HEADER LIGASE 05-MAY-11 3RUI TITLE CRYSTAL STRUCTURE OF ATG7C-ATG8 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-LIKE MODIFIER-ACTIVATING ENZYME ATG7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN (UNP RESIDUES 293-630); COMPND 5 SYNONYM: ATG12-ACTIVATING ENZYME E1 ATG7, AUTOPHAGY-RELATED PROTEIN COMPND 6 7, CYTOPLASM TO VACUOLE TARGETING PROTEIN 2; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: AUTOPHAGY-RELATED PROTEIN 8; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: UNP RESIDUES 1-116; COMPND 13 SYNONYM: AUTOPHAGY-RELATED UBIQUITIN-LIKE MODIFIER ATG8, CYTOPLASM TO COMPND 14 VACUOLE TARGETING PROTEIN 5; COMPND 15 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: S288C; SOURCE 6 GENE: ATG7, APG7, CVT2, YHR171W; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 11 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 12 ORGANISM_TAXID: 559292; SOURCE 13 STRAIN: S288C; SOURCE 14 GENE: ATG8, APG8, AUT7, CVT5, YBL078C, YBL0732; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AUTOPHAGY, AUTOPHAGOSOME FORMATION, NON-CANONICAL E1, ATP BINDING, KEYWDS 2 UBL, ATG8, ATG12, ATG10, ATG3, UBL ACTIVATION, THIOLATION, ZINC KEYWDS 3 FINGER, GXGXXG MOTIF ATP BINDING MOTIF, E1-LIKE PROTEIN, LIGASE, KEYWDS 4 ZINC BINDING, ATG8 PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.B.HONG,B.W.KIM,H.K.SONG REVDAT 2 03-JUL-13 3RUI 1 JRNL REVDAT 1 23-NOV-11 3RUI 0 JRNL AUTH S.B.HONG,B.W.KIM,K.E.LEE,S.W.KIM,H.JEON,J.KIM,H.K.SONG JRNL TITL INSIGHTS INTO NONCANONICAL E1 ENZYME ACTIVATION FROM THE JRNL TITL 2 STRUCTURE OF AUTOPHAGIC E1 ATG7 WITH ATG8. JRNL REF NAT.STRUCT.MOL.BIOL. V. 18 1323 2011 JRNL REFN ISSN 1545-9993 JRNL PMID 22056771 JRNL DOI 10.1038/NSMB.2165 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 43347 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.440 REMARK 3 FREE R VALUE TEST SET COUNT : 1924 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 41.6210 - 4.5917 0.99 3378 156 0.2049 0.2139 REMARK 3 2 4.5917 - 3.6452 1.00 3203 149 0.1703 0.2024 REMARK 3 3 3.6452 - 3.1846 1.00 3153 145 0.1796 0.1954 REMARK 3 4 3.1846 - 2.8935 0.99 3066 140 0.1952 0.2133 REMARK 3 5 2.8935 - 2.6862 0.98 3055 142 0.1943 0.2083 REMARK 3 6 2.6862 - 2.5278 0.97 2986 140 0.1881 0.1978 REMARK 3 7 2.5278 - 2.4012 0.95 2947 137 0.1862 0.2193 REMARK 3 8 2.4012 - 2.2967 0.95 2911 135 0.1905 0.2341 REMARK 3 9 2.2967 - 2.2083 0.96 2962 139 0.2026 0.2459 REMARK 3 10 2.2083 - 2.1321 0.94 2877 135 0.2002 0.2699 REMARK 3 11 2.1321 - 2.0655 0.95 2886 137 0.2090 0.2487 REMARK 3 12 2.0655 - 2.0064 0.92 2821 128 0.2057 0.2619 REMARK 3 13 2.0064 - 1.9536 0.89 2737 123 0.2248 0.2910 REMARK 3 14 1.9536 - 1.9059 0.81 2441 118 0.2287 0.2821 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.06 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 46.03 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.920 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) : 6.12930 REMARK 3 B22 (A**2) : 6.12930 REMARK 3 B33 (A**2) : -12.25850 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.00000 REMARK 3 B23 (A**2) : -0.00000 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 : 0.009 3576 REMARK 3 ANGLE : 1.152 4839 REMARK 3 CHIRALITY : 0.076 552 REMARK 3 PLANARITY : 0.005 617 REMARK 3 DIHEDRAL : 13.224 1348 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 3RUI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAY-11. REMARK 100 THE RCSB ID CODE IS RCSB065392. