HEADER PROTEIN TRANSPORT 17-MAR-11 3R42 TITLE CRYSTAL STRUCTURE OF THE YEAST VPS23 UEV DOMAIN IN COMPLEX WITH A TITLE 2 VPS27 PSDP PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUPPRESSOR PROTEIN STP22 OF TEMPERATURE-SENSITIVE ALPHA- COMPND 3 FACTOR RECEPTOR AND ARGININE PERMEASE; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: N-TERMINAL UEV DOMAIN (UNP RESIDUES 1-160); COMPND 6 SYNONYM: ESCRT-I COMPLEX SUBUNIT VPS23, VACUOLAR PROTEIN SORTING- COMPND 7 ASSOCIATED PROTEIN 23; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 27; COMPND 12 CHAIN: B; COMPND 13 FRAGMENT: PSDP PEPTIDE (UNP RESIDUES 445-453); COMPND 14 SYNONYM: VPS27, GOLGI RETENTION DEFECTIVE PROTEIN 11; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: STP22, VPS23, YCL008C, YCL8C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PGST2; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 13 ORGANISM_COMMON: YEAST; SOURCE 14 ORGANISM_TAXID: 4932 KEYWDS ENDOSOMAL SORTING, ESCRT, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR X.REN,J.H.HURLEY REVDAT 3 13-SEP-23 3R42 1 REMARK SEQADV REVDAT 2 15-JUN-11 3R42 1 JRNL REVDAT 1 04-MAY-11 3R42 0 JRNL AUTH X.REN,J.H.HURLEY JRNL TITL STRUCTURAL BASIS FOR ENDOSOMAL RECRUITMENT OF ESCRT-I BY JRNL TITL 2 ESCRT-0 IN YEAST. JRNL REF EMBO J. V. 30 2130 2011 JRNL REFN ISSN 0261-4189 JRNL PMID 21505419 JRNL DOI 10.1038/EMBOJ.2011.122 REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6_289) 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) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.120 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 17866 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 900 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 30.9776 - 3.3901 1.00 3127 143 0.1835 0.1702 REMARK 3 2 3.3901 - 2.6913 1.00 2943 170 0.1815 0.2197 REMARK 3 3 2.6913 - 2.3513 0.98 2902 146 0.1808 0.2191 REMARK 3 4 2.3513 - 2.1364 0.97 2802 152 0.1734 0.2070 REMARK 3 5 2.1364 - 1.9833 0.96 2787 147 0.1760 0.2267 REMARK 3 6 1.9833 - 1.8663 0.83 2405 142 0.1804 0.2341 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 : 0.40 REMARK 3 B_SOL : 60.74 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.16840 REMARK 3 B22 (A**2) : -2.05050 REMARK 3 B33 (A**2) : -2.11800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.007 1335 REMARK 3 ANGLE : 1.113 1831 REMARK 3 CHIRALITY : 0.074 207 REMARK 3 PLANARITY : 0.006 236 REMARK 3 DIHEDRAL : 15.121 480 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 3R42 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000064462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17866 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.900 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 3R3Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM PHOSPHATE MONOBASIC, 20% REMARK 280 PEG3350, PH 7.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 16.03250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 16.03250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 47.60000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 71.19050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 47.60000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 71.19050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 16.03250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 47.60000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 71.19050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 16.03250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 47.60000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 71.19050 REMARK 290 SMTRY3 8 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: 930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 16.03250 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 217 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 222 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 223 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 266 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 267 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 297 LIES ON A SPECIAL POSITION. 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 -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 ASN A 4 REMARK 465 TYR B 453 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 MET A 107 -8.10 -53.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3R3Q RELATED DB: PDB REMARK 900 THE VPS23 UEV DOMAIN STRUCTURE DBREF 3R42 A 1 160 UNP P25604 STP22_YEAST 1 160 DBREF 3R42 B 445 453 UNP P40343 VPS27_YEAST 445 453 SEQADV 3R42 GLY A -1 UNP P25604 EXPRESSION TAG SEQADV 3R42 ALA A 0 UNP P25604 EXPRESSION TAG SEQADV 3R42 ALA A 133 UNP P25604 CYS 133 ENGINEERED MUTATION SEQRES 1 A 162 GLY ALA MET SER ALA ASN GLY LYS ILE SER VAL PRO GLU SEQRES 2 A 162 ALA VAL VAL ASN TRP LEU PHE LYS VAL ILE GLN PRO ILE SEQRES 3 A 162 TYR ASN ASP GLY ARG THR THR PHE HIS ASP SER LEU ALA SEQRES 4 A 162 LEU LEU ASP ASN PHE HIS SER LEU ARG PRO ARG THR ARG SEQRES 5 A 162 VAL PHE THR HIS SER ASP GLY THR PRO GLN LEU LEU LEU SEQRES 6 A 162 SER ILE TYR GLY THR ILE SER THR GLY GLU ASP GLY SER SEQRES 7 A 162 SER PRO HIS SER ILE PRO VAL ILE MET TRP VAL PRO SER SEQRES 8 A 162 MET TYR PRO VAL LYS PRO PRO PHE ILE SER ILE ASN LEU SEQRES 9 A 162 GLU ASN PHE ASP MET ASN THR ILE SER SER SER LEU PRO SEQRES 10 A 162 ILE GLN GLU TYR ILE ASP SER ASN GLY TRP ILE ALA LEU SEQRES 11 A 162 PRO ILE LEU HIS ALA TRP ASP PRO ALA ALA MET ASN LEU SEQRES 12 A 162 ILE MET VAL VAL GLN GLU LEU MET SER LEU LEU HIS GLU SEQRES 13 A 162 PRO PRO GLN ASP GLN ALA SEQRES 1 B 9 GLN VAL PRO SER ASP PRO TYR ASN TYR FORMUL 3 HOH *151(H2 O) HELIX 1 1 PRO A 10 TYR A 25 1 16 HELIX 2 2 ASP A 27 PHE A 42 1 16 HELIX 3 3 ASP A 106 ILE A 110 5 5 HELIX 4 4 LEU A 114 ILE A 120 5 7 HELIX 5 5 LEU A 128 ALA A 133 1 6 HELIX 6 6 ASN A 140 HIS A 153 1 14 SHEET 1 A 4 ARG A 46 THR A 53 0 SHEET 2 A 4 PRO A 59 SER A 70 -1 O SER A 64 N ARG A 48 SHEET 3 A 4 SER A 80 TRP A 86 -1 O MET A 85 N ILE A 65 SHEET 4 A 4 PHE A 97 ILE A 100 -1 O PHE A 97 N TRP A 86 CISPEP 1 TYR A 91 PRO A 92 0 3.32 CRYST1 95.200 142.381 32.065 90.00 90.00 90.00 C 2 2 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 0.010504 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007023 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031187 0.00000