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- EMDB-4102: Structure of F-ATPase from Pichia angusta, state1 -

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Basic information

Entry
Database: EMDB / ID: 4102
TitleStructure of F-ATPase from Pichia angusta, state1
Map data
SampleYeast F1FO ATP Synthase:
(ATP synthase ...) x 17 / (ligand) x 3
Function / homologyATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase, F0 complex, subunit C / ATP synthase, F0 complex, subunit A / ATPase, OSCP/delta subunit / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, delta/epsilon subunit / V-ATPase proteolipid subunit C-like domain / AAA+ ATPase domain ...ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase, F0 complex, subunit C / ATP synthase, F0 complex, subunit A / ATPase, OSCP/delta subunit / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, delta/epsilon subunit / V-ATPase proteolipid subunit C-like domain / AAA+ ATPase domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, beta subunit / Mitochondrial ATPase inhibitor / ATP synthase, F0 complex, subunit D, mitochondrial / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / ATP synthase, F0 complex, subunit A, active site / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATP synthase, F1 complex, gamma subunit conserved site / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / P-loop containing nucleoside triphosphate hydrolase / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F0 complex, subunit A superfamily / F/V-ATP synthase subunit C superfamily / ATP synthase, F1 complex, gamma subunit superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase alpha and beta subunits signature. / ATP synthase D chain, mitochondrial (ATP5H) / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / Mitochondrial ATPase inhibitor, IATP / ATP synthase gamma subunit signature. / ATP synthase alpha/beta family, beta-barrel domain / F1F0 ATP synthase subunit C superfamily / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase alpha/beta chain, C terminal domain / ATP synthase / ATP synthase delta (OSCP) subunit / ATP synthase subunit C / ATP synthase A chain / ATP synthase a subunit signature. / ATP synthase c subunit signature. / ATP synthase alpha/beta family, nucleotide-binding domain / mitochondrial proton-transporting ATP synthase, central stalk / mitochondrial proton-transporting ATP synthase, catalytic core / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / angiostatin binding / proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / negative regulation of hydrolase activity / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transporter activity / proton-transporting ATPase activity, rotational mechanism / ATP hydrolysis coupled proton transport / negative regulation of endothelial cell proliferation / H+-transporting two-sector ATPase / heme biosynthetic process / ATP synthesis coupled proton transport / mitochondrial nucleoid / negative regulation of ATPase activity / mitochondrial membrane / erythrocyte differentiation / ATPase binding / mitochondrial inner membrane / protein homotetramerization / protein homooligomerization / calmodulin binding / lipid binding / cell surface / mitochondrion / protein homodimerization activity / integral component of membrane / ATP binding / ATP synthase subunit 4, mitochondrial / ATP synthase subunit 5, mitochondrial / F0F1-type ATP synthase, epsilon subunit (Mitochondrial delta subunit) / ATP synthase subunit beta / ATP synthase subunit a / ATP synthase subunit d, mitochondrial / ATP synthase subunit alpha / ATPase inhibitor, mitochondrial / ATP synthase subunit 9, mitochondrial / ATP synthase subunit gamma
Function and homology information
SourceOgataea angusta (fungus)
Methodsingle particle reconstruction / cryo EM / 7 Å resolution
AuthorsVinothkumar KR / Montgomery MG
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Structure of the mitochondrial ATP synthase from Pichia angusta determined by electron cryo-microscopy.
Authors: Kutti R Vinothkumar / Martin G Montgomery / Sidong Liu / John E Walker
Validation ReportPDB-ID: 5lqz

SummaryFull reportAbout validation report
DateDeposition: Sep 30, 2016 / Header (metadata) release: Nov 16, 2016 / Map release: Nov 16, 2016 / Last update: Aug 2, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.145
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.145
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5lqz
  • Surface level: 0.145
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4102.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.75 Å/pix.
= 525. Å
300 pix
1.75 Å/pix.
= 525. Å
300 pix
1.75 Å/pix.
= 525. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.75 Å
Density
Contour Level:0.145 (by author), 0.145 (movie #1):
Minimum - Maximum-0.24618985 - 0.5985556
Average (Standard dev.)9.300444E-5 (0.018973067)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin000
Limit299299299
Spacing300300300
CellA=B=C: 525 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.751.751.75
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z525.000525.000525.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.2460.5990.000

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Supplemental data

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Sample components

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Entire Yeast F1FO ATP Synthase

EntireName: Yeast F1FO ATP Synthase
Details: The complex comprises of the catalytic domain, membrane domain and peripheral stalk of the yeast ATP synthase.
Number of components: 21
MassTheoretical: 550 kDa

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Component #1: protein, Yeast F1FO ATP Synthase

