HEADER LIPID TRANSPORT 13-SEP-24 9JJD TITLE STRUCTURAL ANALYSIS OF AUTOPHAGY-RELATED PROTEIN 8A IN DROSOPHILA TITLE 2 MELANOGASTER COMPND MOL_ID: 1; COMPND 2 MOLECULE: AUTOPHAGY-RELATED 8A, ISOFORM A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LD05816P; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: ATG8A, ATG-8A, ATG8, ATG8, ATG8, ATG8/LC3, ATG8/LC3, ATG8A, SOURCE 6 ATG8A, ATG8A, ATG8A, ATG8ALPHA, BCDNA:LD05816, CG1534, DATG8A, SOURCE 7 DMATG8A, DMEL\CG32672, DRATG8A, LC3, LC3/ATG8, CG32672, SOURCE 8 DMEL_CG32672; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIPID TRAMSPORT, LIPID BINDING PROTEIN, LIPID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.Q.ZHANG,X.LUO,D.X.WU,J.LIU,X.Y.LI REVDAT 2 09-APR-25 9JJD 1 JRNL REVDAT 1 26-MAR-25 9JJD 0 JRNL AUTH S.ZHANG,X.LUO,X.YUAN,D.WU,J.LIU,K.ZHAO,Y.XU,J.ZHOU,X.LI, JRNL AUTH 2 Q.X.LI JRNL TITL CRYSTAL STRUCTURE OF AUTOPHAGY-ASSOCIATED PROTEIN 8 AT 1.36 JRNL TITL 2 ANGSTROM RESOLUTION AND ITS INHIBITORY INTERACTIONS WITH JRNL TITL 3 INDOLE ANALOGS. JRNL REF J.AGRIC.FOOD CHEM. V. 73 7111 2025 JRNL REFN ESSN 1520-5118 JRNL PMID 40066832 JRNL DOI 10.1021/ACS.JAFC.4C11205 REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 29111 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.870 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.7300 - 3.2800 1.00 2086 154 0.1681 0.2236 REMARK 3 2 3.2800 - 2.6000 1.00 1992 147 0.1784 0.1940 REMARK 3 3 2.6000 - 2.2700 1.00 1959 144 0.1761 0.1894 REMARK 3 4 2.2700 - 2.0600 1.00 1945 143 0.1772 0.2113 REMARK 3 5 2.0600 - 1.9200 1.00 1928 143 0.1811 0.2519 REMARK 3 6 1.9200 - 1.8000 1.00 1928 142 0.1874 0.2099 REMARK 3 7 1.8000 - 1.7100 1.00 1925 142 0.1940 0.2469 REMARK 3 8 1.7100 - 1.6400 1.00 1915 141 0.1823 0.2397 REMARK 3 9 1.6400 - 1.5800 1.00 1932 143 0.1804 0.2406 REMARK 3 10 1.5800 - 1.5200 1.00 1901 141 0.1761 0.2075 REMARK 3 11 1.5200 - 1.4700 1.00 1903 140 0.1782 0.2577 REMARK 3 12 1.4700 - 1.4300 1.00 1904 140 0.2150 0.2566 REMARK 3 13 1.4300 - 1.3900 1.00 1911 141 0.2822 0.3335 REMARK 3 14 1.3900 - 1.3600 0.99 1882 139 0.3553 0.4569 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 1057 REMARK 3 ANGLE : 1.098 1423 REMARK 3 CHIRALITY : 0.096 144 REMARK 3 PLANARITY : 0.013 185 REMARK 3 DIHEDRAL : 5.523 141 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9JJD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1300049328. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JAN-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29174 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 29.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.96700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX (1.20.1_4487: ???) REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH=6.5, 26 (W/V) PEG REMARK 280 MME 5000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 16.22500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.42500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.49500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.42500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.22500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.49500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 IN SAME ASYMMETRIC UNIT 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 HE ARG A 28 O HOH A 203 1.46 REMARK 500 O HOH A 283 O HOH A 313 1.89 REMARK 500 O HOH A 203 O HOH A 228 1.90 REMARK 500 OE1 GLU A 97 O HOH A 201 1.98 REMARK 500 O HOH A 252 O HOH A 260 2.08 REMARK 500 O HOH A 201 O HOH A 279 2.09 REMARK 500 O HOH A 281 O HOH A 302 2.11 REMARK 500 O HOH A 287 O HOH A 312 2.11 REMARK 500 O HOH A 312 O HOH A 317 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 265 O HOH A 310 3654 1.77 REMARK 500 O HOH A 285 O HOH A 308 2554 2.10 REMARK 500 REMARK 500 REMARK: NULL DBREF 9JJD A 1 121 UNP Q9W2S2 Q9W2S2_DROME 1 121 SEQRES 1 A 121 MET LYS PHE GLN TYR LYS GLU GLU HIS ALA PHE GLU LYS SEQRES 2 A 121 ARG ARG ALA GLU GLY ASP LYS ILE ARG ARG LYS TYR PRO SEQRES 3 A 121 ASP ARG VAL PRO VAL ILE VAL GLU LYS ALA PRO LYS ALA SEQRES 4 A 121 ARG ILE GLY ASP LEU ASP LYS LYS LYS TYR LEU VAL PRO SEQRES 5 A 121 SER ASP LEU THR VAL GLY GLN PHE TYR PHE LEU ILE ARG SEQRES 6 A 121 LYS ARG ILE HIS LEU ARG PRO GLU ASP ALA LEU PHE PHE SEQRES 7 A 121 PHE VAL ASN ASN VAL ILE PRO PRO THR SER ALA THR MET SEQRES 8 A 121 GLY SER LEU TYR GLN GLU HIS HIS GLU GLU ASP TYR PHE SEQRES 9 A 121 LEU TYR ILE ALA TYR SER ASP GLU ASN VAL TYR GLY MET SEQRES 10 A 121 ALA LYS ILE ASN FORMUL 2 HOH *130(H2 O) HELIX 1 AA1 PHE A 3 HIS A 9 1 7 HELIX 2 AA2 ALA A 10 TYR A 25 1 16 HELIX 3 AA3 THR A 56 HIS A 69 1 14 HELIX 4 AA4 THR A 90 HIS A 99 1 10 HELIX 5 AA5 ASN A 113 MET A 117 5 5 SHEET 1 AA1 4 LYS A 48 PRO A 52 0 SHEET 2 AA1 4 ARG A 28 LYS A 35 -1 N VAL A 31 O TYR A 49 SHEET 3 AA1 4 LEU A 105 SER A 110 1 O ILE A 107 N ILE A 32 SHEET 4 AA1 4 PHE A 77 PHE A 79 -1 N PHE A 77 O SER A 110 CRYST1 32.450 58.990 68.850 90.00 90.00 90.00 P 21 21 21 4 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 0.030817 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016952 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014524 0.00000 MASTER 238 0 0 5 4 0 0 6 1148 1 0 10 END