HEADER PROTEIN TRANSPORT 30-SEP-24 9JSD TITLE CRYO-EM STRUCTURE OF SNF7 LINKER EXTENSION COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR-SORTING PROTEIN SNF7; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DOA4-INDEPENDENT DEGRADATION PROTEIN 1,SUCROSE NONFERMENTING COMPND 5 PROTEIN 7,VACUOLAR PROTEIN-SORTING-ASSOCIATED PROTEIN 32; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_TAXID: 559292; SOURCE 4 GENE: SNF7, DID1, VPS32, YLR025W; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MEMBRANE FISSION, RING POLYMERS, N-TERMINAL DOMAIN, "OPEN" STATUS, KEYWDS 2 PROTEIN TRANSPORT EXPDTA ELECTRON MICROSCOPY AUTHOR Q.T.SHEN,M.D.LIU REVDAT 1 08-OCT-25 9JSD 0 JRNL AUTH Q.T.SHEN,M.D.LIU JRNL TITL CRYO-EM STRUCTURE OF SNF7 LINKER EXTENSION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 7.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 7.370 REMARK 3 NUMBER OF PARTICLES : 199543 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9JSD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 03-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1300052084. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : SNF7-INS15G RING POLYMERS REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.60 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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 MET A 1 REMARK 465 TRP A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 LEU A 5 REMARK 465 PHE A 6 REMARK 465 GLY A 7 REMARK 465 TRP A 8 REMARK 465 THR A 9 REMARK 465 SER A 10 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 465 GLY A 151 REMARK 465 GLY A 152 REMARK 465 GLY A 153 REMARK 465 GLY A 154 REMARK 465 GLY A 155 REMARK 465 GLY A 156 REMARK 465 GLY A 157 REMARK 465 GLY A 158 REMARK 465 GLY A 159 REMARK 465 GLY A 160 REMARK 465 GLY A 161 REMARK 465 GLY A 162 REMARK 465 GLY A 163 REMARK 465 GLY A 164 REMARK 465 GLY A 165 REMARK 465 LEU A 166 REMARK 465 ILE A 167 REMARK 465 THR A 168 REMARK 465 GLY A 169 REMARK 465 ALA A 170 REMARK 465 ASN A 171 REMARK 465 GLU A 172 REMARK 465 VAL A 173 REMARK 465 ASP A 174 REMARK 465 GLU A 175 REMARK 465 ASP A 176 REMARK 465 GLU A 177 REMARK 465 LEU A 178 REMARK 465 ASP A 179 REMARK 465 GLU A 180 REMARK 465 GLU A 181 REMARK 465 LEU A 182 REMARK 465 ASP A 183 REMARK 465 MET A 184 REMARK 465 LEU A 185 REMARK 465 ALA A 186 REMARK 465 GLN A 187 REMARK 465 GLU A 188 REMARK 465 ASN A 189 REMARK 465 ALA A 190 REMARK 465 ASN A 191 REMARK 465 GLN A 192 REMARK 465 GLU A 193 REMARK 465 THR A 194 REMARK 465 SER A 195 REMARK 465 LYS A 196 REMARK 465 ILE A 197 REMARK 465 VAL A 198 REMARK 465 ASN A 199 REMARK 465 ASN A 200 REMARK 465 ASN A 201 REMARK 465 VAL A 202 REMARK 465 ASN A 203 REMARK 465 ALA A 204 REMARK 465 ALA A 205 REMARK 465 PRO A 206 REMARK 465 ILE A 207 REMARK 465 SER A 208 REMARK 465 GLU A 209 REMARK 465 ASN A 210 REMARK 465 LYS A 211 REMARK 465 VAL A 212 REMARK 465 SER A 213 REMARK 465 LEU A 214 REMARK 465 PRO A 215 REMARK 465 SER A 216 REMARK 465 VAL A 217 REMARK 465 PRO A 218 REMARK 465 SER A 219 REMARK 465 ASN A 220 REMARK 465 LYS A 221 REMARK 465 ILE A 222 REMARK 465 LYS A 223 REMARK 465 GLN A 224 REMARK 465 SER A 225 REMARK 465 GLU A 226 REMARK 465 ASN A 227 REMARK 465 SER A 228 REMARK 465 VAL A 229 REMARK 465 LYS A 