+
Open data
-
Basic information
Entry | ![]() | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Human ATP synthase F1 domain, state2 | |||||||||||||||
![]() | ||||||||||||||||
![]() |
| |||||||||||||||
![]() | MEMBRANE PROTEIN | |||||||||||||||
Function / homology | ![]() 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 / proton-transporting ATP synthase complex / oxidative phosphorylation / cellular response to interleukin-7 / response to muscle activity ...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 / proton-transporting ATP synthase complex / oxidative phosphorylation / cellular response to interleukin-7 / response to muscle activity / cellular response to nitric oxide / : / : / : / mitochondrial nucleoid / : / MHC class I protein binding / negative regulation of endothelial cell proliferation / proton motive force-driven ATP synthesis / positive regulation of blood vessel endothelial cell migration / generation of precursor metabolites and energy / proton-transporting ATP synthase complex, catalytic core F(1) / cellular response to dexamethasone stimulus / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / lipid metabolic process / regulation of intracellular pH / Transcriptional activation of mitochondrial biogenesis / mitochondrial membrane / ADP binding / osteoblast differentiation / protease binding / angiogenesis / response to ethanol / mitochondrial inner membrane / mitochondrial matrix / membrane raft / cell surface / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.77 Å | |||||||||||||||
![]() | Lai Y / Zhang Y / Liu F / Gao Y / Gong H / Rao Z | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 484 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 20 KB 20 KB | Display Display | ![]() |
Images | ![]() | 151.8 KB | ||
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() | 474.4 MB 474.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h9iMC ![]() 8h9eC ![]() 8h9fC ![]() 8h9gC ![]() 8h9jC ![]() 8h9kC ![]() 8h9lC ![]() 8h9mC ![]() 8h9nC ![]() 8h9pC ![]() 8h9qC ![]() 8h9rC ![]() 8h9sC ![]() 8h9tC ![]() 8h9uC ![]() 8h9vC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.73 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_34568_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_34568_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Human ATP synthase
Entire | Name: Human ATP synthase |
---|---|
Components |
|
-Supramolecule #1: Human ATP synthase
Supramolecule | Name: Human ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3-#4, #2 |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 600 KDa |
-Macromolecule #1: ATP synthase subunit alpha, mitochondrial
Macromolecule | Name: ATP synthase subunit alpha, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 55.27616 KDa |
Sequence | String: 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 UniProtKB: ATP synthase subunit alpha, mitochondrial |
-Macromolecule #2: ATP synthase subunit beta, mitochondrial
Macromolecule | Name: 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: ![]() |
Molecular weight | Theoretical: 51.821965 KDa |
Sequence | String: 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 UniProtKB: ATP synthase subunit beta, mitochondrial |
-Macromolecule #3: ATP synthase subunit gamma, mitochondrial
Macromolecule | Name: ATP synthase subunit gamma, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 30.207752 KDa |
Sequence | String: 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 UniProtKB: ATP synthase subunit gamma, mitochondrial |
-Macromolecule #4: ATP synthase subunit O, mitochondrial
Macromolecule | Name: ATP synthase subunit O, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 20.904488 KDa |
Sequence | String: FAKLVRPPVQ VYGIEGRYAT ALYSAASKQN KLEQVEKELL RVAQILKEPK VAASVLNPYV KRSIKVKSLN DITAKERFSP LTTNLINLL AENGRLSNTQ GVVSAFSTMM SVHRGEVPCT VTSASPLEEA TLSELKTVLK SFLSQGQVLK LEAKTDPSIL G GMIVRIGE KYVDMSVKTK IQKLGRAMRE IV UniProtKB: ATP synthase subunit O, mitochondrial |
-Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 3 / Formula: ATP |
---|---|
Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 5 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 2 / Formula: ADP |
---|---|
Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.4 |
---|---|
Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: OTHER / Details: AlphaFold |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37480 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |