HEADER PROTEIN BINDING 19-NOV-14 4WZG TITLE STRUCTURE OF HUMAN ATG101 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AUTOPHAGY-RELATED PROTEIN 101; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ATG101, C12ORF44, PP894; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS AUTOPHAGY, ULK1 COMPLEX, HORMA DOMAIN, ATG13 BINDING, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.MICHEL,O.H.WEIERGRAEBER REVDAT 4 03-APR-24 4WZG 1 SSBOND LINK REVDAT 3 13-JAN-16 4WZG 1 JRNL REVDAT 2 19-AUG-15 4WZG 1 JRNL REVDAT 1 17-JUN-15 4WZG 0 JRNL AUTH M.MICHEL,M.SCHWARTEN,C.DECKER,L.NAGEL-STEGER,D.WILLBOLD, JRNL AUTH 2 O.H.WEIERGRABER JRNL TITL THE MAMMALIAN AUTOPHAGY INITIATOR COMPLEX CONTAINS 2 HORMA JRNL TITL 2 DOMAIN PROTEINS. JRNL REF AUTOPHAGY V. 11 2300 2015 JRNL REFN ESSN 1554-8635 JRNL PMID 26236954 JRNL DOI 10.1080/15548627.2015.1076605 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 74.0 REMARK 3 NUMBER OF REFLECTIONS : 13295 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 665 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 3.2512 - 2.5807 0.99 3394 179 0.2395 0.2661 REMARK 3 2 2.5807 - 2.2545 0.85 2869 151 0.2656 0.2919 REMARK 3 3 2.2545 - 2.0483 0.57 1925 101 0.2699 0.4107 REMARK 3 4 2.0483 - 1.9015 0.29 976 51 0.2918 0.2941 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.22 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 : 0.003 1631 REMARK 3 ANGLE : 0.625 2217 REMARK 3 CHIRALITY : 0.025 261 REMARK 3 PLANARITY : 0.004 282 REMARK 3 DIHEDRAL : 13.403 571 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 12.7649 37.1205 15.0227 REMARK 3 T TENSOR REMARK 3 T11: 0.3219 T22: 0.2744 REMARK 3 T33: 0.2865 T12: -0.1233 REMARK 3 T13: 0.0620 T23: -0.0868 REMARK 3 L TENSOR REMARK 3 L11: 2.8235 L22: 3.2481 REMARK 3 L33: 4.4391 L12: -1.7055 REMARK 3 L13: 1.8755 L23: -1.4713 REMARK 3 S TENSOR REMARK 3 S11: -0.2713 S12: 0.0300 S13: 0.2090 REMARK 3 S21: -0.1597 S22: 0.0927 S23: -0.2078 REMARK 3 S31: 0.1787 S32: -0.0097 S33: 0.1719 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 4WZG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000204824. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6-7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90000 REMARK 200 MONOCHROMATOR : SILICON (1 1 1) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS JANUARY 10, 2014 REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13298 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 42.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 73.9 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6200 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) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 22.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE, PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, MES, NACL, BME, PH 5.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL 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 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 405 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 413 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 LEU A 211 REMARK 465 ILE A 212 REMARK 465 LYS A 213 REMARK 465 ASP A 214 REMARK 465 THR A 215 REMARK 465 LEU A 216 REMARK 465 ALA A 217 REMARK 465 LEU A 218 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 1 CG SD CE REMARK 470 ASN A 2 CG OD1 ND2 REMARK 470 ARG A 15 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 