230 REMARK 465 ASP A 231 REMARK 465 GLY A 232 REMARK 465 GLU A 233 REMARK 465 GLU A 234 REMARK 465 GLU A 235 REMARK 465 GLU A 236 REMARK 465 ASP A 237 REMARK 465 GLU A 238 REMARK 465 GLU A 239 REMARK 465 ASP A 240 REMARK 465 GLU A 241 REMARK 465 ASP A 242 REMARK 465 GLU A 243 REMARK 465 LYS A 244 REMARK 465 ALA A 245 REMARK 465 LEU A 246 REMARK 465 ARG A 247 REMARK 465 GLU A 248 REMARK 465 LEU A 249 REMARK 465 GLN A 250 REMARK 465 ALA A 251 REMARK 465 GLU A 252 REMARK 465 MET A 253 REMARK 465 GLY A 254 REMARK 465 LEU A 255 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 SER A 18 CB - CA - C ANGL. DEV. = 11.5 DEGREES REMARK 500 SER A 18 N - CA - CB ANGL. DEV. = 9.7 DEGREES 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 ASP A 124 104.51 -161.58 REMARK 500 LYS A 125 72.74 56.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-61770 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF SNF7 LINKER EXTENSION DBREF 9JSD A 1 255 UNP P39929 SNF7_YEAST 1 240 SEQADV 9JSD GLY A 151 UNP P39929 INSERTION SEQADV 9JSD GLY A 152 UNP P39929 INSERTION SEQADV 9JSD GLY A 153 UNP P39929 INSERTION SEQADV 9JSD GLY A 154 UNP P39929 INSERTION SEQADV 9JSD GLY A 155 UNP P39929 INSERTION SEQADV 9JSD GLY A 156 UNP P39929 INSERTION SEQADV 9JSD GLY A 157 UNP P39929 INSERTION SEQADV 9JSD GLY A 158 UNP P39929 INSERTION SEQADV 9JSD GLY A 159 UNP P39929 INSERTION SEQADV 9JSD GLY A 160 UNP P39929 INSERTION SEQADV 9JSD GLY A 161 UNP P39929 INSERTION SEQADV 9JSD GLY A 162 UNP P39929 INSERTION SEQADV 9JSD GLY A 163 UNP P39929 INSERTION SEQADV 9JSD GLY A 164 UNP P39929 INSERTION SEQADV 9JSD GLY A 165 UNP P39929 INSERTION SEQRES 1 A 255 MET TRP SER SER LEU PHE GLY TRP THR SER SER ASN ALA SEQRES 2 A 255 LYS ASN LYS GLU SER PRO THR LYS ALA ILE VAL ARG LEU SEQRES 3 A 255 ARG GLU HIS ILE ASN LEU LEU SER LYS LYS GLN SER HIS SEQRES 4 A 255 LEU ARG THR GLN ILE THR ASN GLN GLU ASN GLU ALA ARG SEQRES 5 A 255 ILE PHE LEU THR LYS GLY ASN LYS VAL MET ALA LYS ASN SEQRES 6 A 255 ALA LEU LYS LYS LYS LYS THR ILE GLU GLN LEU LEU SER SEQRES 7 A 255 LYS VAL GLU GLY THR MET GLU SER MET GLU GLN GLN LEU SEQRES 8 A 255 PHE SER ILE GLU SER ALA ASN LEU ASN LEU GLU THR MET SEQRES 9 A 255 ARG ALA MET GLN GLU GLY ALA LYS ALA MET LYS THR ILE SEQRES 10 A 255 HIS SER GLY LEU ASP ILE ASP LYS VAL ASP GLU THR MET SEQRES 11 A 255 ASP GLU ILE ARG GLU GLN VAL GLU LEU GLY ASP GLU ILE SEQRES 12 A 255 SER ASP ALA ILE SER ARG PRO GLY GLY GLY GLY GLY GLY SEQRES 13 A 255 GLY GLY GLY GLY GLY GLY GLY GLY GLY LEU ILE THR GLY SEQRES 14 A 255 ALA ASN GLU VAL ASP GLU ASP GLU LEU ASP GLU GLU LEU SEQRES 15 A 255 ASP MET LEU ALA GLN GLU ASN ALA ASN GLN GLU THR SER SEQRES 16 A 255 LYS ILE VAL ASN ASN ASN VAL ASN ALA ALA PRO ILE SER SEQRES 17 A 255 GLU ASN LYS VAL SER LEU PRO SER VAL PRO SER ASN LYS SEQRES 18 A 255 ILE LYS GLN SER GLU ASN SER VAL LYS ASP GLY GLU GLU SEQRES 19 A 255 GLU GLU ASP GLU GLU ASP GLU ASP GLU LYS ALA LEU ARG SEQRES 20 A 255 GLU LEU GLN ALA GLU MET GLY LEU HELIX 1 AA1 SER A 11 GLY A 58 1 48 HELIX 2 AA2 ASN A 59 LEU A 121 1 63 HELIX 3 AA3 LYS A 125 LEU A 139 1 15 HELIX 4 AA4 GLY A 140 GLU A 142 5 3 CISPEP 1 ILE A 123 ASP A 124 0 5.80 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 TER 2018 GLU A 142 MASTER 269 0 0 4 0 0 0 6 1046 1 0 20 END