6YNZ

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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
Ymf66A [auth a],
DC [auth a3],
T [auth A],
WC [auth A3]
446Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
subunit bB [auth b],
EC [auth b3],
U [auth B],
XC [auth B3]
381Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
subunit dC [auth d],
FC [auth d3],
V [auth D],
YC [auth D3]
234Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
subunit fD [auth f],
GC [auth f3],
W [auth F],
ZC [auth F3]
204Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
subunit i/jAD [auth I3],
E [auth i],
HC [auth i3],
X [auth I]
209Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
subunit kBD [auth K3],
F [auth k],
IC [auth k3],
Y [auth K]
179Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ymf56CD [auth C3],
G [auth c],
JC [auth c3],
Z [auth C]
100Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT3AA [auth G],
DD [auth G3],
H [auth g],
KC [auth g3]
286Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT4BA [auth H],
ED [auth H3],
I [auth h],
LC [auth h3]
268Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT5CA [auth J],
FD [auth J3],
J [auth j],
MC [auth j3]
273Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT6DA [auth L],
GD [auth L3],
K [auth l],
NC [auth l3]
247Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT7EA [auth M],
HD [auth M3],
L [auth m],
OC [auth m3]
221Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT8FA [auth N],
ID [auth N3],
M [auth n],
PC [auth n3]
179Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT9GA [auth O],
JD [auth O3],
N [auth o],
QC [auth o3]
154Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT10HA [auth P],
KD [auth P3],
O [auth p],
RC [auth p3]
152Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT11IA [auth Q],
LD [auth Q3],
P [auth q],
SC [auth q3]
152Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT12JA [auth R],
MD [auth R3],
Q [auth r],
TC [auth r3]
149Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT13KA [auth S],
ND [auth S3],
R [auth s],
UC [auth s3]
145Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT1LA [auth E],
OD [auth E3],
S [auth e],
VC [auth e3]
480Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Inhibitor of F1 (IF1)MA [auth i2],
NA [auth i1],
PD [auth i5],
QD [auth i4]
108Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTT2OA [auth t],
RD [auth t3]
460Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Oligomycin sensitivity-conferring protein (OSCP)JB [auth G2],
ME [auth G5],
PA [auth G1],
SD [auth G4]
219Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit gammaKB [auth g2],
NE [auth g5],
QA [auth g1],
TD [auth g4]
299Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha546Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta497Tetrahymena thermophilaMutation(s): 0 
EC: 7.1.2.2
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F0 subunit 976Tetrahymena thermophilaMutation(s): 0 
EC: 3.6.1.34
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
subunit deltaBC [auth d2],
EF [auth d5],
HB [auth d1],
KE [auth d4]
158Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
subunit epsilonCC [auth e2],
FF [auth e5],
IB [auth e1],
LE [auth e4]
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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AG [auth p]
AH [auth L]
AJ [auth B3]
BG [auth r]
BI [auth b3]
AG [auth p],
AH [auth L],
AJ [auth B3],
BG [auth r],
BI [auth b3],
BJ [auth B3],
CH [auth P],
CJ [auth B3],
EG [auth A],
EI [auth f3],
FG [auth B],
FI [auth f3],
FJ [auth F3],
GF [auth a],
GG [auth B],
GI [auth f3],
GJ [auth I3],
HF [auth b],
HG [auth B],
HI [auth i3],
HJ [auth I3],
IG [auth B],
II [auth i3],
IJ [auth I3],
KF [auth f],
KI [auth k3],
KJ [auth K3],
LF [auth f],
LG [auth F],
LJ [auth K3],
MF [auth f],
MG [auth F],
NF [auth i],
NG [auth I],
OG [auth I],
PF [auth k],
PI [auth g3],
QG [auth K],
QI [auth j3],
QJ [auth J3],
RG [auth K],
RI [auth j3],
RJ [auth J3],
SJ [auth L3],
TI [auth l3],
UF [auth g],
UJ [auth P3],
VF [auth j],
VI [auth l3],
WF [auth j],
WG [auth J],
WI [auth p3],
XF [auth l],
XG [auth J],
YF [auth l],
YH [auth a3],
YI [auth A3],
ZG [auth L],
ZH [auth a3],
ZI [auth B3]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1
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CI [auth d3]
DJ [auth D3]
IF [auth d]
JG [auth D]
NI [auth g3]
CI [auth d3],
DJ [auth D3],
IF [auth d],
JG [auth D],
NI [auth g3],
OI [auth g3],
OJ [auth G3],
PJ [auth G3],
SF [auth g],
TF [auth g],
UG [auth G],
VG [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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AI [auth a3]
BH [auth L]
DG [auth A]
SI [auth j3]
TJ [auth L3]
AI [auth a3],
BH [auth L],
DG [auth A],
SI [auth j3],
TJ [auth L3],
UI [auth l3],
YG [auth J],
ZF [auth m]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
UQ8
Query on UQ8

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JI [auth i3],
JJ [auth I3],
OF [auth i],
PG [auth I]
Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
NAD
Query on NAD

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CG [auth e],
DH [auth E],
VJ [auth E3],
XI [auth e3]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
ATP
Query on ATP

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CK [auth B4]
DK [auth A4]
EH [auth C1]
GK [auth C5]
KH [auth B1]
CK [auth B4],
DK [auth A4],
EH [auth C1],
GK [auth C5],
KH [auth B1],
LH [auth A1],
LI [auth g3],
MJ [auth G3],
MK [auth B5],
NK [auth A5],
OH [auth C2],
QF [auth g],
SG [auth G],
UH [auth B2],
VH [auth A2],
WJ [auth C4]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

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BK [auth B4]
GH [auth D1]
IK [auth D5]
JH [auth B1]
LK [auth B5]
BK [auth B4],
GH [auth D1],
IK [auth D5],
JH [auth B1],
LK [auth B5],
QH [auth D2],
TH [auth B2],
YJ [auth D4]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4
Query on PO4

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DI [auth f3],
EJ [auth F3],
JF [auth f],
KG [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG

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AK [auth B4]
EK [auth A4]
FH [auth C1]
FK [auth E4]
HH [auth D1]
AK [auth B4],
EK [auth A4],
FH [auth C1],
FK [auth E4],
HH [auth D1],
HK [auth C5],
IH [auth B1],
JK [auth D5],
KK [auth B5],
MH [auth A1],
MI [auth g3],
NH [auth E1],
NJ [auth G3],
OK [auth A5],
PH [auth C2],
PK [auth E5],
RF [auth g],
RH [auth D2],
SH [auth B2],
TG [auth G],
WH [auth A2],
XH [auth E2],
XJ [auth C4],
ZJ [auth D4]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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