HEADER PROTEIN TRANSPORT 15-DEC-15 5FD7 TITLE X-RAY CRYSTAL STRUCTURE OF ESCRT-III SNF7 CORE DOMAIN (CONFORMATION A) 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 5 27-SEP-23 5FD7 1 REMARK REVDAT 4 25-DEC-19 5FD7 1 REMARK REVDAT 3 20-SEP-17 5FD7 1 REMARK REVDAT 2 23-AUG-17 5FD7 1 REMARK REVDAT 1 30-DEC-15 5FD7 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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 6311 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.259 REMARK 3 R VALUE (WORKING SET) : 0.259 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 315 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 27.0102 - 3.0234 0.97 3019 158 0.2449 0.2386 REMARK 3 2 3.0234 - 2.4002 0.97 2977 157 0.3160 0.3650 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 91.05 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 : 0.015 980 REMARK 3 ANGLE : 1.239 1306 REMARK 3 CHIRALITY : 0.088 154 REMARK 3 PLANARITY : 0.006 167 REMARK 3 DIHEDRAL : 16.387 396 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 18 THROUGH 59 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.7799 -15.5377 -2.6062 REMARK 3 T TENSOR REMARK 3 T11: 0.5432 T22: 0.6641 REMARK 3 T33: 0.7876 T12: 0.0726 REMARK 3 T13: -0.0688 T23: -0.1619 REMARK 3 L TENSOR REMARK 3 L11: 3.3697 L22: 3.9832 REMARK 3 L33: 7.2983 L12: 1.4117 REMARK 3 L13: 3.4373 L23: 1.5203 REMARK 3 S TENSOR REMARK 3 S11: 0.8583 S12: 0.2058 S13: -2.0080 REMARK 3 S21: -0.5610 S22: 0.2039 S23: 0.6185 REMARK 3 S31: 1.0025 S32: -0.0099 S33: -0.8180 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 60 THROUGH 119 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.6101 -7.2802 5.2759 REMARK 3 T TENSOR REMARK 3 T11: 0.3272 T22: 0.5133 REMARK 3 T33: 0.6036 T12: 0.0314 REMARK 3 T13: 0.1037 T23: -0.0298 REMARK 3 L TENSOR REMARK 3 L11: 2.8157 L22: 1.1716 REMARK 3 L33: 2.0837 L12: -2.1346 REMARK 3 L13: 0.9240 L23: -0.7762 REMARK 3 S TENSOR REMARK 3 S11: -0.1240 S12: -0.5166 S13: 0.3206 REMARK 3 S21: -0.0113 S22: 0.0818 S23: -0.1200 REMARK 3 S31: -0.0335 S32: -0.0238 S33: -0.0189 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 120 THROUGH 125 ) REMARK 3 ORIGIN FOR THE GROUP (A): 44.0364 -6.5519 23.6775 REMARK 3 T TENSOR REMARK 3 T11: 3.0874 T22: 1.3345 REMARK 3 T33: 2.0937 T12: 0.9324 REMARK 3 T13: -0.3194 T23: -0.1675 REMARK 3 L TENSOR REMARK 3 L11: 3.3594 L22: 1.0732 REMARK 3 L33: 4.4790 L12: 0.7201 REMARK 3 L13: 3.5657 L23: -0.0513 REMARK 3 S TENSOR REMARK 3 S11: -0.7006 S12: -0.3915 S13: 4.5677 REMARK 3 S21: 0.6659 S22: -1.0445 S23: -0.1183 REMARK 3 S31: -1.6691 S32: -1.7615 S33: 1.3693 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 126 THROUGH 140 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.1662 -1.0475 37.4111 REMARK 3 T TENSOR REMARK 3 T11: 0.7087 T22: 0.9277 REMARK 3 T33: 0.9779 T12: -0.0001 REMARK 3 T13: -0.1860 T23: -0.0028 REMARK 3 L TENSOR REMARK 3 L11: 2.2710 L22: 9.8340 REMARK 3 L33: 9.3006 L12: 1.2208 REMARK 3 L13: 3.3537 L23: 3.9480 REMARK 3 S TENSOR REMARK 3 S11: -0.1428 S12: 1.8358 S13: 1.2158 REMARK 3 S21: -1.7599 S22: -0.4334 S23: 0.4250 REMARK 3 S31: -0.1854 S32: 1.2160 S33: 0.8451 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 5FD7 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_1000216392. 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6376 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08840 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.24900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.910 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 (%): 53.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM NACL, 100MM MES:NAOH PH5.5, 3% 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 26.09800 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 GLY A 11 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 ASP A 141 REMARK 465 GLU A 142 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 NH1 ARG A 41 O HOH A 201 1.81 REMARK 500 SD MET A 84 O HOH A 204 1.89 REMARK 500 O ASN A 31 OG SER A 34 1.91 REMARK 500 O THR A 56 N GLY A 58 2.03 REMARK 500 OE2 GLU A 74 O HOH A 202 2.08 REMARK 500 O THR A 116 OG SER A 119 2.11 REMARK 500 C LEU A 33 O HOH A 204 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 NZ LYS A 79 OG SER A 96 1455 2.13 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 THR A 56 -95.92 -99.57 REMARK 500 LYS A 57 39.11 -47.79 REMARK 500 VAL A 61 -42.07 -28.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FD7 RELATED DB: PDB DBREF 5FD7 A 12 150 UNP P39929 SNF7_YEAST 12 150 SEQADV 5FD7 GLY A 11 UNP P39929 EXPRESSION TAG SEQRES 1 A 140 GLY ASN ALA LYS ASN LYS GLU SER PRO THR LYS ALA ILE SEQRES 2 A 140 VAL ARG LEU ARG GLU HIS ILE ASN LEU LEU SER LYS LYS SEQRES 3 A 140 GLN SER HIS LEU ARG THR GLN ILE THR ASN GLN GLU ASN SEQRES 4 A 140 GLU ALA ARG ILE PHE LEU THR LYS GLY ASN LYS VAL MET SEQRES 5 A 140 ALA LYS ASN ALA LEU LYS LYS LYS LYS THR ILE GLU GLN SEQRES 6 A 140 LEU LEU SER LYS VAL GLU GLY THR MET GLU SER MET GLU SEQRES 7 A 140 GLN GLN LEU PHE SER ILE GLU SER ALA ASN LEU ASN LEU SEQRES 8 A 140 GLU THR MET ARG ALA MET GLN GLU GLY ALA LYS ALA MET SEQRES 9 A 140 LYS THR ILE HIS SER GLY LEU ASP ILE ASP LYS VAL ASP SEQRES 10 A 140 GLU THR MET ASP GLU ILE ARG GLU GLN VAL GLU LEU GLY SEQRES 11 A 140 ASP GLU ILE SER ASP ALA ILE SER ARG PRO FORMUL 2 HOH *7(H2 O) HELIX 1 AA1 SER A 18 LYS A 57 1 40 HELIX 2 AA2 ASN A 59 GLY A 120 1 62 HELIX 3 AA3 LYS A 125 GLY A 140 1 16 CRYST1 29.451 52.196 54.486 90.00 97.52 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 0.033955 0.000000 0.004484 0.00000 SCALE2 0.000000 0.019159 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018513 0.00000