HEADER MEMBRANE PROTEIN 19-JAN-12 4DDP
TITLE CRYSTAL STRUCTURE OF BECLIN 1 EVOLUTIONARILY CONSERVED DOMAIN(ECD)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BECLIN-1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 241-450;
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;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID
KEYWDS BECLIN 1, ECD, AUTOPHAGY, MEMBRANE BINDING, MEMBRANE PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR W.J.HUANG,W.Y.CHOI,J.W.WANG,Y.G.SHI
REVDAT 2 20-MAR-24 4DDP 1 REMARK
REVDAT 1 22-FEB-12 4DDP 0
JRNL AUTH W.HUANG,W.CHOI,W.HU,N.MI,Q.GUO,M.MA,M.LIU,Y.TIAN,P.LU,
JRNL AUTH 2 F.L.WANG,H.DENG,L.LIU,N.GAO,L.YU,Y.SHI
JRNL TITL CRYSTAL STRUCTURE AND BIOCHEMICAL ANALYSES REVEAL BECLIN 1
JRNL TITL 2 AS A NOVEL MEMBRANE BINDING PROTEIN
JRNL REF CELL RES. 2012
JRNL REFN ISSN 1001-0602
JRNL PMID 22310240
JRNL DOI 10.1038/CR.2012.24
REMARK 2
REMARK 2 RESOLUTION. 1.55 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_596)
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) : 1.55
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.41
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 90.7
REMARK 3 NUMBER OF REFLECTIONS : 24700
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.177
REMARK 3 R VALUE (WORKING SET) : 0.176
REMARK 3 FREE R VALUE : 0.203
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030
REMARK 3 FREE R VALUE TEST SET COUNT : 1243
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 32.4151 - 3.2161 0.92 2725 147 0.1700 0.1767
REMARK 3 2 3.2161 - 2.5530 0.98 2840 152 0.1655 0.2140
REMARK 3 3 2.5530 - 2.2304 0.98 2825 147 0.1514 0.2016
REMARK 3 4 2.2304 - 2.0265 0.97 2797 148 0.1614 0.1816
REMARK 3 5 2.0265 - 1.8813 0.96 2723 143 0.1788 0.2078
REMARK 3 6 1.8813 - 1.7704 0.92 2629 120 0.1894 0.2579
REMARK 3 7 1.7704 - 1.6817 0.88 2505 112 0.2132 0.2324
REMARK 3 8 1.6817 - 1.6085 0.84 2358 150 0.2520 0.2897
REMARK 3 9 1.6085 - 1.5466 0.72 2055 124 0.2951 0.3269
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 : 1.01
REMARK 3 K_SOL : 0.44
REMARK 3 B_SOL : 43.95
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.890
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.97
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 19.20430
REMARK 3 B22 (A**2) : -9.67440
REMARK 3 B33 (A**2) : -9.52990
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -6.58550
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 : 0.012 1625
REMARK 3 ANGLE : 1.274 2190
REMARK 3 CHIRALITY : 0.083 225
REMARK 3 PLANARITY : 0.007 277
REMARK 3 DIHEDRAL : 16.034 582
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): 28.8198 -3.9292 17.3240
REMARK 3 T TENSOR
REMARK 3 T11: 0.2124 T22: 0.2068
REMARK 3 T33: 0.1896 T12: 0.0417
REMARK 3 T13: 0.0034 T23: 0.0037
REMARK 3 L TENSOR
REMARK 3 L11: 0.8275 L22: 1.8621
REMARK 3 L33: 1.5292 L12: 0.2464
REMARK 3 L13: 0.0823 L23: 0.0560
REMARK 3 S TENSOR
REMARK 3 S11: -0.0182 S12: 0.0220 S13: -0.0268
REMARK 3 S21: -0.0437 S22: -0.0418 S23: -0.0853
REMARK 3 S31: 0.0665 S32: 0.1095 S33: 0.0077
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 4DDP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-FEB-12.
