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- EMDB-34578: Human ATP synthase state 3b subregion 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-34578
TitleHuman ATP synthase state 3b subregion 2
Map data
Sample
  • Complex: Human ATP synthase
    • Protein or peptide: ATP synthase F(0) complex subunit B1, mitochondrial
    • Protein or peptide: ATP synthase-coupling factor 6, mitochondrial
    • Protein or peptide: ATP synthase subunit d, mitochondrial
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / : / proton-transporting ATP synthase complex / : / : / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton transmembrane transporter activity / Mitochondrial protein degradation ...Formation of ATP by chemiosmotic coupling / Cristae formation / : / proton-transporting ATP synthase complex / : / : / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton transmembrane transporter activity / Mitochondrial protein degradation / substantia nigra development / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / membrane / nucleus
Similarity search - Function
ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial
Similarity search - Domain/homology
ATP synthase subunit d, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.97 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 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34578.png

Downloads & links

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Map

FileDownload / File: emd_34578.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.19935133 - 0.29790384
Average (Standard dev.)-0.000018825984 (±0.008951606)
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: #1

Fileemd_34578_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34578_half_map_2.map
Projections & Slices
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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 F(0) complex subunit B1, mitochondrial
    • Protein or peptide: ATP synthase-coupling factor 6, mitochondrial
    • Protein or peptide: ATP synthase subunit d, mitochondrial

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Supramolecule #1: Human ATP synthase

SupramoleculeName: Human ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: ATP synthase F(0) complex subunit B1, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit B1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.658586 KDa
SequenceString: PVPPLPEYGG KVRYGLIPEE FFQFLYPKTG VTGPYVLGTG LILYALSKEI YVISAETFTA LSVLGVMVYG IKKYGPFVAD FADKLNEQK LAQLEEAKQA SIQHIQNAID TEKSQQALVQ KRHYLFDVQR NNIAMALEVT YRERLYRVYK EVKNRLDYHI S VQNMMRRK ...String:
PVPPLPEYGG KVRYGLIPEE FFQFLYPKTG VTGPYVLGTG LILYALSKEI YVISAETFTA LSVLGVMVYG IKKYGPFVAD FADKLNEQK LAQLEEAKQA SIQHIQNAID TEKSQQALVQ KRHYLFDVQR NNIAMALEVT YRERLYRVYK EVKNRLDYHI S VQNMMRRK EQEHMINWVE KHVVQSISTQ QEKETIAKCI ADLKLLAKKA QAQPVM

UniProtKB: ATP synthase F(0) complex subunit B1, mitochondrial

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Macromolecule #2: ATP synthase-coupling factor 6, mitochondrial

MacromoleculeName: ATP synthase-coupling factor 6, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.606499 KDa
SequenceString:
MILQRLFRFS SVIRSAVSVH LRRNIGVTAV AFNKELDPIQ KLFVDKIREY KSKRQTSGGP VDASSEYQQE LERELFKLKQ MFGNADMNT FPTFKFEDPK FEVIEKPQA

UniProtKB: ATP synthase-coupling factor 6, mitochondrial

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Macromolecule #3: ATP synthase subunit d, mitochondrial

MacromoleculeName: ATP synthase subunit d, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.383982 KDa
SequenceString:
AGRKLALKTI DWVAFAEIIP QNQKAIASSL KSWNETLTSR LAALPENPPA IDWAYYKANV AKAGLVDDFE KKFNALKVPV PEDKYTAQV DAEEKEDVKS CAEWVSLSKA RIVEYEKEME KMKNLIPFDQ MTIEDLNEAF PETKLDKKKY PYWPHQPIEN L

UniProtKB: ATP synthase subunit d, mitochondrial

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

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Image processing

Startup modelType of model: OTHER / Details: AlphaFold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23272
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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