HEADER CELL CYCLE 10-JAN-16 5HHE TITLE HUMAN BECLIN 1 COILED-COIL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BECLIN-1; COMPND 3 CHAIN: D, A; COMPND 4 FRAGMENT: UNP ENTRIES 175-265; COMPND 5 SYNONYM: COILED-COIL MYOSIN-LIKE BCL2-INTERACTING PROTEIN,PROTEIN COMPND 6 GT197; COMPND 7 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: BECN1, GT197; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET29B KEYWDS AUTOPHAGY REGULATOR, COILED-COIL DOMAIN, ANTI-PARALLEL DIMER, CELL KEYWDS 2 CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR Y.MEI,S.SINHA REVDAT 6 27-SEP-23 5HHE 1 REMARK REVDAT 5 31-AUG-16 5HHE 1 REMARK REVDAT 4 17-AUG-16 5HHE 1 JRNL REVDAT 3 03-AUG-16 5HHE 1 JRNL REVDAT 2 27-JUL-16 5HHE 1 JRNL REVDAT 1 20-JUL-16 5HHE 0 JRNL AUTH Y.MEI,M.SU,R.SANISHVILI,S.CHAKRAVARTHY,C.L.COLBERT,S.C.SINHA JRNL TITL IDENTIFICATION OF BECN1 AND ATG14 COILED-COIL INTERFACE JRNL TITL 2 RESIDUES THAT ARE IMPORTANT FOR STARVATION-INDUCED JRNL TITL 3 AUTOPHAGY. JRNL REF BIOCHEMISTRY V. 55 4239 2016 JRNL REFN ISSN 0006-2960 JRNL PMID 27383850 JRNL DOI 10.1021/ACS.BIOCHEM.6B00246 REMARK 2 REMARK 2 RESOLUTION. 1.46 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) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 38429 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1921 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 40.1500 - 3.5093 0.99 2653 140 0.1876 0.2009 REMARK 3 2 3.5093 - 2.7857 1.00 2634 139 0.1700 0.1700 REMARK 3 3 2.7857 - 2.4336 1.00 2618 137 0.1707 0.2276 REMARK 3 4 2.4336 - 2.2111 1.00 2650 140 0.1463 0.1838 REMARK 3 5 2.2111 - 2.0526 1.00 2628 138 0.1478 0.1998 REMARK 3 6 2.0526 - 1.9316 1.00 2608 137 0.1562 0.2163 REMARK 3 7 1.9316 - 1.8349 1.00 2616 138 0.1635 0.2382 REMARK 3 8 1.8349 - 1.7550 1.00 2629 139 0.1610 0.2595 REMARK 3 9 1.7550 - 1.6874 1.00 2628 137 0.1512 0.2258 REMARK 3 10 1.6874 - 1.6292 1.00 2585 137 0.1484 0.2036 REMARK 3 11 1.6292 - 1.5783 1.00 2621 137 0.1574 0.2157 REMARK 3 12 1.5783 - 1.5331 1.00 2602 138 0.1869 0.2611 REMARK 3 13 1.5331 - 1.4928 0.97 2560 133 0.2038 0.3080 REMARK 3 14 1.4928 - 1.4564 0.94 2476 131 0.2444 0.3170 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.34 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 : 0.007 1589 REMARK 3 ANGLE : 0.704 2122 REMARK 3 CHIRALITY : 0.043 229 REMARK 3 PLANARITY : 0.002 291 REMARK 3 DIHEDRAL : 14.350 664 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 5HHE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000217036. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : CRYOGENICALLY-COOLED SINGLE REMARK 200 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38596 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 40.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.020 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3Q8T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 39% 2-METHYL-2, 4-PENTADIOL, 9% PEG400 REMARK 280 AND 100 MM TRIS BUFFER, PH 7.5., EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 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 3555 X+1/2,Y+1/2,Z 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 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 SMTRY1 3 1.000000 0.000000 0.000000 