HEADER MEMBRANE PROTEIN 25-OCT-22 8H9R TITLE HUMAN ATP SYNTHASE STATE 3B SUBREGION 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP SYNTHASE F(0) COMPLEX SUBUNIT B1, MITOCHONDRIAL; COMPND 3 CHAIN: K; COMPND 4 SYNONYM: ATP SYNTHASE PERIPHERAL STALK-MEMBRANE SUBUNIT B,ATP COMPND 5 SYNTHASE PROTON-TRANSPORTING MITOCHONDRIAL F(0) COMPLEX SUBUNIT B1, COMPND 6 ATP SYNTHASE SUBUNIT B,ATPASE SUBUNIT B; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL; COMPND 9 CHAIN: L; COMPND 10 SYNONYM: ATPASE SUBUNIT F6,ATP SYNTHASE PERIPHERAL STALK SUBUNIT F6; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: ATP SYNTHASE SUBUNIT D, MITOCHONDRIAL; COMPND 13 CHAIN: M; COMPND 14 SYNONYM: ATPASE SUBUNIT D,ATP SYNTHASE PERIPHERAL STALK SUBUNIT D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 6 ORGANISM_COMMON: HUMAN; SOURCE 7 ORGANISM_TAXID: 9606; SOURCE 8 MOL_ID: 3; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.LAI,Y.ZHANG,F.LIU,Y.GAO,H.GONG,Z.RAO REVDAT 3 05-JUL-23 8H9R 1 JRNL REVDAT 2 07-JUN-23 8H9R 1 JRNL REVDAT 1 31-MAY-23 8H9R 0 JRNL AUTH Y.LAI,Y.ZHANG,S.ZHOU,J.XU,Z.DU,Z.FENG,L.YU,Z.ZHAO,W.WANG, JRNL AUTH 2 Y.TANG,X.YANG,L.W.GUDDAT,F.LIU,Y.GAO,Z.RAO,H.GONG JRNL TITL STRUCTURE OF THE HUMAN ATP SYNTHASE. JRNL REF MOL.CELL V. 83 2137 2023 JRNL REFN ISSN 1097-2765 JRNL PMID 37244256 JRNL DOI 10.1016/J.MOLCEL.2023.04.029 REMARK 2 REMARK 2 RESOLUTION. 3.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC 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) : 3.970 REMARK 3 NUMBER OF PARTICLES : 23272 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 8H9R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE DEPOSITION ID IS D_1300033013. 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 : HUMAN ATP SYNTHASE 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 : 7.40 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 : FEI FALCON IV (4K X 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: K, L, M 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 PRO K 1 REMARK 465 VAL K 2 REMARK 465 ILE K 185 REMARK 465 SER K 186 REMARK 465 THR K 187 REMARK 465 GLN K 188 REMARK 465 GLN K 189 REMARK 465 GLU K 190 REMARK 465 LYS K 191 REMARK 465 GLU K 192 REMARK 465 GLN K 209 REMARK 465 ALA K 210 REMARK 465 GLN K 211 REMARK 465 PRO K 212 REMARK 465 VAL K 213 REMARK 465 MET K 214 REMARK 465 MET L 1 REMARK 465 ILE L 2 REMARK 465 LEU L 3 REMARK 465 GLN L 4 REMARK 465 ARG L 5 REMARK 465 LEU L 6 REMARK 465 PHE L 7 REMARK 465 ARG L 8 REMARK 465 PHE L 9 REMARK 465 SER L 10 REMARK 465 SER L 11 REMARK 465 VAL L 