HEADER VIRAL PROTEIN 09-FEB-16 5FVL TITLE CRYSTAL STRUCTURE OF VPS4-VPS20 COMPLEX FROM S.CEREVISIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: MIT DOMAIN, RESIDUES 1-82; COMPND 5 SYNONYM: VPS4, DOA4-INDEPENDENT DEGRADATION PROTEIN 6, PROTEIN END13, COMPND 6 VACUOLAR PROTEIN-TARGETING PROTEIN 10; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 20; COMPND 10 CHAIN: C, D; COMPND 11 FRAGMENT: RESIDUES 170-195; COMPND 12 SYNONYM: VPS20, AMINO ACID SENSOR-INDEPENDENT PROTEIN 10, CHARGED COMPND 13 MULTIVESICULAR BODY PROTEIN 6, ESCRT-III COMPLEX SUBUNIT VPS20, COMPND 14 VACUOLAR PROTEIN-TARGETING PROTEIN 20; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: POPTH; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 12 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 13 ORGANISM_TAXID: 4932; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 18 EXPRESSION_SYSTEM_VECTOR: POPTG KEYWDS VIRAL PROTEIN, MIT DOMAIN, ATPASE, YEAST EXPDTA X-RAY DIFFRACTION AUTHOR R.KOJIMA,T.OBITA,K.ONOUE,M.MIZUGUCHI REVDAT 3 10-JAN-24 5FVL 1 REMARK REVDAT 2 08-JUN-16 5FVL 1 JRNL REVDAT 1 27-APR-16 5FVL 0 JRNL AUTH R.KOJIMA,T.OBITA,K.ONOUE,M.MIZUGUCHI JRNL TITL STRUCTURAL FINE-TUNING OF MIT INTERACTING MOTIF 2 (MIM2) AND JRNL TITL 2 ALLOSTERIC REGULATION OF ESCRT-III BY VPS4 IN YEAST. JRNL REF J.MOL.BIOL. V. 428 2392 2016 JRNL REFN ISSN 0022-2836 JRNL PMID 27075672 JRNL DOI 10.1016/J.JMB.2016.04.007 REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 13369 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 659 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 39.7043 - 3.3737 1.00 2675 132 0.1788 0.2281 REMARK 3 2 3.3737 - 2.6780 1.00 2520 141 0.1886 0.2244 REMARK 3 3 2.6780 - 2.3395 1.00 2508 135 0.1863 0.2451 REMARK 3 4 2.3395 - 2.1256 1.00 2519 118 0.1787 0.2384 REMARK 3 5 2.1256 - 1.9733 1.00 2488 133 0.1893 0.2429 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.94 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 1716 REMARK 3 ANGLE : 0.942 2313 REMARK 3 CHIRALITY : 0.042 253 REMARK 3 PLANARITY : 0.004 301 REMARK 3 DIHEDRAL : 15.527 667 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 5FVL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1290066196. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.6 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 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13410 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 39.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.30 REMARK 200 R MERGE (I) : 0.16000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.30 REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.100 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: PDB ENTRY 2V6X REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 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 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 24.07000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.08500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.94500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.08500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.07000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.94500 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: 1820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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: 1620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 HIS B 0 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 THR B 3 REMARK 465 ALA B 82 REMARK 465 GLN C 193 REMARK 465 GLY C 194 REMARK 465 GLU C 195 REMARK 465 MET D 169 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FVK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VPS4-VFA1 COMPLEX FROM S. CEREVISIAE AT 1.66 A REMARK 900 RESOLUTION. DBREF 5FVL A 1 82 UNP P52917 VPS4_YEAST 1 82 DBREF 5FVL B 1 82 UNP P52917 VPS4_YEAST 1 82 DBREF 5FVL C 170 195 UNP Q04272 VPS20_YEAST 170 195 DBREF 5FVL D 170 195 UNP Q04272 VPS20_YEAST 170 195 SEQADV 5FVL HIS A 0 UNP P52917 EXPRESSION TAG SEQADV 5FVL HIS B 0 UNP P52917 EXPRESSION TAG SEQADV 5FVL MET C 169 UNP Q04272 EXPRESSION TAG SEQADV 5FVL MET D 169 UNP Q04272 EXPRESSION TAG SEQRES 1 A 83 HIS MET SER THR GLY ASP PHE LEU THR LYS GLY ILE GLU SEQRES 2 A 83 LEU VAL GLN LYS ALA ILE ASP LEU ASP THR ALA THR GLN SEQRES 3 A 83 TYR GLU GLU ALA TYR THR ALA TYR TYR ASN GLY LEU ASP SEQRES 4 A 83 TYR LEU MET LEU ALA LEU LYS TYR GLU LYS ASN PRO LYS SEQRES 5 A 83 SER LYS ASP LEU ILE ARG ALA LYS PHE THR GLU TYR LEU SEQRES 6 A 83 ASN ARG ALA GLU GLN LEU LYS LYS HIS LEU GLU SER GLU SEQRES 7 A 83 GLU ALA ASN ALA ALA SEQRES 1 B 83 HIS MET SER THR GLY ASP PHE LEU THR LYS GLY ILE GLU SEQRES 2 B 83 LEU VAL GLN LYS ALA ILE ASP LEU ASP THR ALA THR GLN SEQRES 3 B 83 TYR GLU GLU ALA TYR THR ALA TYR TYR ASN GLY LEU ASP SEQRES 4 B 83 TYR LEU MET LEU ALA LEU LYS TYR GLU LYS ASN PRO LYS SEQRES 5 B 83 SER LYS ASP LEU ILE ARG ALA LYS PHE THR GLU TYR LEU SEQRES 6 B 83 ASN ARG ALA GLU GLN LEU LYS LYS HIS LEU GLU SER GLU SEQRES 7 B 83 GLU ALA ASN ALA ALA SEQRES 1 C 27 MET ASN PRO GLU LYS MET ASN ASN ALA LYS VAL ALA ASN SEQRES 2 C 27 MET PRO SER THR GLU GLY LEU PRO SER LEU PRO GLN GLY SEQRES 3 C 27 GLU SEQRES 1 D 27 MET ASN PRO GLU LYS MET ASN ASN ALA LYS VAL ALA ASN SEQRES 2 D 27 MET PRO SER THR GLU GLY LEU PRO SER LEU PRO GLN GLY SEQRES 3 D 27 GLU FORMUL 5 HOH *25(H2 O) HELIX 1 1 ASP A 5 ALA A 23 1 19 HELIX 2 2 GLN A 25 TYR A 46 1 22 HELIX 3 3 ASN A 49 ALA A 81 1 33 HELIX 4 4 GLY B 4 ALA B 23 1 20 HELIX 5 5 GLN B 25 GLU B 47 1 23 HELIX 6 6 ASN B 49 ASN B 80 1 32 HELIX 7 7 ASN C 170 ASN C 181 1 12 HELIX 8 8 ASN D 170 ASN D 181 1 12 CRYST1 48.140 53.890 70.170 90.00 90.00 90.00 P 21 21 21 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 0.020773 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018556 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014251 0.00000