HEADER TRANSFERASE 02-APR-20 6YJ5 TITLE FOCUSED REFINEMENT CRYO-EM STRUCTURE OF THE YEAST MITOCHONDRIAL TITLE 2 COMPLEX I SUB-STOICHIOMETRIC SULFUR TRANSFERASE SUBUNIT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHODANESE-LIKE DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: q; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YARROWIA LIPOLYTICA; SOURCE 3 ORGANISM_TAXID: 4952; SOURCE 4 GENE: B0I71DRAFT_128700, YALI1_F30877G; SOURCE 5 EXPRESSION_SYSTEM: YARROWIA LIPOLYTICA; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4952; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS NADH:UBIQUINONE OXIDOREDUCTASE, SULFUR TRANSFERASE, SUB- KEYWDS 2 STOICHIOMETRIC, COMPLEX I, TRANSFERASE EXPDTA ELECTRON MICROSCOPY AUTHOR J.HIRST,D.GRBA REVDAT 5 22-MAY-24 6YJ5 1 REMARK REVDAT 4 10-FEB-21 6YJ5 1 JRNL REVDAT 3 21-OCT-20 6YJ5 1 JRNL REVDAT 2 19-AUG-20 6YJ5 1 JRNL REVDAT 1 12-AUG-20 6YJ5 0 JRNL AUTH T.NI,S.GERARD,G.ZHAO,K.DENT,J.NING,J.ZHOU,J.SHI, JRNL AUTH 2 J.ANDERSON-DANIELS,W.LI,S.JANG,A.N.ENGELMAN,C.AIKEN,P.ZHANG JRNL TITL INTRINSIC CURVATURE OF THE HIV-1 CA HEXAMER UNDERLIES CAPSID JRNL TITL 2 TOPOLOGY AND INTERACTION WITH CYCLOPHILIN A. JRNL REF NAT.STRUCT.MOL.BIOL. V. 27 855 2020 JRNL REFN ESSN 1545-9985 JRNL PMID 32747784 JRNL DOI 10.1038/S41594-020-0467-8 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.N.GRBA,J.HIRST REMARK 1 TITL MITOCHONDRIAL COMPLEX I STRUCTURE REVEALS ORDERED WATER REMARK 1 TITL 2 MOLECULES FOR CATALYSIS AND PROTON TRANSLOCATION. REMARK 1 REF NAT.STRUCT.MOL.BIOL. V. 27 892 2020 REMARK 1 REFN ESSN 1545-9985 REMARK 1 PMID 32747785 REMARK 1 DOI 10.1038/S41594-020-0473-X REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, EPU, RELION, GCTF, UCSF REMARK 3 CHIMERA, PHENIX, PHENIX, RELION, RELION, REMARK 3 RELION, RELION REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1RHD 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 : SWISS-MODEL USED TO GENERATE INITIAL MODEL REMARK 3 USING PDB 1RHD AS A TEMPLATE 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) : 3.500 REMARK 3 NUMBER OF PARTICLES : 25456 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 6YJ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292107683. 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 : ST1 (SULFUR TRANSFERASE) REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : GOLD GRIDS SATURATED WITH PEG REMARK 245 THIOL REAGENT REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.45 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 2540 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4400.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 130000 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: q 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 q 1 REMARK 465 ASN q 308 REMARK 465 LEU q 309 REMARK 465 ASN q 310 REMARK 465 GLU q 311 REMARK 465 ALA q 312 REMARK 465 ASN q 313 REMARK 465 ARG q 314 REMARK 465 ALA q 315 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 THR q 30 OG1 CG2 REMARK 470 PRO q 31 CG CD REMARK 470 ASN q 33 CG OD1 ND2 REMARK 470 VAL q 34 CG1 CG2 REMARK 470 LYS q 36 CG CD CE NZ REMARK 470 LYS q 45 CG CD CE NZ REMARK 470 ASP q 54 CG OD1 OD2 REMARK 470 ILE q 55 CG1 CG2 CD1 REMARK 470 ASP q 56 CG OD1 