12 REMARK 465 ILE L 13 REMARK 465 ARG L 14 REMARK 465 SER L 15 REMARK 465 ALA L 16 REMARK 465 VAL L 17 REMARK 465 SER L 18 REMARK 465 VAL L 19 REMARK 465 HIS L 20 REMARK 465 LEU L 21 REMARK 465 ARG L 22 REMARK 465 ARG L 23 REMARK 465 ASN L 24 REMARK 465 ILE L 25 REMARK 465 GLY L 26 REMARK 465 VAL L 27 REMARK 465 THR L 28 REMARK 465 ALA L 29 REMARK 465 VAL L 30 REMARK 465 ALA L 31 REMARK 465 PHE L 32 REMARK 465 ASN L 33 REMARK 465 LYS L 34 REMARK 465 GLU L 35 REMARK 465 LEU L 36 REMARK 465 ASP L 37 REMARK 465 PRO L 38 REMARK 465 ILE L 39 REMARK 465 GLN L 107 REMARK 465 ALA L 108 REMARK 465 ALA M 1 REMARK 465 GLY M 2 REMARK 465 ARG M 3 REMARK 465 LYS M 4 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 K 193 OG1 CG2 REMARK 470 ILE K 194 CG1 CG2 CD1 REMARK 470 LYS K 196 CG CD CE NZ REMARK 470 CYS K 197 SG REMARK 470 ILE K 198 CG1 CG2 CD1 REMARK 470 ASP K 200 CG OD1 OD2 REMARK 470 LEU K 201 CG CD1 CD2 REMARK 470 LYS K 202 CG CD CE NZ REMARK 470 LEU K 203 CG CD1 CD2 REMARK 470 LEU K 204 CG CD1 CD2 REMARK 470 LYS K 206 CG CD CE NZ REMARK 470 LYS K 207 CG CD CE NZ REMARK 470 LYS L 53 CG CD CE NZ REMARK 470 TYR L 67 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS M 72 CG CD CE NZ REMARK 470 LYS M 84 CG CD CE NZ 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 ARG K 121 -39.92 -37.91 REMARK 500 SER L 65 -4.09 65.65 REMARK 500 GLU L 66 -168.06 -168.24 REMARK 500 TYR L 67 -5.05 75.48 REMARK 500 LYS M 84 12.82 57.21 REMARK 500 ASN M 123 36.72 -96.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-34578 RELATED DB: EMDB REMARK 900 HUMAN ATP SYNTHASE PERIPHERAL STALK DOMAIN, STATE 3B DBREF 8H9R K 1 214 UNP P24539 AT5F1_HUMAN 43 256 DBREF 8H9R L 1 108 UNP P18859 ATP5J_HUMAN 1 108 DBREF 8H9R M 1 160 UNP O75947 ATP5H_HUMAN 2 161 SEQRES 1 K 214 PRO VAL PRO PRO LEU PRO GLU TYR GLY GLY LYS VAL ARG SEQRES 2 K 214 TYR GLY LEU ILE PRO GLU GLU PHE PHE GLN PHE LEU TYR SEQRES 3 K 214 PRO LYS THR GLY VAL THR GLY PRO TYR VAL LEU GLY THR SEQRES 4 K 214 GLY LEU ILE LEU TYR ALA LEU SER LYS GLU ILE TYR VAL SEQRES 5 K 214 ILE SER ALA GLU THR PHE THR ALA LEU SER VAL LEU GLY SEQRES 6 K 214 VAL MET VAL TYR GLY ILE LYS LYS TYR GLY PRO PHE VAL SEQRES 7 K 214 ALA ASP PHE ALA ASP LYS LEU ASN GLU GLN LYS LEU ALA SEQRES 8 K 214 GLN LEU GLU GLU ALA LYS GLN ALA SER ILE GLN HIS ILE SEQRES 9 K 214 GLN ASN ALA ILE ASP THR GLU LYS SER GLN GLN ALA LEU SEQRES 10 K 214 VAL GLN LYS ARG HIS TYR LEU PHE ASP VAL GLN ARG ASN SEQRES 11 K 214 ASN ILE ALA MET ALA LEU GLU VAL THR TYR ARG GLU ARG SEQRES 12 K 214 LEU TYR ARG VAL TYR LYS GLU VAL LYS ASN