HEADER MEMBRANE PROTEIN 14-APR-20 6YNV TITLE CRYO-EM STRUCTURE OF TETRAHYMENA THERMOPHILA MITOCHONDRIAL ATP TITLE 2 SYNTHASE - FO-WING REGION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATPTT1; COMPND 3 CHAIN: e SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TETRAHYMENA THERMOPHILA; SOURCE 3 ORGANISM_TAXID: 5911 KEYWDS MITOCHONDRIA, ATP SYNTHASE, OXIDOREDUCTASE, NAD, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR R.KOCK FLYGAARD,A.MUHLEIP,A.AMUNTS REVDAT 3 22-MAY-24 6YNV 1 REMARK REVDAT 2 11-NOV-20 6YNV 1 JRNL REVDAT 1 30-SEP-20 6YNV 0 JRNL AUTH R.K.FLYGAARD,A.MUHLEIP,V.TOBIASSON,A.AMUNTS JRNL TITL TYPE III ATP SYNTHASE IS A SYMMETRY-DEVIATED DIMER THAT JRNL TITL 2 INDUCES MEMBRANE CURVATURE THROUGH TETRAMERIZATION. JRNL REF NAT COMMUN V. 11 5342 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 33093501 JRNL DOI 10.1038/S41467-020-18993-6 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, EPU, CTFFIND, RELION, RELION, REMARK 3 RELION 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) : 2.800 REMARK 3 NUMBER OF PARTICLES : 61157 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 6YNV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292107809. 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 : MITOCHONDRIAL ATP SYNTHASE, FO REMARK 245 -WING REGION REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.75 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 QUANTUM (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 : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 3090.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 165000 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: 1240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: e 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 e 1 REMARK 465 ILE e 2 REMARK 465 HIS e 3 REMARK 465 CYS e 4 REMARK 465 LEU e 5 REMARK 465 ARG e 6 REMARK 465 ASN e 7 REMARK 465 ILE e 8 REMARK 465 ARG e 9 REMARK 465 THR e 10 REMARK 465 VAL e 11 REMARK 465 SER e 12 REMARK 465 ALA e 13 REMARK 465 LEU e 14 REMARK 465 GLN e 15 REMARK 465 SER e 16 REMARK 465 LYS e 17 REMARK 465 ILE e 18 REMARK 465 SER e 19 REMARK 465 TYR e 20 REMARK 465 ASN e 21 REMARK 465 LEU e 22 REMARK 465 GLY e 23 REMARK 465 GLY e 24 REMARK 465 GLY e 25 REMARK 465 ASN e 26 REMARK 465 TYR e 444 REMARK 465 HIS e 445 REMARK 465 LYS e 446 REMARK 465 VAL e 447 REMARK 465 LEU e 448 REMARK 465 LYS e 449 REMARK 465 SER e 450 REMARK 465 PHE e 451 REMARK 465 PRO e 452 REMARK 465 GLU e 453 REMARK 465 LEU e 454 REMARK 465 PRO e 455 REMARK 465 GLY e 456 REMARK 465 SER e 457 REMARK 465 PRO e 458 REMARK 465 GLU e 459 REMARK 465 SER e 460 REMARK 465 GLN e 461 REMARK 465 GLN e 462 REMARK 465 SER e 463 REMARK 465 SER e 464 REMARK 465 GLY e 465 REMARK 465 ILE e 466 REMARK 465 SER e 467 REMARK 465 LYS e 468 REMARK 465 TYR e 469 REMARK 