HEADER APOPTOSIS 23-OCT-15 5EFM TITLE BECLIN 1 FLEXIBLE-HELICAL DOMIAN (FHD) (141-171) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BECLIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: COILED-COIL MYOSIN-LIKE BCL2-INTERACTING PROTEIN,PROTEIN COMPND 5 GT197; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS FLEXIBLE HELIX, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR S.SINHA,Y.MEI REVDAT 3 16-OCT-24 5EFM 1 REMARK REVDAT 2 22-NOV-17 5EFM 1 JRNL REMARK REVDAT 1 20-JUL-16 5EFM 0 JRNL AUTH Y.MEI,A.RAMANATHAN,K.GLOVER,C.STANLEY,R.SANISHVILI, JRNL AUTH 2 S.CHAKRAVARTHY,Z.YANG,C.L.COLBERT,S.C.SINHA JRNL TITL CONFORMATIONAL FLEXIBILITY ENABLES THE FUNCTION OF A BECN1 JRNL TITL 2 REGION ESSENTIAL FOR STARVATION-MEDIATED AUTOPHAGY. JRNL REF BIOCHEMISTRY V. 55 1945 2016 JRNL REFN ISSN 0006-2960 JRNL PMID 26937551 JRNL DOI 10.1021/ACS.BIOCHEM.5B01264 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 3490 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 169 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 0.0000 - 1.9500 1.00 3321 169 0.2116 0.2164 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) : 0.040 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.53 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 : 0.009 147 REMARK 3 ANGLE : 1.298 196 REMARK 3 CHIRALITY : 0.068 19 REMARK 3 PLANARITY : 0.004 27 REMARK 3 DIHEDRAL : 13.696 61 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 5EFM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214787. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.3776 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3490 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 44.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 75.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.16000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 78.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 250MM POTASSIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE, 2.2 M AMMONIUM SULFATE, 100MM SODIUM CITRATE REMARK 280 TRIBASIC DIHYDRATE (PH 5.6), EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 3 2 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 REMARK 290 13555 Y+1/4,X+3/4,-Z+3/4 REMARK 290 14555 -Y+1/4,-X+1/4,-Z+1/4 REMARK 290 15555 Y+3/4,-X+3/4,Z+1/4 REMARK 290 16555 -Y+3/4,X+1/4,Z+3/4 REMARK 290 17555 X+1/4,Z+3/4,-Y+3/4 REMARK 290 18555 -X+3/4,Z+1/4,Y+3/4 REMARK 290 19555 -X+1/4,-Z+1/4,-Y+1/4 REMARK 290 20555 X+3/4,-Z+3/4,Y+1/4 REMARK 290 21555 Z+1/4,Y+3/4,-X+3/4 REMARK 290 22555 Z+3/4,-Y+3/4,X+1/4 REMARK 290 23555 -Z+3/4,Y+1/4,X+3/4 REMARK 290 24555 -Z+1/4,-Y+1/4,-X+1/4 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 31.58150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.58150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.58150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.58150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.58150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.58150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 31.58150 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 31.58150 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 31.58150 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 31.58150 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 31.58150 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 31.58150 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 31.58150 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 31.58150 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 31.58150 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 31.58150 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 31.58150 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 31.58150 REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 15.79075 REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 47.37225 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 47.37225 REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 15.79075 REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 15.79075 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 15.79075 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 47.37225 REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 47.37225 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 15.79075 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 47.37225 REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 15.79075 REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 47.37225 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 15.79075 REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 47.37225 REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 47.37225 REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 47.37225 REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 15.79075 REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 47.37225 REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 15.79075 REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 15.79075 REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 15.79075 REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 47.37225 REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 47.37225 REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 15.79075 REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 15.79075 REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 47.37225 REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 47.37225 REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 47.37225 REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 47.37225 REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 15.79075 REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 47.37225 REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 15.79075 REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 47.37225 REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 15.79075 REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 15.79075 REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 15.79075 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 350 BIOMT1 2 0.000000 0.000000 1.000000 31.58150 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 94.74450 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 63.16300 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 94.74450 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 63.16300 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 -31.58150 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 S SO4 A 201 LIES ON A SPECIAL POSITION. REMARK 375 O3 SO4 A 201 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 306 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 THR A 141 REMARK 465 ASP A 142 REMARK 465 THR A 143 REMARK 465 LEU A 144 REMARK 465 LEU A 145 REMARK 465 ASP A 146 REMARK 465 GLN A 147 REMARK 465 LEU A 148 REMARK 465 ASP A 149 REMARK 465 THR A 150 REMARK 465 GLN A 151 REMARK 465 LEU A 152 REMARK 465 ASN A 153 REMARK 465 VAL A 154 REMARK 465 THR A 155 REMARK 465 GLU A 156 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 DBREF 5EFM A 141 171 UNP Q14457 BECN1_HUMAN 141 171 SEQRES 1 A 31 THR ASP THR LEU LEU ASP GLN LEU ASP THR GLN LEU ASN SEQRES 2 A 31 VAL THR GLU ASN GLU CYS GLN ASN TYR LYS ARG CYS LEU SEQRES 3 A 31 GLU ILE LEU GLU GLN HET SO4 A 201 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *8(H2 O) HELIX 1 AA1 CYS A 159 GLU A 170 1 12 SSBOND 1 CYS A 159 CYS A 165 1555 6566 2.06 SITE 1 AC1 2 ASN A 161 TYR A 162 CRYST1 63.163 63.163 63.163 90.00 90.00 90.00 P 43 3 2 24 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 0.015832 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015832 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015832 0.00000