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- EMDB-34568: Human ATP synthase F1 domain, state2 -

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Basic information

Entry
Database: EMDB / ID: EMD-34568
TitleHuman ATP synthase F1 domain, state2
Map data
Sample
  • Complex: Human ATP synthase
    • Protein or peptide: ATP synthase subunit alpha, mitochondrial
    • Protein or peptide: ATP synthase subunit gamma, mitochondrial
    • Protein or peptide: ATP synthase subunit O, mitochondrial
    • Protein or peptide: ATP synthase subunit beta, mitochondrial
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / Cristae formation / ATP biosynthetic process / angiostatin binding / Mitochondrial protein import / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / cellular response to interleukin-7 / proton-transporting ATP synthase complex ...negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / Cristae formation / ATP biosynthetic process / angiostatin binding / Mitochondrial protein import / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / cellular response to interleukin-7 / proton-transporting ATP synthase complex / oxidative phosphorylation / response to muscle activity / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / negative regulation of endothelial cell proliferation / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / cellular response to nitric oxide / proton-transporting ATP synthase complex, catalytic core F(1) / positive regulation of blood vessel endothelial cell migration / MHC class I protein binding / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / cellular response to dexamethasone stimulus / generation of precursor metabolites and energy / ADP binding / regulation of intracellular pH / mitochondrial membrane / Transcriptional activation of mitochondrial biogenesis / lipid metabolic process / osteoblast differentiation / angiogenesis / response to ethanol / mitochondrial inner membrane / protease binding / mitochondrial matrix / membrane raft / cell surface / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane
Similarity search - Function
ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit ...ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase subunit beta, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit O, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human) / human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsLai Y / Zhang Y / Liu F / Gao Y / Gong H / Rao Z
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)813300237 China
National Natural Science Foundation of China (NSFC)32100976 China
National Natural Science Foundation of China (NSFC)82222042 China
CitationJournal: Mol Cell / Year: 2023
Title: Structure of the human ATP synthase.
Authors: Yuezheng Lai / Yuying Zhang / Shan Zhou / Jinxu Xu / Zhanqiang Du / Ziyan Feng / Long Yu / Ziqing Zhao / Weiwei Wang / Yanting Tang / Xiuna Yang / Luke W Guddat / Fengjiang Liu / Yan Gao / ...Authors: Yuezheng Lai / Yuying Zhang / Shan Zhou / Jinxu Xu / Zhanqiang Du / Ziyan Feng / Long Yu / Ziqing Zhao / Weiwei Wang / Yanting Tang / Xiuna Yang / Luke W Guddat / Fengjiang Liu / Yan Gao / Zihe Rao / Hongri Gong /
Abstract: Biological energy currency ATP is produced by FF-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main ...Biological energy currency ATP is produced by FF-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main rotational states and one substate of human ATP synthase using cryoelectron microscopy. These structures reveal that the release of ADP occurs when the β subunit of FF-ATP synthase is in the open conformation, showing how ADP binding is coordinated during synthesis. The accommodation of the symmetry mismatch between F and F motors is resolved by the torsional flexing of the entire complex, especially the γ subunit, and the rotational substep of the c subunit. Water molecules are identified in the inlet and outlet half-channels, suggesting that the proton transfer in these two half-channels proceed via a Grotthus mechanism. Clinically relevant mutations are mapped to the structure, showing that they are mainly located at the subunit-subunit interfaces, thus causing instability of the complex.
History
DepositionOct 25, 2022-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateJul 5, 2023-
Current statusJul 5, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34568.png

Downloads & links

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Map

FileDownload / File: emd_34568.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.73 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.43314973 - 0.78501016
Average (Standard dev.)0.000028771483 (±0.023402873)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 373.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34568_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34568_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human ATP synthase

EntireName: Human ATP synthase
Components
  • Complex: Human ATP synthase
    • Protein or peptide: ATP synthase subunit alpha, mitochondrial
    • Protein or peptide: ATP synthase subunit gamma, mitochondrial
    • Protein or peptide: ATP synthase subunit O, mitochondrial
    • Protein or peptide: ATP synthase subunit beta, mitochondrial
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Human ATP synthase

SupramoleculeName: Human ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3-#4, #2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: ATP synthase subunit alpha, mitochondrial

