A 117 LYS ARG LYS ALA GLU SER GLU ARG ILE ALA ASP ARG PHE SEQRES 3 A 117 PRO ASN ARG ILE PRO VAL ILE CYS GLU LYS ALA GLU LYS SEQRES 4 A 117 SER ASP ILE PRO GLU ILE ASP LYS ARG LYS TYR LEU VAL SEQRES 5 A 117 PRO ALA ASP LEU THR VAL GLY GLN PHE VAL TYR VAL ILE SEQRES 6 A 117 ARG LYS ARG ILE MET LEU PRO PRO GLU LYS ALA ILE PHE SEQRES 7 A 117 ILE PHE VAL ASN ASP THR LEU PRO PRO THR ALA ALA LEU SEQRES 8 A 117 MET SER ALA ILE TYR GLN GLU HIS LYS ASP LYS ASP GLY SEQRES 9 A 117 PHE LEU TYR VAL THR TYR SER GLY GLU ASN THR PHE GLY SEQRES 1 B 34 GLY PRO HIS MET ILE SER GLY LEU SER VAL ILE LYS GLN SEQRES 2 B 34 GLU VAL GLU ARG LEU GLY ASN ASP VAL PHE GLU TRP GLU SEQRES 3 B 34 ASP ASP GLU SER ASP GLU ILE ALA HELIX 1 1 PRO A 10 PHE A 25 1 16 HELIX 2 2 THR A 56 ILE A 68 1 13 HELIX 3 3 LEU A 90 TYR A 95 1 6 HELIX 4 4 GLY B 615 PHE B 619 5 5 HELIX 5 5 SER B 626 ALA B 630 5 5 SHEET 1 A 2 ARG A 28 VAL A 31 0 SHEET 2 A 2 TYR A 49 PRO A 52 -1 O TYR A 49 N VAL A 31 SHEET 1 B 2 PHE A 77 PHE A 79 0 SHEET 2 B 2 THR A 108 SER A 110 -1 O SER A 110 N PHE A 77 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