REMARK 100 THE DEPOSITION ID IS D_1000070199.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 02-DEC-09
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SPRING-8
REMARK 200 BEAMLINE : BL41XU
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000
REMARK 200 MONOCHROMATOR : SI 111 CHANNEL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26572
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.547
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61
REMARK 200 COMPLETENESS FOR SHELL (%) : 93.3
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 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 35.24
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 3350, 0.3M NACL, 0.1M TRIS PH
REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
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 40.37300
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.78150
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.37300
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.78150
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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 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 241
REMARK 465 GLU A 242
REMARK 465 LEU A 243
REMARK 465 ASP A 244
REMARK 465 ASP A 245
REMARK 465 GLU A 246
REMARK 465 LEU A 247
REMARK 465 LYS A 265
REMARK 465 LYS A 266
REMARK 465 THR A 267
REMARK 465 ASN A 268
REMARK 465 GLU A 387
REMARK 465 TYR A 448
REMARK 465 ASN A 449
REMARK 465 LYS A 450
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 ARG A 389 CG CD NE CZ NH1 NH2
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 546 O HOH A 596 2.08
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 HD22 ASN A 271 HD22 ASN A 271 2655 0.63
REMARK 500 ND2 ASN A 271 HD22 ASN A 271 2655 1.57
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 TRP A 277 -158.21 -152.20
REMARK 500 ARG A 327 -31.70 76.49
REMARK 500 TYR A 333 49.56 -154.14
REMARK 500 LEU A 351 56.31 -104.29
REMARK 500
REMARK 500 REMARK: NULL
DBREF 4DDP A 241 450 UNP Q14457 BECN1_HUMAN 241 450
SEQRES 1 A 210 LEU GLU LEU ASP ASP GLU LEU LYS SER VAL GLU ASN GLN
SEQRES 2 A 210 MET ARG TYR ALA GLN THR GLN LEU ASP LYS LEU LYS LYS
SEQRES 3 A 210 THR ASN VAL PHE ASN ALA THR PHE HIS ILE TRP HIS SER
SEQRES 4 A 210 GLY GLN PHE GLY THR ILE ASN ASN PHE ARG LEU GLY ARG
SEQRES 5 A 210 LEU PRO SER VAL PRO VAL GLU TRP ASN GLU ILE ASN ALA
SEQRES 6 A 210 ALA TRP GLY GLN THR VAL LEU LEU LEU HIS ALA LEU ALA
SEQRES 7 A 210 ASN LYS MET GLY LEU LYS PHE GLN ARG TYR ARG LEU VAL
SEQRES 8 A 210 PRO TYR GLY ASN HIS SER TYR LEU GLU SER LEU THR ASP
SEQRES 9 A 210 LYS SER LYS GLU LEU PRO LEU TYR CYS SER GLY GLY LEU
SEQRES 10 A 210 ARG PHE PHE TRP ASP ASN LYS PHE ASP HIS ALA MET VAL
SEQRES 11 A 210 ALA PHE LEU ASP CYS VAL GLN GLN PHE LYS GLU GLU VAL
SEQRES 12 A 210 GLU LYS GLY GLU THR ARG PHE CYS LEU PRO TYR ARG MET
SEQRES 13 A 210 ASP VAL GLU LYS GLY LYS ILE GLU ASP THR GLY GLY SER
SEQRES 14 A 210 GLY GLY SER TYR SER ILE LYS THR GLN PHE ASN SER GLU
SEQRES 15 A 210 GLU GLN TRP THR LYS ALA LEU LYS PHE MET LEU THR ASN
SEQRES 16 A 210 LEU LYS TRP GLY LEU ALA TRP VAL SER SER GLN PHE TYR
SEQRES 17 A 210 ASN LYS
FORMUL 2 HOH *115(H2 O)
HELIX 1 1 SER A 249 LYS A 263 1 15
HELIX 2 2 GLU A 299 GLY A 322 1 24
HELIX 3 3 TYR A 333 HIS A 336 5 4
HELIX 4 4 LEU A 357 TRP A 361 5 5
HELIX 5 5 ASN A 363 LYS A 385 1 23
HELIX 6 6 SER A 421 PHE A 447 1 27
SHEET 1 A 3 ILE A 276 SER A 279 0
SHEET 2 A 3 PHE A 282 ILE A 285 -1 O THR A 284 N TRP A 277
SHEET 3 A 3 PHE A 288 ARG A 289 -1 O PHE A 288 N ILE A 285
SHEET 1 B 3 TYR A 328 VAL A 331 0
SHEET 2 B 3 TYR A 338 SER A 341 -1 O TYR A 338 N VAL A 331
SHEET 3 B 3 LEU A 349 PRO A 350 -1 O LEU A 349 N LEU A 339
SHEET 1 C 3 MET A 396 ASP A 397 0
SHEET 2 C 3 LYS A 402 GLU A 404 -1 O LYS A 402 N ASP A 397
SHEET 3 C 3 SER A 412 SER A 414 -1 O TYR A 413 N ILE A 403
CRYST1 80.746 33.563 74.765 90.00 113.49 90.00 C 1 2 1 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 0.012385 0.000000 0.005383 0.00000
SCALE2 0.000000 0.029795 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014584 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