OD2 REMARK 470 VAL q 58 CG1 CG2 REMARK 470 ASN q 59 CG OD1 ND2 REMARK 470 THR q 60 OG1 CG2 REMARK 470 PRO q 61 CG CD REMARK 470 SER q 62 OG REMARK 470 LYS q 63 CG CD CE NZ REMARK 470 PHE q 64 CG CD1 CD2 CE1 CE2 CZ REMARK 470 PRO q 65 CG CD REMARK 470 HIS q 66 CG ND1 CD2 CE1 NE2 REMARK 470 TRP q 139 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP q 139 CZ3 CH2 REMARK 470 THR q 144 OG1 CG2 REMARK 470 GLN q 145 CG CD OE1 NE2 REMARK 470 VAL q 146 CG1 CG2 REMARK 470 PRO q 147 CG CD REMARK 470 LYS q 149 CG CD CE NZ REMARK 470 SER q 169 OG REMARK 470 PHE q 170 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU q 171 CG CD OE1 OE2 REMARK 470 ASP q 172 CG OD1 OD2 REMARK 470 VAL q 173 CG1 CG2 REMARK 470 LEU q 174 CG CD1 CD2 REMARK 470 ILE q 176 CG1 CG2 CD1 REMARK 470 VAL q 177 CG1 CG2 REMARK 470 GLU q 178 CG CD OE1 OE2 REMARK 470 LYS q 179 CG CD CE NZ REMARK 470 HIS q 180 CG ND1 CD2 CE1 NE2 REMARK 470 ASN q 181 CG OD1 ND2 REMARK 470 ASP q 183 CG OD1 OD2 REMARK 470 LYS q 186 CG CD CE NZ REMARK 470 ILE q 187 CG1 CG2 CD1 REMARK 470 ARG q 188 CG CD NE CZ NH1 NH2 REMARK 470 ASN q 189 CG OD1 ND2 REMARK 470 GLU q 190 CG CD OE1 OE2 REMARK 470 VAL q 191 CG1 CG2 REMARK 470 THR q 192 OG1 CG2 REMARK 470 ARG q 197 CG CD NE CZ NH1 NH2 REMARK 470 ARG q 201 CG CD NE CZ NH1 NH2 REMARK 470 PHE q 202 CG CD1 CD2 CE1 CE2 CZ REMARK 470 THR q 203 OG1 CG2 REMARK 470 LYS q 205 CG CD CE NZ REMARK 470 ASP q 206 CG OD1 OD2 REMARK 470 GLU q 208 CG CD OE1 OE2 REMARK 470 PRO q 209 CG CD REMARK 470 ARG q 210 CG CD NE CZ NH1 NH2 REMARK 470 GLU q 212 CG CD OE1 OE2 REMARK 470 LEU q 213 CG CD1 CD2 REMARK 470 SER q 214 OG REMARK 470 SER q 215 OG REMARK 470 HIS q 217 CG ND1 CD2 CE1 NE2 REMARK 470 VAL q 218 CG1 CG2 REMARK 470 PRO q 219 CG CD REMARK 470 TYR q 222 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 SER q 223 OG REMARK 470 ILE q 224 CG1 CG2 CD1 REMARK 470 LYS q 234 CG CD CE NZ REMARK 470 LYS q 236 CG CD CE NZ REMARK 470 SER q 237 OG REMARK 470 PRO q 238 CG CD REMARK 470 GLU q 239 CG CD OE1 OE2 REMARK 470 GLU q 240 CG CD OE1 OE2 REMARK 470 LEU q 241 CG CD1 CD2 REMARK 470 LYS q 242 CG CD CE NZ REMARK 470 LEU q 244 CG CD1 CD2 REMARK 470 SER q 247 OG REMARK 470 LYS q 248 CG CD CE NZ REMARK 470 ILE q 250 CG1 CG2 CD1 REMARK 470 ASP q 251 CG OD1 OD2 REMARK 470 SER q 253 OG REMARK 470 LYS q 254 CG CD CE NZ REMARK 470 PRO q 255 CG CD REMARK 470 THR q 292 OG1 CG2 REMARK 470 GLU q 293 CG CD OE1 OE2 REMARK 470 TRP q 294 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP q 294 CZ3 CH2 REMARK 470 GLN q 296 CG CD OE1 NE2 REMARK 470 ARG q 297 CG CD NE CZ NH1 NH2 REMARK 470 PRO q 299 CG CD REMARK 470 THR q 300 OG1 CG2 REMARK 470 LYS q 301 CG CD CE NZ REMARK 470 TYR q 302 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ILE q 303 CG1 CG2 CD1 REMARK 470 VAL q 304 CG1 CG2 REMARK 470 LYS q 305 CG CD CE NZ REMARK 470 GLU q 306 CG CD OE1 OE2 REMARK 470 GLU q 307 CG CD OE1 OE2 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 NZ LYS q 108 OE2 GLU q 274 2.18 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 PRO q 29 46.76 -86.76 REMARK 500 LYS q 45 118.52 -162.31 REMARK 500 HIS q 66 56.39 -96.51 REMARK 500 THR q 138 -9.70 75.02 REMARK 500 ASN q 232 -18.26 70.53 REMARK 500 SER q 262 -3.59 69.01 REMARK 500 ASN q 284 80.70 -69.88 REMARK 500 PRO q 299 -178.90 -69.