HEADER PROTEIN TRANSPORT 15-DEC-15 5FD9 TITLE X-RAY CRYSTAL STRUCTURE OF ESCRT-III SNF7 CORE DOMAIN (CONFORMATION B) COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR-SORTING PROTEIN SNF7; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DOA4-INDEPENDENT DEGRADATION PROTEIN 1,VACUOLAR PROTEIN- COMPND 5 SORTING-ASSOCIATED PROTEIN 32; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 STRAIN: ATCC 204508 / S288C; SOURCE 7 GENE: SNF7, DID1, VPS32, YLR025W; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PET28A; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET28A HIS6-SUMO-SNF7N12-P150 KEYWDS ESCRT, SNF7, ACTIVE, CORE, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.TANG,W.M.HENNE,P.P.BORBAT,N.J.BUCHKOVICH,J.H.FREED,Y.MAO, AUTHOR 2 J.C.FROMME,S.D.EMR REVDAT 4 27-SEP-23 5FD9 1 REMARK REVDAT 3 25-DEC-19 5FD9 1 REMARK REVDAT 2 20-SEP-17 5FD9 1 REMARK REVDAT 1 30-DEC-15 5FD9 0 JRNL AUTH S.TANG,W.M.HENNE,P.P.BORBAT,N.J.BUCHKOVICH,J.H.FREED,Y.MAO, JRNL AUTH 2 J.C.FROMME,S.D.EMR JRNL TITL STRUCTURAL BASIS FOR ACTIVATION, ASSEMBLY AND MEMBRANE JRNL TITL 2 BINDING OF ESCRT-III SNF7 FILAMENTS. JRNL REF ELIFE V. 4 2015 JRNL REFN ESSN 2050-084X JRNL PMID 26670543 JRNL DOI 10.7554/ELIFE.12548 REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 15389 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 775 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 24.9103 - 2.9061 0.96 2488 134 0.1961 0.2145 REMARK 3 2 2.9061 - 2.3072 0.98 2468 129 0.2198 0.2361 REMARK 3 3 2.3072 - 2.0157 0.97 2450 131 0.1989 0.2129 REMARK 3 4 2.0157 - 1.8315 0.97 2427 128 0.2270 0.2419 REMARK 3 5 1.8315 - 1.7002 0.96 2414 129 0.2509 0.2852 REMARK 3 6 1.7002 - 1.6000 0.94 2367 124 0.2818 0.2511 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.71 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 : 0.006 997 REMARK 3 ANGLE : 0.808 1329 REMARK 3 CHIRALITY : 0.034 156 REMARK 3 PLANARITY : 0.003 171 REMARK 3 DIHEDRAL : 13.488 403 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 5FD9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000216396. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16849 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.8500 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) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.07820 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.350 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: 4ABM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 110MM NACL, 70MM MES:NAOH PH5.5, 6% REMARK 280 PEG20,000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 23.10050 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 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 ASN A 12 REMARK 465 ALA A 13 REMARK 465 LYS A 14 REMARK 465 ASN A 15 REMARK 465 LYS A 16 REMARK 465 GLU A 17 REMARK 465 ILE A 143 REMARK 465 SER A 144 REMARK 465 ASP A 145 REMARK 465 ALA A 146 REMARK 465 ILE A 147 REMARK 465 SER A 148 REMARK 465 ARG A 149 REMARK 465 PRO A 150 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 255 O HOH A 297 1.82 REMARK 500 NZ LYS A 125 O HOH A 201 1.84 REMARK 500 O HOH A 288 O HOH A 293 1.86 REMARK 500 OE1 GLU A 142 O HOH A 202 1.90 REMARK 500 NE2 GLN A 43 O HOH A 203 1.94 REMARK 500 O HOH A 282 O HOH A 292 1.97 REMARK 500 CD GLU A 142 O HOH A 202 1.98 REMARK 500 O HOH A 201 O HOH A 228 1.99 REMARK 500 NZ LYS A 79 O HOH A 204 2.01 REMARK 500 O HOH A 207 O HOH A 286 2.02 REMARK 500 OE1 GLU A 48 O HOH A 205 2.07 REMARK 500 NE2 GLN A 108 O HOH A 206 2.08 REMARK 500 O HOH A 205 O HOH A 266 2.12 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 NZ LYS A 36 OE2 GLU A 142 1745 1.73 REMARK 500 CE LYS A 36 OE2 GLU A 142 1745 1.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FD7 RELATED DB: PDB DBREF 5FD9 A 12 150 UNP P39929 SNF7_YEAST 12 150 SEQRES 1 A 139 ASN ALA LYS ASN LYS GLU SER PRO THR LYS ALA ILE VAL SEQRES 2 A 139 ARG LEU ARG GLU HIS ILE ASN LEU LEU SER LYS LYS GLN SEQRES 3 A 139 SER HIS LEU ARG THR GLN ILE THR ASN GLN GLU ASN GLU SEQRES 4 A 139 ALA ARG ILE PHE LEU THR LYS GLY ASN LYS VAL MET ALA SEQRES 5 A 139 LYS ASN ALA LEU LYS LYS LYS LYS THR ILE GLU GLN LEU SEQRES 6 A 139 LEU SER LYS VAL GLU GLY THR MET GLU SER MET GLU GLN SEQRES 7 A 139 GLN LEU PHE SER ILE GLU SER ALA ASN LEU ASN LEU GLU SEQRES 8 A 139 THR MET ARG ALA MET GLN GLU GLY ALA LYS ALA MET LYS SEQRES 9 A 139 THR ILE HIS SER GLY LEU ASP ILE ASP LYS VAL ASP GLU SEQRES 10 A 139 THR MET ASP GLU ILE ARG GLU GLN VAL GLU LEU GLY ASP SEQRES 11 A 139 GLU ILE SER ASP ALA ILE SER ARG PRO FORMUL 2 HOH *105(H2 O) HELIX 1 AA1 SER A 18 LYS A 57 1 40 HELIX 2 AA2 ASN A 59 SER A 119 1 61 HELIX 3 AA3 VAL A 126 LEU A 139 1 14 CISPEP 1 ILE A 123 ASP A 124 0 -8.49 CRYST1 29.901 46.201 44.601 90.00 98.50 90.00 P 1 21 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 0.033444 0.000000 0.004996 0.00000 SCALE2 0.000000 0.021645 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022670 0.00000