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- PDB-9evd: In situ structure of the peripheral stalk of the mitochondrial AT... -

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Basic information

Entry
Database: PDB / ID: 9evd
TitleIn situ structure of the peripheral stalk of the mitochondrial ATPsynthase in whole Polytomella cells
Components
  • (Mitochondrial ATP synthase subunit ...) x 3
  • (Mitochondrial F1F0 ATP synthase associated ...) x 2
  • ASA-10: Polytomella F-ATP synthase associated subunit 10
  • ASA-9: Polytomella F-ATP synthase associated subunit 9
  • ATP synthase associated protein ASA1
  • Mitochondrial ATP synthase associated protein ASA7
KeywordsMEMBRANE PROTEIN / ATP synthesis / in situ / OXPHOS
Function / homology
Function and homology information


thylakoid / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / mitochondrion / membrane
Similarity search - Function
F1F0 ATP synthase subunit ASA5 / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature.
Similarity search - Domain/homology
Mitochondrial F1F0 ATP synthase associated 14 kDa protein / ASA-9: Polytomella F-ATP synthase associated subunit 9 / ASA-10: Polytomella F-ATP synthase associated subunit 10 / Mitochondrial ATP synthase subunit ASA6 / Mitochondrial ATP synthase associated protein ASA7 / Mitochondrial ATP synthase subunit ASA8 / F-ATPase protein 6 / Mitochondrial F1F0 ATP synthase associated 32 kDa protein / ATP synthase associated protein ASA1
Similarity search - Component
Biological speciesPolytomella sp. Pringsheim 198.80 (plant)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 5.6 Å
AuthorsDietrich, L. / Agip, A.N.A. / Kuehlbrandt, W.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)FOR2848 Germany
Citation
Journal: Science / Year: 2024
Title: In situ structure and rotary states of mitochondrial ATP synthase in whole cells.
Authors: Lea Dietrich / Ahmed-Noor A Agip / Christina Kunz / Andre Schwarz / Werner Kühlbrandt /
Abstract: Cells depend on a continuous supply of adenosine triphosphate (ATP), the universal energy currency. In mitochondria, ATP is produced by a series of redox reactions, whereby an electrochemical ...Cells depend on a continuous supply of adenosine triphosphate (ATP), the universal energy currency. In mitochondria, ATP is produced by a series of redox reactions, whereby an electrochemical gradient is established across the inner mitochondrial membrane. The ATP synthase harnesses the energy of the gradient to generate ATP from adenosine diphosphate (ADP) and inorganic phosphate. We determined the structure of ATP synthase within mitochondria of the unicellular flagellate by electron cryo-tomography and subtomogram averaging at up to 4.2-angstrom resolution, revealing six rotary positions of the central stalk, subclassified into 21 substates of the F head. The ATP synthase forms helical arrays with multiple adjacent rows defining the cristae ridges. The structure of ATP synthase under native operating conditions in the presence of a membrane potential represents a pivotal step toward the analysis of membrane protein complexes in situ.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography.
Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams /
Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
#2: Journal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
History
DepositionMar 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: ASA-10: Polytomella F-ATP synthase associated subunit 10
1: ATP synthase associated protein ASA1
3: Mitochondrial F1F0 ATP synthase associated 32 kDa protein
5: Mitochondrial F1F0 ATP synthase associated 14 kDa protein
6: Mitochondrial ATP synthase subunit ASA6
7: Mitochondrial ATP synthase associated protein ASA7
8: Mitochondrial ATP synthase subunit ASA8
9: ASA-9: Polytomella F-ATP synthase associated subunit 9
M: Mitochondrial ATP synthase subunit 6


Theoretical massNumber of molelcules
Total (without water)218,4119
Polymers218,4119
Non-polymers00
Water00
1
0: ASA-10: Polytomella F-ATP synthase associated subunit 10
1: ATP synthase associated protein ASA1
3: Mitochondrial F1F0 ATP synthase associated 32 kDa protein
5: Mitochondrial F1F0 ATP synthase associated 14 kDa protein
6: Mitochondrial ATP synthase subunit ASA6
7: Mitochondrial ATP synthase associated protein ASA7
8: Mitochondrial ATP synthase subunit ASA8
9: ASA-9: Polytomella F-ATP synthase associated subunit 9
M: Mitochondrial ATP synthase subunit 6

0: ASA-10: Polytomella F-ATP synthase associated subunit 10
1: ATP synthase associated protein ASA1
3: Mitochondrial F1F0 ATP synthase associated 32 kDa protein
5: Mitochondrial F1F0 ATP synthase associated 14 kDa protein
6: Mitochondrial ATP synthase subunit ASA6
7: Mitochondrial ATP synthase associated protein ASA7
8: Mitochondrial ATP synthase subunit ASA8
9: ASA-9: Polytomella F-ATP synthase associated subunit 9
M: Mitochondrial ATP synthase subunit 6


Theoretical massNumber of molelcules
Total (without water)436,82318
Polymers436,82318
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1

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Components

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Protein , 4 types, 4 molecules 0179

#1: Protein ASA-10: Polytomella F-ATP synthase associated subunit 10


Mass: 8731.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: A0A5H1ZR95
#2: Protein ATP synthase associated protein ASA1


Mass: 68679.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: Q85JD5
#6: Protein Mitochondrial ATP synthase associated protein ASA7


Mass: 20553.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: D8V7I2
#8: Protein ASA-9: Polytomella F-ATP synthase associated subunit 9 / Mitochondrial ATP synthase subunit ASA9


Mass: 11001.712 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: A0A5H1ZR73

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Mitochondrial F1F0 ATP synthase associated ... , 2 types, 2 molecules 35

#3: Protein Mitochondrial F1F0 ATP synthase associated 32 kDa protein


Mass: 34850.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: K0J903
#4: Protein Mitochondrial F1F0 ATP synthase associated 14 kDa protein


Mass: 14004.376 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: A0A024FSR7

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Mitochondrial ATP synthase subunit ... , 3 types, 3 molecules 68M

#5: Protein Mitochondrial ATP synthase subunit ASA6


Mass: 15904.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: D7P897
#7: Protein Mitochondrial ATP synthase subunit ASA8


Mass: 9883.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: D8V7I7
#9: Protein Mitochondrial ATP synthase subunit 6


Mass: 34802.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: H8PGG3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Polytomella sp. / Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)Organism: Polytomella (plant)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K / Details: GP2

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 53000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 2500 nm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.9 e/Å2 / Avg electron dose per subtomogram: 120 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4040

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Processing

EM software
IDNameCategory
1STOPGAPvolume selection
2SerialEMimage acquisition
4WarpCTF correction
7PHENIXmodel fitting
10RELIONfinal Euler assignment
12Coot3D reconstruction
13ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 238622 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 255 / Num. of volumes extracted: 363061

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