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- EMDB-0670: Cryo-EM structure of the mammalian DP-state ATP synthase FO section -

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Basic information

Entry
Database: EMDB / ID: EMD-0670
TitleCryo-EM structure of the mammalian DP-state ATP synthase FO section
Map data
Sample
  • Complex: Cryo-EM structure of the mammalian DP-state ATP synthase FO section
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / ATP biosynthetic process / Mitochondrial protein degradation / proton channel activity / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex ...Formation of ATP by chemiosmotic coupling / Cristae formation / ATP biosynthetic process / Mitochondrial protein degradation / proton channel activity / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / mitochondrial membrane / mitochondrial inner membrane / intracellular membrane-bounded organelle / lipid binding / cytoplasm
Similarity search - Function
ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase protein 8, metazoa / Mitochondrial F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / Mitochondrial F1F0-ATP synthase, subunit f / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) ...ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase protein 8, metazoa / Mitochondrial F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / Mitochondrial F1F0-ATP synthase, subunit f / 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 / 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. / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
ATP synthase subunit b / ATP synthase peripheral stalk subunit d / ATP synthase membrane subunit k / ATP synthase F(0) complex subunit 8 / ATP synthase F(0) complex subunit a / ATP synthase lipid-binding protein / ATP synthase F(0) complex subunit f, mitochondrial
Similarity search - Component
Biological speciesSus (mammal)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.35 Å
AuthorsGu JK / Zhang LX / Yi JB / Yang MJ
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFA0504600 and 2016YFA0501100 China
National Natural Science Foundation of China21532004, 31570733 and 31800620 China
National Natural Science Foundation of China31625008 China
CitationJournal: Science / Year: 2019
Title: Cryo-EM structure of the mammalian ATP synthase tetramer bound with inhibitory protein IF1.
Authors: Jinke Gu / Laixing Zhang / Shuai Zong / Runyu Guo / Tianya Liu / Jingbo Yi / Peiyi Wang / Wei Zhuo / Maojun Yang /
Abstract: The mitochondrial adenosine triphosphate (ATP) synthase produces most of the ATP required by mammalian cells. We isolated porcine tetrameric ATP synthase and solved its structure at 6.2-angstrom ...The mitochondrial adenosine triphosphate (ATP) synthase produces most of the ATP required by mammalian cells. We isolated porcine tetrameric ATP synthase and solved its structure at 6.2-angstrom resolution using a single-particle cryo-electron microscopy method. Two classical V-shaped ATP synthase dimers lie antiparallel to each other to form an H-shaped ATP synthase tetramer, as viewed from the matrix. ATP synthase inhibitory factor subunit 1 (IF1) is a well-known in vivo inhibitor of mammalian ATP synthase at low pH. Two IF1 dimers link two ATP synthase dimers, which is consistent with the ATP synthase tetramer adopting an inhibited state. Within the tetramer, we refined structures of intact ATP synthase in two different rotational conformations at 3.34- and 3.45-Å resolution.
History
DepositionJan 10, 2019-
Header (metadata) releaseJun 19, 2019-
Map releaseJun 26, 2019-
UpdateJun 26, 2019-
Current statusJun 26, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0189
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0189
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6j5a
  • Surface level: 0.0189
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0670.png

Downloads & links

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Map

FileDownload / File: emd_0670.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 240 pix.
= 331.2 Å		1.38 Å/pix.
x 240 pix.
= 331.2 Å		1.38 Å/pix.
x 240 pix.
= 331.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0189 / Movie #1: 0.0189
Minimum - Maximum-0.08010008 - 0.14653581
Average (Standard dev.)0.00013069986 (±0.0020781406)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z331.200331.200331.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ304304304
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0800.1470.000

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of the mammalian DP-state ATP synthase FO section

EntireName: Cryo-EM structure of the mammalian DP-state ATP synthase FO section
Components
  • Complex: Cryo-EM structure of the mammalian DP-state ATP synthase FO section

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Supramolecule #1: Cryo-EM structure of the mammalian DP-state ATP synthase FO section

SupramoleculeName: Cryo-EM structure of the mammalian DP-state ATP synthase FO section
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Sus (mammal)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.56 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114103
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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