465 PHE e 470 REMARK 465 PRO e 471 REMARK 465 THR e 472 REMARK 465 LYS e 473 REMARK 465 THR e 474 REMARK 465 GLU e 475 REMARK 465 ASN e 476 REMARK 465 LYS e 477 REMARK 465 ALA e 478 REMARK 465 ALA e 479 REMARK 465 HIS e 480 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 O HIS e 157 HZ2 LYS e 177 1.58 REMARK 500 OE1 GLN e 85 OH TYR e 420 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 ASP e 34 68.30 -101.19 REMARK 500 ASP e 70 -32.28 -130.82 REMARK 500 GLU e 202 -72.97 -64.46 REMARK 500 ASN e 294 104.96 -160.38 REMARK 500 TYR e 331 73.00 61.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD e 900 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-10857 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF TETRAHYMENA THERMOPHILA MITOCHONDRIAL ATP REMARK 900 SYNTHASE - FO-WING REGION DBREF 6YNV e 1 480 UNP I7LVQ8 I7LVQ8_TETTS 1 480 SEQRES 1 e 480 MET ILE HIS CYS LEU ARG ASN ILE ARG THR VAL SER ALA SEQRES 2 e 480 LEU GLN SER LYS ILE SER TYR ASN LEU GLY GLY GLY ASN SEQRES 3 e 480 LYS ARG LYS LYS THR SER GLY ASP LEU ASP ASN TYR ASP SEQRES 4 e 480 VAL LEU PHE VAL GLY ALA ASN LEU GLY GLY ILE CYS SER SEQRES 5 e 480 ASN HIS PHE ASP LYS ASP THR HIS GLY LYS TYR LYS CYS SEQRES 6 e 480 PHE VAL SER PHE ASP GLN PRO ILE ASN GLN ILE TYR SER SEQRES 7 e 480 VAL ARG ILE PRO TYR GLU GLN GLN ARG VAL ARG LYS SER SEQRES 8 e 480 GLU TYR ILE HIS PHE SER LYS LYS SER ILE ASN GLN PHE SEQRES 9 e 480 THR PRO SER GLU MET LEU ALA VAL LYS GLU ILE LEU PRO SEQRES 10 e 480 GLU GLN ASN ALA VAL VAL LEU SER SER GLY ARG ARG ILE SEQRES 11 e 480 GLY TYR ASN GLN LEU VAL LEU ALA THR GLY LEU LYS HIS SEQRES 12 e 480 ASP PHE SER GLN ILE LYS GLY PHE TYR GLU ALA LEU GLU SEQRES 13 e 480 HIS PRO GLU HIS PRO VAL TYR ALA ASN ARG ASP PRO GLU SEQRES 14 e 480 THR TRP ARG SER ALA GLN HIS LYS TYR SER LYS TYR ILE SEQRES 15 e 480 SER ASN PHE LYS SER GLY ASP GLY TYR PHE CYS ILE PRO SEQRES 16 e 480 GLU TYR PRO TYR ALA GLY GLU VAL GLU CYS PHE ASN PHE SEQRES 17 e 480 PHE VAL SER ASP GLU VAL TRP LYS TRP ALA GLN HIS HIS SEQRES 18 e 480 GLY ALA LEU SER PRO LYS HIS THR PHE THR ILE VAL ASN SEQRES 19 e 480 ALA ASN GLU LYS PHE VAL HIS TYR CYS ASP SER ALA ASP SEQRES 20 e 480 ALA PHE ILE LYS GLU ARG LEU GLU LYS ARG GLY ILE ARG SEQRES 21 e 480 VAL GLU TYR ASN THR LYS LEU LEU GLU VAL HIS GLN ASP SEQRES 22 e 480 GLY GLN LYS ALA THR PHE ILE ASN THR LYS THR GLY GLU SEQRES 23 e 480 LYS SER VAL ARG ASP TYR ASN ASN LEU TYR SER ILE VAL SEQRES 24 e 480 PRO SER LYS ARG GLN GLU PHE LEU ASP LYS ALA GLY LEU SEQRES 25 e 480 THR ASN GLY ASN GLY LEU LEU ASN VAL ASP HIS GLN THR SEQRES 26 e 480 LEU GLN HIS LYS LYS TYR LYS ASN ILE PHE GLY LEU GLY SEQRES 27 e 480 ASP ALA ALA ASP LEU PRO THR THR LYS THR PHE TRP ALA SEQRES 28 e 480 GLY TRP TYR GLN ILE ALA VAL VAL ARG ASN ASN VAL LYS SEQRES 29 e 480 ARG ASN LEU GLN GLY GLN THR LEU ASN ALA HIS TYR ASP