ProteinName: Yeast F1FO ATP Synthase
Details: The complex comprises of the catalytic domain, membrane domain and peripheral stalk of the yeast ATP synthase.
Recombinant expression: No
MassTheoretical: 550 kDa
SourceSpecies: Ogataea angusta (fungus) / Strain: A16

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Component #2: protein, ATP synthase subunit f

ProteinName: ATP synthase subunit f / Recombinant expression: No
MassTheoretical: 2.571161 kDa
SourceSpecies: Ogataea angusta (fungus)

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Component #3: protein, ATP synthase subunit AAP1

ProteinName: ATP synthase subunit AAP1 / Recombinant expression: No
MassTheoretical: 2.145636 kDa
SourceSpecies: Ogataea angusta (fungus)

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Component #4: protein, ATP synthase subunit a

ProteinName: ATP synthase subunit a / Details: Helix 1 of subunit a / Recombinant expression: No
MassTheoretical: 1.464797 kDa
SourceSpecies: Ogataea angusta (fungus)

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Component #5: protein, ATP synthase subunit b

ProteinName: ATP synthase subunit b / Recombinant expression: No
MassTheoretical: 2.315846 kDa
SourceSpecies: Ogataea angusta (fungus)

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Component #6: protein, ATP synthase alpha subunit

ProteinName: ATP synthase alpha subunit / Recombinant expression: No
MassTheoretical: 55.007535 kDa
SourceSpecies: Ogataea angusta (fungus)

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Component #7: protein, ATP synthase beta subunit

ProteinName: ATP synthase beta subunit / Recombinant expression: No
MassTheoretical: 50.852434 kDa
SourceSpecies: Ogataea angusta (fungus)

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Component #8: protein, ATP synthase gamma subunit

ProteinName: ATP synthase gamma subunit / Recombinant expression: No
MassTheoretical: 29.418238 kDa
SourceSpecies: Ogataea angusta (fungus)

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Component #9: protein, ATP synthase delta subunit

ProteinName: ATP synthase delta subunit / Recombinant expression: No
MassTheoretical: 14.171783 kDa
SourceSpecies: Ogataea angusta (fungus)

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Component #10: protein, ATP synthase epsilon subunit

ProteinName: ATP synthase epsilon subunit / Recombinant expression: No
MassTheoretical: 6.910886 kDa
SourceSpecies: Ogataea angusta (fungus)

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Component #11: protein, ATP synthase inhibitor protein IF1

ProteinName: ATP synthase inhibitor protein IF1 / Recombinant expression: No
MassTheoretical: 7.462098 kDa
SourceSpecies: Ogataea angusta (fungus)

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Component #12: protein, ATP synthase subunit c

ProteinName: ATP synthase subunit c / Recombinant expression: No
MassTheoretical: 7.83738 kDa
SourceSpecies: Ogataea angusta (fungus)

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Component #13: protein, ATP synthase OSCP subunit

ProteinName: ATP synthase OSCP subunit / Recombinant expression: No
MassTheoretical: 20.678812 kDa
SourceSpecies: Ogataea angusta (fungus)

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Component #14: protein, ATP synthase subunit b

ProteinName: ATP synthase subunit b / Recombinant expression: No
MassTheoretical: 22.292332 kDa
SourceSpecies: Ogataea angusta (fungus)

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Component #15: protein, ATP synthase subunit d

ProteinName: ATP synthase subunit d / Recombinant expression: No
MassTheoretical: 16.427818 kDa
SourceSpecies: Ogataea angusta (fungus)

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Component #16: protein, ATP synthase subunit h

ProteinName: ATP synthase subunit h / Recombinant expression: No
MassTheoretical: 1.805216 kDa
SourceSpecies: Ogataea angusta (fungus)

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Component #17: protein, ATP synthase subunit a

ProteinName: ATP synthase subunit a / Details: Helices 4, 5 and 6 of subunit aHelix / Recombinant expression: No
MassTheoretical: 27.559775 kDa
SourceSpecies: Ogataea angusta (fungus)

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Component #18: protein, ATP synthase subunit a

ProteinName: ATP synthase subunit a / Details: Helices 2 and 3 of subunit a / Recombinant expression: No
MassTheoretical: 3.762629 kDa
SourceSpecies: Ogataea angusta (fungus)

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Component #19: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Component #20: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #21: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3.5 mg/ml / pH: 7.5
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %
Details: Grids were blotted for 12-14 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 64 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 47000 X (nominal), 81395 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1800 - 5000 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 87.5 - K)
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 14 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 42771
Details: The total exposure was 4 seconds resulting in 69 frames and a total dose of 64 e/A2. Frames were captured with an in-house protocol. For processing frames 1-32 were used.
3D reconstructionSoftware: RELION
CTF correction: CTF was estimated using the whole micrograph using all the frames. CTF was corrected per particle in RELION.
Resolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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