[English] 日本語
Yorodumi
- EMDB-4102: Structure of F-ATPase from Pichia angusta, state1 -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 4102
TitleStructure of F-ATPase from Pichia angusta, state1
SampleYeast F1FO ATP Synthase
SourceOgataea angusta / fungus
Map data
Methodsingle particle reconstruction, at 7 Å resolution
AuthorsVinothkumar KR / Montgomery MG
CitationProc. Natl. Acad. Sci. U.S.A., 2016

Proc. Natl. Acad. Sci. U.S.A., 2016 StrPapers
Structure of the mitochondrial ATP synthase from Pichia angusta determined by electron cryo-microscopy.
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

-
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
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5lqz
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
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 package.

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

-
Supplemental data

-
Sample components

+
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

+
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

+
Component #2: protein, ATP synthase subunit f

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

+
Component #3: protein, ATP synthase subunit AAP1

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

+
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

+
Component #5: protein, ATP synthase subunit b

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

+
Component #6: protein, ATP synthase alpha subunit

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

+
Component #7: protein, ATP synthase beta subunit

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

+
Component #8: protein, ATP synthase gamma subunit

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

+
Component #9: protein, ATP synthase delta subunit

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

+
Component #10: protein, ATP synthase epsilon subunit

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

+
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

+
Component #12: protein, ATP synthase subunit c

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

+
Component #13: protein, ATP synthase OSCP subunit

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

+
Component #14: protein, ATP synthase subunit b

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

+
Component #15: protein, ATP synthase subunit d

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

+
Component #16: protein, ATP synthase subunit h

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

+
Component #17: protein, ATP synthase subunit a

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

+
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

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

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

+
Component #20: ligand, MAGNESIUM ION

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

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

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

-
Experimental details

-
Sample preparation

Specimen stateparticle
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.

-
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)

-
Image acquisition

Image acquisitionSampling size: 14 microns

-
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 assessment)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more