29.10000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.78750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.10000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.78750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 -1.000000 0.000000 0.000000 -44.82686 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 107.95505 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: 4990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 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 -1.000000 0.000000 0.000000 -44.82686 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 107.95505 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 GLU A 267 CG CD OE1 OE2 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 OE1 GLN A 240 O HOH A 301 1.61 REMARK 500 OE1 GLU D 235 O HOH D 301 1.91 REMARK 500 O HOH D 302 O HOH D 402 1.94 REMARK 500 O HOH D 302 O HOH D 332 2.03 REMARK 500 O HOH D 327 O HOH D 423 2.05 REMARK 500 O HOH D 371 O HOH D 423 2.07 REMARK 500 O HOH A 377 O HOH A 405 2.08 REMARK 500 O HOH D 409 O HOH D 429 2.11 REMARK 500 O HOH A 312 O HOH A 358 2.13 REMARK 500 O HOH D 381 O HOH D 406 2.14 REMARK 500 O HOH D 301 O HOH D 400 2.17 REMARK 500 O HOH A 378 O HOH A 397 2.17 REMARK 500 O HOH A 389 O HOH A 402 2.18 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 D 423 O HOH A 324 2557 2.05 REMARK 500 O HOH D 370 O HOH D 423 2557 2.05 REMARK 500 O HOH A 380 O HOH A 389 2557 2.07 REMARK 500 O HOH A 387 O HOH A 398 1455 2.07 REMARK 500 O HOH D 313 O HOH D 353 2558 2.08 REMARK 500 O HOH A 361 O HOH A 389 2557 2.11 REMARK 500 O HOH D 423 O HOH A 336 2557 2.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 5HHE D 175 265 UNP Q14457 BECN1_HUMAN 175 265 DBREF 5HHE A 175 265 UNP Q14457 BECN1_HUMAN 175 265 SEQADV 5HHE LEU D 266 UNP Q14457 EXPRESSION TAG SEQADV 5HHE GLU D 267 UNP Q14457 EXPRESSION TAG SEQADV 5HHE LEU A 266 UNP Q14457 EXPRESSION TAG SEQADV 5HHE GLU A 267 UNP Q14457 EXPRESSION TAG SEQRES 1 D 93 ASP ASP SER GLU GLN LEU GLN MET GLU LEU LYS GLU LEU SEQRES 2 D 93 ALA LEU GLU GLU GLU ARG LEU ILE GLN GLU LEU GLU ASP SEQRES 3 D 93 VAL GLU LYS ASN ARG LYS ILE VAL ALA GLU ASN LEU GLU SEQRES 4 D 93 LYS VAL GLN ALA GLU ALA GLU ARG LEU ASP GLN GLU GLU SEQRES 5 D 93 ALA GLN TYR GLN ARG GLU TYR SER GLU PHE LYS ARG GLN SEQRES 6 D 93 GLN LEU GLU LEU ASP ASP GLU LEU LYS SER VAL GLU ASN SEQRES 7 D 93 GLN MET ARG TYR ALA GLN THR GLN LEU ASP LYS LEU LYS SEQRES 8 D 93 LEU GLU SEQRES 1 A 93 ASP ASP SER GLU GLN LEU GLN MET GLU LEU LYS GLU LEU SEQRES 2 A 93 ALA LEU GLU GLU GLU ARG LEU ILE GLN GLU LEU GLU ASP SEQRES 3 A 93 VAL GLU LYS ASN ARG LYS ILE VAL ALA GLU ASN LEU GLU SEQRES 4 A 93 LYS VAL GLN ALA GLU ALA GLU ARG LEU ASP GLN GLU GLU SEQRES 5 A 93 ALA GLN TYR GLN ARG GLU TYR SER GLU PHE LYS ARG GLN SEQRES 6 A 93 GLN LEU GLU LEU ASP ASP GLU LEU LYS SER VAL GLU ASN SEQRES 7 A 93 GLN MET ARG TYR ALA GLN THR GLN LEU ASP LYS LEU LYS SEQRES 8 A 93 LEU GLU FORMUL 3 HOH *255(H2 O) HELIX 1 AA1 ASP D 175 GLU D 267 1 93 HELIX 2 AA2 ASP A 176 GLU A 267 1 92 CRYST1 58.200 71.575 58.446 90.00 112.55 90.00 C 1 2 1 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 0.017182 0.000000 0.007133 0.00000 SCALE2 0.000000 0.013971 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018526 0.00000