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-10; 28-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : PAL/PLS; PHOTON FACTORY REMARK 200 BEAMLINE : 4A; AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796, 0.9799, 0.95; 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR; REMARK 200 NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL MONOCHROMATOR, REMARK 200 LIQUID NITROGEN COOLING REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R; ADSC QUANTUM REMARK 200 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43347 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 41.611 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02M PROLINE, 0.1M HEPES PH 7.5, 10~ REMARK 280 7% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 110.45800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.66300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.66300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 165.68700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.66300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.66300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.22900 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.66300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.66300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 165.68700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.66300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.66300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 55.22900 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 110.45800 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 71.32600 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 -71.32600 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 220.91600 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 188 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 291 REMARK 465 SER A 292 REMARK 465 TRP A 621 REMARK 465 GLU A 622 REMARK 465 ASP A 623 REMARK 465 ASP A 624 REMARK 465 GLU A 625 REMARK 465 SER A 626 REMARK 465 ASP A 627 REMARK 465 GLU A 628 REMARK 465 ILE A 629 REMARK 465 ALA A 630 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 SER B 3 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 O HOH A 240 O HOH A 275 1.85 REMARK 500 O HOH A 98 O HOH A 646 1.86 REMARK 500 O HOH A 272 O HOH A 647 2.00 REMARK 500 O HOH A 154 O HOH A 161 2.04 REMARK 500 O HOH A 221 O HOH A 225 2.07 REMARK 500 O HOH A 261 O HOH A 285 2.08 REMARK 500 O HOH B 262 O HOH B 317 2.09 REMARK 500 O HOH A 237 O HOH A 244 2.13 REMARK 500 O HOH A 252 O HOH A 273 2.19 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 ILE A 313 -53.09 -123.94 REMARK 500 THR A 502 -167.97 -61.14 REMARK 500 LEU A 503 72.36 47.96 REMARK 500 GLU A 538 63.16 -104.03 REMARK 500 ASN A 616 33.61 -70.21 REMARK 500 PHE A 619 -158.74 -125.19 REMARK 500 TYR B 9 -3.33 81.03 REMARK 500 PRO B 10 46.65 -106.21 REMARK 500 LYS B 38 -11.79 73.19 REMARK 500 ILE B 41 141.47 -172.