6TDV

Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase, membrane region


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structure of a mitochondrial ATP synthase with bound native cardiolipin.

Muhleip, A.McComas, S.E.Amunts, A.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.51179
  • Primary Citation of Related Structures:  
    6TDU, 6TDV, 6TDW, 6TDX, 6TDY, 6TDZ, 6TE0

  • PubMed Abstract: 

    The mitochondrial ATP synthase fuels eukaryotic cells with chemical energy. Here we report the cryo-EM structure of a divergent ATP synthase dimer from mitochondria of Euglena gracilis , a member of the phylum Euglenozoa that also includes human parasites. It features 29 different subunits, 8 of which are newly identified. The membrane region was determined to 2.8 Å resolution, enabling the identification of 37 associated lipids, including 25 cardiolipins, which provides insight into protein-lipid interactions and their functional roles. The rotor-stator interface comprises four membrane-embedded horizontal helices, including a distinct subunit a . The dimer interface is formed entirely by phylum-specific components, and a peripherally associated subcomplex contributes to the membrane curvature. The central and peripheral stalks directly interact with each other. Last, the ATPase inhibitory factor 1 (IF 1 ) binds in a mode that is different from human, but conserved in Trypanosomatids.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB1A,
T [auth a]
487Euglena gracilisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB3B,
U [auth b]
338Euglena gracilisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB6C [auth D],
V [auth d]
187Euglena gracilisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB12D [auth E],
W [auth e]
97Euglena gracilisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
subunit aE [auth F],
X [auth f]
274Euglena gracilisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
subunit bF [auth G],
Y [auth g]
112Euglena gracilisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
subunit dG [auth H],
Z [auth h]
476Euglena gracilisMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
subunit fAA [auth i],
H [auth I]
98Euglena gracilisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
subunit i/jBA [auth j],
I [auth J]
104Euglena gracilisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
subunit kCA [auth k],
J [auth K]
113Euglena gracilisMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
subunit 8DA [auth l],
K [auth L]
57Euglena gracilisMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG1EA [auth m],
L [auth M]
169Euglena gracilisMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG2FA [auth n],
M [auth N]
137Euglena gracilisMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG3GA [auth o],
N [auth O]
116Euglena gracilisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG4HA [auth p],
O [auth P]
120Euglena gracilisMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG5IA [auth q],
P [auth Q]
90Euglena gracilisMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG6JA [auth r],
Q [auth R]
78Euglena gracilisMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG7KA [auth s],
R [auth S]
74Euglena gracilisMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG8LA [auth t],
S [auth T]
66Euglena gracilisMutation(s): 0 
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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BB [auth M]
CB [auth M]
EC [auth m]
FC [auth m]
HB [auth O]
BB [auth M],
CB [auth M],
EC [auth m],
FC [auth m],
HB [auth O],
KB [auth P],
LC [auth o],
MA [auth A],
NA [auth A],
OA [auth A],
OB [auth R],
OC [auth p],
PA [auth A],
PC [auth p],
QA [auth D],
RA [auth D],
RB [auth a],
SB [auth a],
SC [auth r],
TA [auth E],
TB [auth a],
UB [auth a],
VB [auth d],
WB [auth d],
YB [auth e]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
LPP (Subject of Investigation/LOI)
Query on LPP

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DC [auth i]
FB [auth N]
IB [auth O]
JB [auth O]
LB [auth P]
DC [auth i],
FB [auth N],
IB [auth O],
JB [auth O],
LB [auth P],
MC [auth o],
NC [auth o],
PB [auth R],
TC [auth r],
UA [auth F],
YA [auth I],
ZB [auth f]
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
C35 H69 O8 P
PORPENFLTBBHSG-MGBGTMOVSA-N
LMT
Query on LMT

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AC [auth f]
GB [auth N]
IC [auth n]
NB [auth Q]
RC [auth q]
AC [auth f],
GB [auth N],
IC [auth n],
NB [auth Q],
RC [auth q],
SA [auth D],
VA [auth F],
XB [auth d]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
TRT
Query on TRT

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AB [auth M]
BC [auth g]
CC [auth g]
DB [auth N]
EB [auth N]
AB [auth M],
BC [auth g],
CC [auth g],
DB [auth N],
EB [auth N],
GC [auth m],
HC [auth m],
JC [auth n],
KC [auth n],
MB [auth P],
QB [auth R],
QC [auth p],
UC [auth r],
WA [auth G],
XA [auth G],
ZA [auth M]
FRAGMENT OF TRITON X-100
C21 H36 O4
HEUDUECKTWTQQR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Database references, Structure summary