SEQRES 30 e 480 GLY PHE SER LYS VAL PRO LEU PHE THR GLY HIS GLN THR SEQRES 31 e 480 LEU THR TYR VAL ALA HIS SER TYR GLY GLY VAL GLY ASN SEQRES 32 e 480 TRP GLN HIS LEU LYS HIS ASN ASN GLY GLY ILE LEU ALA SEQRES 33 e 480 TRP MET ARG TYR ARG SER TRP ALA LYS GLY MET ALA LYS SEQRES 34 e 480 LYS PHE GLN ASP PHE TYR ASN GLY ALA ARG LEU GLY PRO SEQRES 35 e 480 PRO TYR HIS LYS VAL LEU LYS SER PHE PRO GLU LEU PRO SEQRES 36 e 480 GLY SER PRO GLU SER GLN GLN SER SER GLY ILE SER LYS SEQRES 37 e 480 TYR PHE PRO THR LYS THR GLU ASN LYS ALA ALA HIS HET NAD e 900 70 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 2 NAD C21 H27 N7 O14 P2 HELIX 1 AA1 ASN e 46 HIS e 60 1 15 HELIX 2 AA2 VAL e 79 GLN e 85 1 7 HELIX 3 AA3 ARG e 89 GLU e 92 5 4 HELIX 4 AA4 SER e 97 ILE e 101 1 5 HELIX 5 AA5 PHE e 145 ILE e 148 5 4 HELIX 6 AA6 GLY e 150 HIS e 157 1 8 HELIX 7 AA7 HIS e 176 TYR e 178 5 3 HELIX 8 AA8 SER e 179 ASN e 184 1 6 HELIX 9 AA9 PHE e 209 GLN e 219 1 11 HELIX 10 AB1 CYS e 243 GLY e 258 1 16 HELIX 11 AB2 GLU e 305 ALA e 310 1 6 HELIX 12 AB3 THR e 348 GLN e 368 1 21 HELIX 13 AB4 GLY e 413 LYS e 425 1 13 HELIX 14 AB5 LYS e 430 GLY e 437 1 8 SHEET 1 AA1 5 SER e 107 GLU e 108 0 SHEET 2 AA1 5 CYS e 65 SER e 68 1 N VAL e 67 O GLU e 108 SHEET 3 AA1 5 VAL e 40 VAL e 43 1 N PHE e 42 O PHE e 66 SHEET 4 AA1 5 LEU e 135 LEU e 137 1 O VAL e 136 N LEU e 41 SHEET 5 AA1 5 ILE e 334 GLY e 336 1 O PHE e 335 N LEU e 135 SHEET 1 AA2 2 ILE e 73 GLN e 75 0 SHEET 2 AA2 2 ILE e 94 PHE e 96 -1 O HIS e 95 N ASN e 74 SHEET 1 AA3 3 VAL e 112 LEU e 116 0 SHEET 2 AA3 3 ALA e 121 LEU e 124 -1 O VAL e 123 N GLU e 114 SHEET 3 AA3 3 ARG e 129 GLY e 131 -1 O ILE e 130 N VAL e 122 SHEET 1 AA4 2 LYS e 142 HIS e 143 0 SHEET 2 AA4 2 SER e 301 LYS e 302 -1 O LYS e 302 N LYS e 142 SHEET 1 AA5 5 VAL e 162 ALA e 164 0 SHEET 2 AA5 5 ASN e 294 SER e 297 1 O LEU e 295 N TYR e 163 SHEET 3 AA5 5 GLY e 188 ILE e 194 1 N CYS e 193 O TYR e 296 SHEET 4 AA5 5 HIS e 228 ASN e 234 1 O THR e 229 N GLY e 190 SHEET 5 AA5 5 ARG e 260 TYR e 263 1 O ARG e 260 N ILE e 232 SHEET 1 AA6 3 THR e 265 HIS e 271 0 SHEET 2 AA6 3 LYS e 276 ASN e 281 -1 O LYS e 276 N HIS e 271 SHEET 3 AA6 3 GLU e 286 ASP e 291 -1 O SER e 288 N PHE e 279 SHEET 1 AA7 2 THR e 313 ASN e 314 0 SHEET 2 AA7 2 LEU e 318 LEU e 319 -1 O LEU e 318 N ASN e 314 SHEET 1 AA8 2 SER e 380 GLY e 387 0 SHEET 2 AA8 2 THR e 390 HIS e 396 -1 O THR e 392 N LEU e 384 CISPEP 1 TYR e 197 PRO e 198 0 -3.03 SITE 1 AC1 27 VAL e 43 GLY e 44 ALA e 45 ASN e 46 SITE 2 AC1 27 LEU e 47 SER e 68 PHE e 69 ASP e 70 SITE 3 AC1 27 GLN e 71 TYR e 77 ALA e 111 VAL e 112 SITE 4 AC1 27 ALA e 138 THR e 139 GLY e 140 HIS e 143 SITE 5 AC1 27 ASN e 165 ALA e 200 GLY e 201 GLU e 204 SITE 6 AC1 27 CYS e 205 GLN e 304 PHE e 306 GLY e 338 SITE 7 AC1 27 ASP e 339 THR e 348 PHE e 349 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