40 CE NZ REMARK 470 LYS A 41 CG CD CE NZ REMARK 470 GLU A 42 OE1 OE2 REMARK 470 ASP A 61 CG OD1 OD2 REMARK 470 LYS A 84 CG CD CE NZ REMARK 470 ARG A 88 NE CZ NH1 NH2 REMARK 470 LYS A 105 CE NZ REMARK 470 LYS A 106 CE NZ REMARK 470 LYS A 107 CG CD CE NZ REMARK 470 ARG A 109 NE CZ NH1 NH2 REMARK 470 ASP A 114 CG OD1 OD2 REMARK 470 LYS A 125 CE NZ REMARK 470 GLU A 134 CG CD OE1 OE2 REMARK 470 GLU A 142 CG CD OE1 OE2 REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 GLU A 146 CG CD OE1 OE2 REMARK 470 LYS A 147 CE NZ REMARK 470 GLU A 150 CG CD OE1 OE2 REMARK 470 GLU A 157 CD OE1 OE2 REMARK 470 GLU A 163 CG CD OE1 OE2 REMARK 470 LYS A 167 CD CE NZ REMARK 470 MET A 208 CG SD CE REMARK 470 ARG A 209 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 210 CG CD NE CZ NH1 NH2 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 LYS A 40 -158.67 -110.69 REMARK 500 GLU A 42 17.87 59.23 REMARK 500 LYS A 107 106.19 -58.69 REMARK 500 PHE A 112 -72.50 -61.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME A 301 DBREF 4WZG A 1 218 UNP Q9BSB4 ATGA1_HUMAN 1 218 SEQRES 1 A 218 MET ASN CYS ARG SER GLU VAL LEU GLU VAL SER VAL GLU SEQRES 2 A 218 GLY ARG GLN VAL GLU GLU ALA MET LEU ALA VAL LEU HIS SEQRES 3 A 218 THR VAL LEU LEU HIS ARG SER THR GLY LYS PHE HIS TYR SEQRES 4 A 218 LYS LYS GLU GLY THR TYR SER ILE GLY THR VAL GLY THR SEQRES 5 A 218 GLN ASP VAL ASP CYS ASP PHE ILE ASP PHE THR TYR VAL SEQRES 6 A 218 ARG VAL SER SER GLU GLU LEU ASP ARG ALA LEU ARG LYS SEQRES 7 A 218 VAL VAL GLY GLU PHE LYS ASP ALA LEU ARG ASN SER GLY SEQRES 8 A 218 GLY ASP GLY LEU GLY GLN MET SER LEU GLU PHE TYR GLN SEQRES 9 A 218 LYS LYS LYS SER ARG TRP PRO PHE SER ASP GLU CYS ILE SEQRES 10 A 218 PRO TRP GLU VAL TRP THR VAL LYS VAL HIS VAL VAL ALA SEQRES 11 A 218 LEU ALA THR GLU GLN GLU ARG GLN ILE CYS ARG GLU LYS SEQRES 12 A 218 VAL GLY GLU LYS LEU CYS GLU LYS ILE ILE ASN ILE VAL SEQRES 13 A 218 GLU VAL MET ASN ARG HIS GLU TYR LEU PRO LYS MET PRO SEQRES 14 A 218 THR GLN SER GLU VAL ASP ASN VAL PHE ASP THR GLY LEU SEQRES 15 A 218 ARG ASP VAL GLN PRO TYR LEU TYR LYS ILE SER PHE GLN SEQRES 16 A 218 ILE THR ASP ALA LEU GLY THR SER VAL THR THR THR MET SEQRES 17 A 218 ARG ARG LEU ILE LYS ASP THR LEU ALA LEU HET BME A 301 4 HETNAM BME BETA-MERCAPTOETHANOL FORMUL 2 BME C2 H6 O S FORMUL 3 HOH *31(H2 O) HELIX 1 AA1 GLN A 16 HIS A 31 1 16 HELIX 2 AA2 LYS A 41 GLY A 43 5 3 HELIX 3 AA3 SER A 69 ASN A 89 1 21 HELIX 4 AA4 THR A 133 HIS A 162 1 30 HELIX 5 AA5 THR A 170 VAL A 177 5 8 SHEET 1 AA1 5 ARG A 4 GLU A 13 0 SHEET 2 AA1 5 GLU A 115 VAL A 129 1 O LYS A 125 N LEU A 8 SHEET 3 AA1 5 LEU A 95 LYS A 106 -1 N LEU A 100 O TRP A 122 SHEET 4 AA1 5 TYR A 190 THR A 197 -1 O SER A 193 N SER A 99 SHEET 5 AA1 5 THR A 202 THR A 207 -1 O SER A 203 N ILE A 196 SHEET 1 AA2 2 SER A 33 THR A 34 0 SHEET 2 AA2 2 GLN A 186 PRO A 187 -1 O GLN A 186 N THR A 34 SHEET 1 AA3 2 PHE A 37 TYR A 39 0 SHEET 2 AA3 2 TYR A 45 ILE A 47 -1 O SER A 46 N HIS A 38 SHEET 1 AA4 2 THR A 52 ASP A 56 0 SHEET 2 AA4 2 THR A 63 VAL A 67 -1 O TYR A 64 N VAL A 55 LINK SG CYS A 140 S2 BME A 301 1555 1555 2.03 CISPEP 1 TRP A 110 PRO A 111 0 0.17 SITE 1 AC1 3 SER A 11 VAL A 129 CYS A 140 CRYST1 40.150 42.620 67.210 90.00 97.31 90.00 P 1 2 1 2 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 0.024907 0.000000 0.003197 0.00000 SCALE2 0.000000 0.023463 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015001 0.00000