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 488 SG REMARK 620 2 CYS A 572 SG 95.6 REMARK 620 3 CYS A 569 SG 112.1 108.1 REMARK 620 4 CYS A 485 SG 122.6 116.9 101.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZPN RELATED DB: PDB REMARK 900 THE SAME PROTEIN, YEAST ATG8, C-TERM GLY EXPOSED STATE, REMARK 900 COMPLEXED WITH ATG7C REMARK 900 RELATED ID: 3RUJ RELATED DB: PDB DBREF 3RUI A 293 630 UNP P38862 ATG7_YEAST 293 630 DBREF 3RUI B 1 116 UNP P38182 ATG8_YEAST 1 116 SEQADV 3RUI GLY A 291 UNP P38862 EXPRESSION TAG SEQADV 3RUI SER A 292 UNP P38862 EXPRESSION TAG SEQADV 3RUI SER A 507 UNP P38862 CYS 507 ENGINEERED MUTATION SEQADV 3RUI GLY B -1 UNP P38182 EXPRESSION TAG SEQADV 3RUI SER B 0 UNP P38182 EXPRESSION TAG SEQRES 1 A 340 GLY SER ASP PRO LEU LYS ILE ALA ASP GLN SER VAL ASP SEQRES 2 A 340 LEU ASN LEU LYS LEU MSE LYS TRP ARG ILE LEU PRO ASP SEQRES 3 A 340 LEU ASN LEU ASP ILE ILE LYS ASN THR LYS VAL LEU LEU SEQRES 4 A 340 LEU GLY ALA GLY THR LEU GLY CYS TYR VAL SER ARG ALA SEQRES 5 A 340 LEU ILE ALA TRP GLY VAL ARG LYS ILE THR PHE VAL ASP SEQRES 6 A 340 ASN GLY THR VAL SER TYR SER ASN PRO VAL ARG GLN ALA SEQRES 7 A 340 LEU TYR ASN PHE GLU ASP CYS GLY LYS PRO LYS ALA GLU SEQRES 8 A 340 LEU ALA ALA ALA SER LEU LYS ARG ILE PHE PRO LEU MSE SEQRES 9 A 340 ASP ALA THR GLY VAL LYS LEU SER ILE PRO MSE ILE GLY SEQRES 10 A 340 HIS LYS LEU VAL ASN GLU GLU ALA GLN HIS LYS ASP PHE SEQRES 11 A 340 ASP ARG LEU ARG ALA LEU ILE LYS GLU HIS ASP ILE ILE SEQRES 12 A 340 PHE LEU LEU VAL ASP SER ARG GLU SER ARG TRP LEU PRO SEQRES 13 A 340 SER LEU LEU SER ASN ILE GLU ASN LYS THR VAL ILE ASN SEQRES 14 A 340 ALA ALA LEU GLY PHE ASP SER TYR LEU VAL MSE ARG HIS SEQRES 15 A 340 GLY ASN ARG ASP GLU GLN SER SER LYS GLN LEU GLY CYS SEQRES 16 A 340 TYR PHE CYS HIS ASP VAL VAL ALA PRO THR ASP SER LEU SEQRES 17 A 340 THR ASP ARG THR LEU ASP GLN MSE SER THR VAL THR ARG SEQRES 18 A 340 PRO GLY VAL ALA MSE MSE ALA SER SER LEU ALA VAL GLU SEQRES 19 A 340 LEU MSE THR SER LEU LEU GLN THR LYS TYR SER GLY SER SEQRES 20 A 340 GLU THR THR VAL LEU GLY ASP ILE PRO HIS GLN ILE ARG SEQRES 21 A 340 GLY PHE LEU HIS ASN PHE SER ILE LEU LYS LEU GLU THR SEQRES 22 A 340 PRO ALA TYR GLU HIS CYS PRO ALA CYS SER PRO LYS VAL SEQRES 23 A 340 ILE GLU ALA PHE THR ASP LEU GLY TRP GLU PHE VAL LYS SEQRES 24 A 340 LYS ALA LEU GLU HIS PRO LEU TYR LEU GLU GLU ILE SER SEQRES 25 A 340 GLY LEU SER VAL ILE LYS GLN GLU VAL GLU ARG LEU GLY SEQRES 26 A 340 ASN ASP VAL PHE GLU TRP GLU ASP ASP GLU SER ASP GLU SEQRES 27 A 340 ILE ALA SEQRES 1 B 118 GLY SER MET LYS SER THR PHE LYS SER GLU TYR PRO PHE SEQRES 2 B 118 GLU LYS ARG LYS ALA GLU SER GLU ARG ILE ALA ASP ARG SEQRES 3 B 118 PHE LYS ASN ARG ILE PRO VAL ILE CYS GLU LYS ALA GLU SEQRES 4 B 118 LYS SER ASP ILE PRO GLU ILE ASP LYS ARG LYS TYR LEU SEQRES 5 B 118 VAL PRO ALA ASP LEU THR VAL GLY GLN PHE VAL TYR VAL SEQRES 6 B 118 ILE ARG LYS ARG ILE MET LEU PRO PRO GLU LYS ALA ILE SEQRES 7 B 118 PHE ILE PHE VAL ASN ASP THR LEU PRO PRO THR ALA ALA SEQRES 8 B 118 LEU MET SER ALA ILE TYR GLN GLU HIS LYS ASP LYS