ARG LEU ASP SEQRES 13 K 214 TYR HIS ILE SER VAL GLN ASN MET MET ARG ARG LYS GLU SEQRES 14 K 214 GLN GLU HIS MET ILE ASN TRP VAL GLU LYS HIS VAL VAL SEQRES 15 K 214 GLN SER ILE SER THR GLN GLN GLU LYS GLU THR ILE ALA SEQRES 16 K 214 LYS CYS ILE ALA ASP LEU LYS LEU LEU ALA LYS LYS ALA SEQRES 17 K 214 GLN ALA GLN PRO VAL MET SEQRES 1 L 108 MET ILE LEU GLN ARG LEU PHE ARG PHE SER SER VAL ILE SEQRES 2 L 108 ARG SER ALA VAL SER VAL HIS LEU ARG ARG ASN ILE GLY SEQRES 3 L 108 VAL THR ALA VAL ALA PHE ASN LYS GLU LEU ASP PRO ILE SEQRES 4 L 108 GLN LYS LEU PHE VAL ASP LYS ILE ARG GLU TYR LYS SER SEQRES 5 L 108 LYS ARG GLN THR SER GLY GLY PRO VAL ASP ALA SER SER SEQRES 6 L 108 GLU TYR GLN GLN GLU LEU GLU ARG GLU LEU PHE LYS LEU SEQRES 7 L 108 LYS GLN MET PHE GLY ASN ALA ASP MET ASN THR PHE PRO SEQRES 8 L 108 THR PHE LYS PHE GLU ASP PRO LYS PHE GLU VAL ILE GLU SEQRES 9 L 108 LYS PRO GLN ALA SEQRES 1 M 160 ALA GLY ARG LYS LEU ALA LEU LYS THR ILE ASP TRP VAL SEQRES 2 M 160 ALA PHE ALA GLU ILE ILE PRO GLN ASN GLN LYS ALA ILE SEQRES 3 M 160 ALA SER SER LEU LYS SER TRP ASN GLU THR LEU THR SER SEQRES 4 M 160 ARG LEU ALA ALA LEU PRO GLU ASN PRO PRO ALA ILE ASP SEQRES 5 M 160 TRP ALA TYR TYR LYS ALA ASN VAL ALA LYS ALA GLY LEU SEQRES 6 M 160 VAL ASP ASP PHE GLU LYS LYS PHE ASN ALA LEU LYS VAL SEQRES 7 M 160 PRO VAL PRO GLU ASP LYS TYR THR ALA GLN VAL ASP ALA SEQRES 8 M 160 GLU GLU LYS GLU ASP VAL LYS SER CYS ALA GLU TRP VAL SEQRES 9 M 160 SER LEU SER LYS ALA ARG ILE VAL GLU TYR GLU LYS GLU SEQRES 10 M 160 MET GLU LYS MET LYS ASN LEU ILE PRO PHE ASP GLN MET SEQRES 11 M 160 THR ILE GLU ASP LEU ASN GLU ALA PHE PRO GLU THR LYS SEQRES 12 M 160 LEU ASP LYS LYS LYS TYR PRO TYR TRP PRO HIS GLN PRO SEQRES 13 M 160 ILE GLU ASN LEU HELIX 1 AA1 GLU K 19 TYR K 26 1 8 HELIX 2 AA2 THR K 29 VAL K 31 5 3 HELIX 3 AA3 THR K 32 LYS K 48 1 17 HELIX 4 AA4 SER K 54 ARG K 121 1 68 HELIX 5 AA5 HIS K 122 VAL K 182 1 61 HELIX 6 AA6 ILE K 194 LYS K 206 1 13 HELIX 7 AA7 LYS L 41 GLN L 55 1 15 HELIX 8 AA8 TYR L 67 GLY L 83 1 17 HELIX 9 AA9 TRP M 12 ILE M 18 1 7 HELIX 10 AB1 ILE M 19 ASN M 22 5 4 HELIX 11 AB2 GLN M 23 ALA M 43 1 21 HELIX 12 AB3 TRP M 53 ALA M 58 1 6 HELIX 13 AB4 GLY M 64 ALA M 75 1 12 HELIX 14 AB5 TYR M 85 ASN M 123 1 39 HELIX 15 AB6 PRO M 126 MET M 130 5 5 HELIX 16 AB7 THR M 131 PHE M 139 1 9 HELIX 17 AB8 PRO M 140 LYS M 143 5 4 HELIX 18 AB9 PRO M 156 LEU M 160 5 5 SHEET 1 AA1 2 VAL K 12 ARG K 13 0 SHEET 2 AA1 2 ILE K 17 PRO K 18 -1 O ILE K 17 N ARG K 13 CISPEP 1 TRP M 152 PRO M 153 0 -6.06 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