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- EMDB-0677: Cryo-EM structure of the mammalian DP-state ATP synthase -

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Basic information

Entry
Database: EMDB / ID: EMD-0677
TitleCryo-EM structure of the mammalian DP-state ATP synthase
Map data
Sample
  • Complex: Cryo-EM structure of the mammalian DP-state ATP synthase
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / : / mitochondrial proton-transporting ATP synthase complex binding / regulation of protein targeting to mitochondrion / positive regulation of proteolysis involved in protein catabolic process / negative regulation of mitochondrial ATP synthesis coupled proton transport / Mitochondrial protein import / angiostatin binding / negative regulation of hydrolase activity ...Formation of ATP by chemiosmotic coupling / Cristae formation / : / mitochondrial proton-transporting ATP synthase complex binding / regulation of protein targeting to mitochondrion / positive regulation of proteolysis involved in protein catabolic process / negative regulation of mitochondrial ATP synthesis coupled proton transport / Mitochondrial protein import / angiostatin binding / negative regulation of hydrolase activity / ATP biosynthetic process / mitochondrial depolarization / ATPase inhibitor activity / Mitochondrial protein degradation / positive regulation of type 2 mitophagy / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / proton channel activity / heme biosynthetic process / negative regulation of endothelial cell proliferation / 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 / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / reactive oxygen species metabolic process / erythrocyte differentiation / ADP binding / mitochondrial membrane / ATPase binding / calmodulin binding / mitochondrial inner membrane / intracellular membrane-bounded organelle / lipid binding / cell surface / protein-containing complex / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / plasma membrane / 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 / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / ATP synthase-coupling factor 6, mitochondrial ...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 / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / 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, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / 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. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / 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. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase subunit b / ATP synthase subunit gamma / ATP synthase peripheral stalk subunit d / ATP synthase, H+ transporting, mitochondrial F1 complex, epsilon subunit / ATP synthase membrane subunit k / ATP synthase subunit beta / ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial / ATPase inhibitor, mitochondrial ...ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase subunit b / ATP synthase subunit gamma / ATP synthase peripheral stalk subunit d / ATP synthase, H+ transporting, mitochondrial F1 complex, epsilon subunit / ATP synthase membrane subunit k / ATP synthase subunit beta / ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial / ATPase inhibitor, mitochondrial / ATP synthase peripheral stalk subunit OSCP, mitochondrial / 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: 3.34 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: 0.0188
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0188
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6j5i
  • Surface level: 0.0188
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0677.png

Downloads & links

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Map

FileDownload / File: emd_0677.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: 0.0188 / Movie #1: 0.0188
Minimum - Maximum-0.12620464 - 0.21504733
Average (Standard dev.)0.0003670495 (±0.005396946)
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-0.1260.2150.000

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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

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

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

SupramoleculeName: Cryo-EM structure of the mammalian DP-state ATP synthase
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: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 291128
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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