ASP SEQRES 9 B 118 GLY PHE LEU TYR VAL THR TYR SER GLY GLU ASN THR PHE SEQRES 10 B 118 GLY MODRES 3RUI MSE A 309 MET SELENOMETHIONINE MODRES 3RUI MSE A 394 MET SELENOMETHIONINE MODRES 3RUI MSE A 405 MET SELENOMETHIONINE MODRES 3RUI MSE A 470 MET SELENOMETHIONINE MODRES 3RUI MSE A 506 MET SELENOMETHIONINE MODRES 3RUI MSE A 516 MET SELENOMETHIONINE MODRES 3RUI MSE A 517 MET SELENOMETHIONINE MODRES 3RUI MSE A 526 MET SELENOMETHIONINE HET MSE A 309 8 HET MSE A 394 8 HET MSE A 405 8 HET MSE A 470 8 HET MSE A 506 8 HET MSE A 516 8 HET MSE A 517 8 HET MSE A 526 8 HET ZN A 1 1 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *318(H2 O) HELIX 1 1 ASP A 293 ILE A 313 1 21 HELIX 2 2 ASN A 318 ASN A 324 1 7 HELIX 3 3 GLY A 333 TRP A 346 1 14 HELIX 4 4 ASN A 371 CYS A 375 5 5 HELIX 5 5 PRO A 378 PHE A 391 1 14 HELIX 6 6 ASN A 412 HIS A 430 1 19 HELIX 7 7 ARG A 440 SER A 442 5 3 HELIX 8 8 ARG A 443 GLU A 453 1 11 HELIX 9 9 CYS A 485 ASP A 490 5 6 HELIX 10 10 LEU A 503 VAL A 509 5 7 HELIX 11 11 PRO A 512 LEU A 530 1 19 HELIX 12 12 SER A 573 GLY A 584 1 12 HELIX 13 13 GLY A 584 HIS A 594 1 11 HELIX 14 14 HIS A 594 GLY A 603 1 10 HELIX 15 15 GLY A 603 ARG A 613 1 11 HELIX 16 16 PRO B 10 PHE B 25 1 16 HELIX 17 17 THR B 56 ILE B 68 1 13 HELIX 18 18 LEU B 90 LYS B 99 1 10 SHEET 1 A 8 ASP A 395 VAL A 399 0 SHEET 2 A 8 LYS A 350 VAL A 354 1 N PHE A 353 O THR A 397 SHEET 3 A 8 LYS A 326 LEU A 330 1 N LEU A 329 O THR A 352 SHEET 4 A 8 ILE A 432 LEU A 435 1 O PHE A 434 N LEU A 328 SHEET 5 A 8 THR A 456 LEU A 462 1 O ILE A 458 N LEU A 435 SHEET 6 A 8 SER A 466 ARG A 471 -1 O MSE A 470 N ASN A 459 SHEET 7 A 8 GLN A 548 PHE A 552 -1 O ILE A 549 N VAL A 469 SHEET 8 A 8 SER A 557 LEU A 561 -1 O LEU A 561 N GLN A 548 SHEET 1 B 2 THR A 539 THR A 540 0 SHEET 2 B 2 GLY A 543 ASP A 544 -1 O GLY A 543 N THR A 540 SHEET 1 C 4 LYS B 48 PRO B 52 0 SHEET 2 C 4 ARG B 28 LYS B 35 -1 N VAL B 31 O TYR B 49 SHEET 3 C 4 LEU B 105 GLY B 111 1 O VAL B 107 N ILE B 32 SHEET 4 C 4 ILE B 76 PHE B 79 -1 N PHE B 79 O THR B 108 LINK C LEU A 308 N MSE A 309 1555 1555 1.33 LINK C MSE A 309 N LYS A 310 1555 1555 1.33 LINK C LEU A 393 N MSE A 394 1555 1555 1.33 LINK C MSE A 394 N ASP A 395 1555 1555 1.34 LINK C PRO A 404 N MSE A 405 1555 1555 1.33 LINK C MSE A 405 N ILE A 406 1555 1555 1.33 LINK C VAL A 469 N MSE A 470 1555 1555 1.33 LINK C MSE A 470 N ARG A 471 1555 1555 1.33 LINK C GLN A 505 N MSE A 506 1555 1555 1.33 LINK C MSE A 506 N SER A 507 1555 1555 1.33 LINK C ALA A 515 N MSE A 516 1555 1555 1.32 LINK C MSE A 516 N MSE A 517 1555 1555 1.33 LINK C MSE A 517 N ALA A 518 1555 1555 1.33 LINK C LEU A 525 N MSE A 526 1555 1555 1.33 LINK C MSE A 526 N THR A 527 1555 1555 1.33 LINK SG CYS A 488 ZN ZN A 1 1555 1555 2.32 LINK SG CYS A 572 ZN ZN A 1 1555 1555 2.34 LINK SG CYS A 569 ZN ZN A 1 1555 1555 2.39 LINK SG CYS A 485 ZN ZN A 1 1555 1555 2.39 SITE 1 AC1 4 CYS A 485 CYS A 488 CYS A 569 CYS A 572 CRYST1 71.326 71.326 220.916 90.00 90.00 90.00 P 43 21 2 8 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 0.014020 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014020 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004527 0.00000