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6YJ4 RELATED DB: PDB REMARK 900 MAJOR COMPLEX REMARK 900 RELATED ID: EMD-10815 RELATED DB: EMDB REMARK 900 MAJOR COMPLEX REMARK 900 RELATED ID: EMD-10816 RELATED DB: EMDB REMARK 900 FOCUSED REFINEMENT CRYO-EM STRUCTURE OF THE YEAST MITOCHONDRIAL REMARK 900 COMPLEX I SUB-STOICHIOMETRIC SULFUR TRANSFERASE SUBUNIT DBREF1 6YJ5 q 1 315 UNP A0A1D8NPQ4_YARLL DBREF2 6YJ5 q A0A1D8NPQ4 1 315 SEQRES 1 q 315 MET SER LYS LEU ILE SER PRO ALA GLU LEU ALA LYS ARG SEQRES 2 q 315 LEU SER SER LYS GLU THR LYS ILE PHE ASP ALA THR TRP SEQRES 3 q 315 TYR LEU PRO THR PRO ALA ASN VAL GLY LYS ASN ALA TYR SEQRES 4 q 315 ASP ASN TYR MET LYS LYS ARG ILE PRO GLY ALA LEU TYR SEQRES 5 q 315 PHE ASP ILE ASP ALA VAL ASN THR PRO SER LYS PHE PRO SEQRES 6 q 315 HIS MET LEU PRO SER PRO GLN THR PHE GLU ASN GLU LEU SEQRES 7 q 315 THR LYS LEU GLY VAL SER SER ASP SER PRO ILE VAL VAL SEQRES 8 q 315 TYR ASP THR GLN GLY VAL PHE SER GLY PRO ARG LEU VAL SEQRES 9 q 315 TRP THR PHE LYS VAL PHE GLY HIS ASP ASN VAL GLN PHE SEQRES 10 q 315 LEU ASN GLY PHE GLU ALA TYR THR GLN LEU PRO GLY ILE SEQRES 11 q 315 PRO SER ARG PRO ASP ALA TYR THR TRP GLY ILE TRP ASP SEQRES 12 q 315 THR GLN VAL PRO GLY LYS ILE ASP PRO ALA ASP PRO PRO SEQRES 13 q 315 TYR LYS VAL THR LYS ALA ARG PRO GLU LEU VAL LYS SER SEQRES 14 q 315 PHE GLU ASP VAL LEU ALA ILE VAL GLU LYS HIS ASN GLY SEQRES 15 q 315 ASP GLY ALA LYS ILE ARG ASN GLU VAL THR PHE ILE ASP SEQRES 16 q 315 ALA ARG PRO ASN GLY ARG PHE THR GLY LYS ASP ALA GLU SEQRES 17 q 315 PRO ARG ALA GLU LEU SER SER GLY HIS VAL PRO GLY ALA SEQRES 18 q 315 TYR SER ILE ALA PHE PRO GLU VAL VAL GLU ASN GLY LYS SEQRES 19 q 315 PHE LYS SER PRO GLU GLU LEU LYS ALA LEU PHE ALA SER SEQRES 20 q 315 LYS GLY ILE ASP GLY SER LYS PRO ILE ILE SER MET CYS SEQRES 21 q 315 GLY SER GLY VAL THR ALA CYS VAL ILE ASP LEU ALA LEU SEQRES 22 q 315 GLU ILE ALA GLY ILE GLY SER ARG ASP THR ASN ALA VAL SEQRES 23 q 315 TYR ASP GLY SER TRP THR GLU TRP ALA GLN ARG ALA PRO SEQRES 24 q 315 THR LYS TYR ILE VAL LYS GLU GLU ASN LEU ASN GLU ALA SEQRES 25 q 315 ASN ARG ALA HELIX 1 AA1 SER q 6 SER q 15 1 10 HELIX 2 AA2 ALA q 38 MET q 43 1 6 HELIX 3 AA3 ASP q 54 ASN q 59 1 6 HELIX 4 AA4 PHE q 74 THR q 79 1 6 HELIX 5 AA5 GLY q 100 PHE q 110 1 11 HELIX 6 AA6 GLY q 120 GLN q 126 1 7 HELIX 7 AA7 SER q 169 ALA q 175 1 7 HELIX 8 AA8 ILE q 176 LYS q 179 5 4 HELIX 9 AA9 ASN q 181 ALA q 185 5 5 HELIX 10 AB1 LYS q 186 VAL q 191 1 6 HELIX 11 AB2 SER q 237 SER q 247 1 11 HELIX 12 AB3 CYS q 260 VAL q 264 5 5 HELIX 13 AB4 THR q 265 ALA q 266 5 2 HELIX 14 AB5 CYS q 267 GLY q 277 1 11 HELIX 15 AB6 SER q 290 ARG q 297 1 8 SHEET 1 AA1 5 LYS q 3 ILE q 5 0 SHEET 2 AA1 5 VAL q 115 LEU q 118 1 O PHE q 117 N ILE q 5 SHEET 3 AA1 5 ILE q 89 TYR q 92 1 N VAL q 91 O LEU q 118 SHEET 4 AA1 5 LYS q 20 ASP q 23 1 N PHE q 22 O VAL q 90 SHEET 5 AA1 5 LEU q 51 TYR q 52 1 O LEU q 51 N ASP q 23 SHEET 1 AA2 3 THR q 192 PHE q 193 0 SHEET 2 AA2 3 ILE q 256 SER q 258 1 O ILE q 257 N THR q 192 SHEET 3 AA2 3 ALA q 285 VAL q 286 1 O ALA q 285 N ILE q 256 CISPEP 1 ASP q 154 PRO q 155 0 -9.05 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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