MacromoleculeName: ATP synthase subunit alpha, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 55.27616 KDa
SequenceString: QKTGTAEMSS ILEERILGAD TSVDLEETGR VLSIGDGIAR VHGLRNVQAE EMVEFSSGLK GMSLNLEPDN VGVVVFGNDK LIKEGDIVK RTGAIVDVPV GEELLGRVVD ALGNAIDGKG PIGSKTRRRV GLKAPGIIPR ISVREPMQTG IKAVDSLVPI G RGQRELII ...String:
QKTGTAEMSS ILEERILGAD TSVDLEETGR VLSIGDGIAR VHGLRNVQAE EMVEFSSGLK GMSLNLEPDN VGVVVFGNDK LIKEGDIVK RTGAIVDVPV GEELLGRVVD ALGNAIDGKG PIGSKTRRRV GLKAPGIIPR ISVREPMQTG IKAVDSLVPI G RGQRELII GDRQTGKTSI AIDTIINQKR FNDGSDEKKK LYCIYVAIGQ KRSTVAQLVK RLTDADAMKY TIVVSATASD AA PLQYLAP YSGCSMGEYF RDNGKHALII YDDLSKQAVA YRQMSLLLRR PPGREAYPGD VFYLHSRLLE RAAKMNDAFG GGS LTALPV IETQAGDVSA YIPTNVISIT DGQIFLETEL FYKGIRPAIN VGLSVSRVGS AAQTRAMKQV AGTMKLELAQ YREV AAFAQ FGSDLDAATQ QLLSRGVRLT ELLKQGQYSP MAIEEQVAVI YAGVRGYLDK LEPSKITKFE NAFLSHVVSQ HQALL GTIR ADGKISEQSD AKLKEIVTNF LAGFEA

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Macromolecule #2: ATP synthase subunit beta, mitochondrial

MacromoleculeName: ATP synthase subunit beta, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: human (human)
Molecular weightTheoretical: 51.821965 KDa
SequenceString: AQTSPSPKAG AATGRIVAVI GAVVDVQFDE GLPPILNALE VQGRETRLVL EVAQHLGEST VRTIAMDGTE GLVRGQKVLD SGAPIKIPV GPETLGRIMN VIGEPIDERG PIKTKQFAPI HAEAPEFMEM SVEQEILVTG IKVVDLLAPY AKGGKIGLFG G AGVGKTVL ...String:
AQTSPSPKAG AATGRIVAVI GAVVDVQFDE GLPPILNALE VQGRETRLVL EVAQHLGEST VRTIAMDGTE GLVRGQKVLD SGAPIKIPV GPETLGRIMN VIGEPIDERG PIKTKQFAPI HAEAPEFMEM SVEQEILVTG IKVVDLLAPY AKGGKIGLFG G AGVGKTVL IMELINNVAK AHGGYSVFAG VGERTREGND LYHEMIESGV INLKDATSKV ALVYGQMNEP PGARARVALT GL TVAEYFR DQEGQDVLLF IDNIFRFTQA GSEVSALLGR IPSAVGYQPT LATDMGTMQE RITTTKKGSI TSVQAIYVPA DDL TDPAPA TTFAHLDATT VLSRAIAELG IYPAVDPLDS TSRIMDPNIV GSEHYDVARG VQKILQDYKS LQDIIAILGM DELS EEDKL TVSRARKIQR FLSQPFQVAE VFTGHMGKLV PLKETIKGFQ QILAGEYDHL PEQAFYMVGP IEEAVAKADK LAEEH SS

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Macromolecule #3: ATP synthase subunit gamma, mitochondrial

MacromoleculeName: ATP synthase subunit gamma, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 30.207752 KDa
SequenceString: ATLKDITRRL KSIKNIQKIT KSMKMVAAAK YARAERELKP ARIYGLGSLA LYEKADIKGP EDKKKHLLIG VSSDRGLCGA IHSSIAKQM KSEVATLTAA GKEVMLVGIG DKIRGILYRT HSDQFLVAFK EVGRKPPTFG DASVIALELL NSGYEFDEGS I IFNKFRSV ...String:
ATLKDITRRL KSIKNIQKIT KSMKMVAAAK YARAERELKP ARIYGLGSLA LYEKADIKGP EDKKKHLLIG VSSDRGLCGA IHSSIAKQM KSEVATLTAA GKEVMLVGIG DKIRGILYRT HSDQFLVAFK EVGRKPPTFG DASVIALELL NSGYEFDEGS I IFNKFRSV ISYKTEEKPI FSLNTVASAD SMSIYDDIDA DVLQNYQEYN LANIIYYSLK ESTTSEQSAR MTAMDNASKN AS EMIDKLT LTFNRTRQAV ITKELIEIIS GAAALD

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Macromolecule #4: ATP synthase subunit O, mitochondrial

MacromoleculeName: ATP synthase subunit O, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 20.904488 KDa
SequenceString:
FAKLVRPPVQ VYGIEGRYAT ALYSAASKQN KLEQVEKELL RVAQILKEPK VAASVLNPYV KRSIKVKSLN DITAKERFSP LTTNLINLL AENGRLSNTQ GVVSAFSTMM SVHRGEVPCT VTSASPLEEA TLSELKTVLK SFLSQGQVLK LEAKTDPSIL G GMIVRIGE KYVDMSVKTK IQKLGRAMRE IV

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: AlphaFold
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37480

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