6YNY

Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - F1Fo composite dimer model


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization.

Flygaard, R.K.Muhleip, A.Tobiasson, V.Amunts, A.

(2020) Nat Commun 11: 5342-5342

  • DOI: https://doi.org/10.1038/s41467-020-18993-6
  • Primary Citation of Related Structures:  
    6YNV, 6YNW, 6YNX, 6YNY, 6YNZ, 6YO0

  • PubMed Abstract: 

    Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we characterized the unique type III mitochondrial ATP synthase in its dimeric and tetrameric form. The cryo-EM structure of a ciliate ATP synthase dimer reveals an unusual U-shaped assembly of 81 proteins, including a substoichiometrically bound ATPTT2, 40 lipids, and co-factors NAD and CoQ. A single copy of subunit ATPTT2 functions as a membrane anchor for the dimeric inhibitor IF 1 . Type III specific linker proteins stably tie the ATP synthase monomers in parallel to each other. The intricate dimer architecture is scaffolded by an extended subunit-a that provides a template for both intra- and inter-dimer interactions. The latter results in the formation of tetramer assemblies, the membrane part of which we determined to 3.1 Å resolution. The structure of the type III ATP synthase tetramer and its associated lipids suggests that it is the intact unit propagating the membrane curvature.


  • Organizational Affiliation

    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
subunit aA [auth a],
T [auth A]
446Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
subunit bB [auth b],
U [auth B]
381Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
subunit dC [auth d],
V [auth D]
234Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
subunit fD [auth f],
W [auth F]
204Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
subunit i/jE [auth i],
X [auth I]
209Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
subunit kF [auth k],
Y [auth K]
179Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
subunit 8G [auth c],
Z [auth C]
100Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT3AA [auth G],
H [auth g]
286Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT4BA [auth H],
I [auth h]
268Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT5CA [auth J],
J [auth j]
273Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT6DA [auth L],
K [auth l]
247Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT7EA [auth M],
L [auth m]
221Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT8FA [auth N],
M [auth n]
179Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT9GA [auth O],
N [auth o]
154Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT10HA [auth P],
O [auth p]
152Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT11IA [auth Q],
P [auth q]
152Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT12JA [auth R],
Q [auth r]
149Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT13KA [auth S],
R [auth s]
145Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT1LA [auth E],
S [auth e]
480Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Inhibitor of F1 (IF1)MA [auth i2],
NA [auth i1]
108Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT2OA [auth t]460Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Oligomycin sensitivity-conferring protein (OSCP)JB [auth G2],
PA [auth G1]
219Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
subunit gammaKB [auth g2],
QA [auth g1]
299Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
subunit alpha546Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
subunit beta497Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
subunit c76Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
subunit deltaBC [auth d2],
HB [auth d1]
158Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
subunit epsilonCC [auth e2],
IB [auth e1]
71Tetrahymena thermophilaMutation(s): 0 
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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CD [auth A]
DC [auth a]
DD [auth B]
EC [auth a]
ED [auth B]
CD [auth A],
DC [auth a],
DD [auth B],
EC [auth a],
ED [auth B],
FC [auth b],
FD [auth B],
GD [auth B],
IC [auth f],
JC [auth f],
JD [auth F],
KC [auth f],
KD [auth I],
LC [auth i],
LD [auth I],
NC [auth k],
ND [auth K],
OC [auth k],
OD [auth K],
TC [auth j],
TD [auth J],
UC [auth j],
UD [auth J],
VC [auth l],
WC [auth l],
WD [auth L],
XD [auth L],
YC [auth p],
ZC [auth r],
ZD [auth P]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1
Query on PC1

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GC [auth d]
HD [auth D]
RC [auth g]
RD [auth G]
SC [auth g]
GC [auth d],
HD [auth D],
RC [auth g],
RD [auth G],
SC [auth g],
SD [auth G]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
PEE
Query on PEE

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BD [auth A],
VD [auth J],
XC [auth m],
YD [auth L]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
UQ8
Query on UQ8

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MC [auth i],
MD [auth I]
Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
NAD
Query on NAD

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AD [auth e],
AE [auth E]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
ATP
Query on ATP

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BE [auth C1]
FE [auth B1]
IE [auth A1]
LE [auth C2]
PC [auth g]
BE [auth C1],
FE [auth B1],
IE [auth A1],
LE [auth C2],
PC [auth g],
PD [auth G],
PE [auth B2],
SE [auth A2]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

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DE [auth D1],
HE [auth B1],
NE [auth D2],
RE [auth B2]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4
Query on PO4

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HC [auth f],
ID [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG

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CE [auth C1]
EE [auth D1]
GE [auth B1]
JE [auth A1]
KE [auth E1]
CE [auth C1],
EE [auth D1],
GE [auth B1],
JE [auth A1],
KE [auth E1],
ME [auth C2],
OE [auth D2],
QC [auth g],
QD [auth G],
QE [auth B2],
TE [auth A2],
UE [auth E2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSwedenNT_2015-04107
European Research Council (ERC)SwedenERC-2018-StG-805230
Knut and Alice Wallenberg FoundationSweden2018.0080

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references