6TDU

Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase, full dimer, rotational states 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.32 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,
S [auth a]
487Euglena gracilisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB6B [auth D],
T [auth d]
187Euglena gracilisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB12C [auth E],
U [auth e]
97Euglena gracilisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aD [auth F],
V [auth f]
274Euglena gracilisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit bE [auth G],
W [auth g]
112Euglena gracilisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit dF [auth H],
X [auth h]
476Euglena gracilisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit fG [auth I],
Y [auth i]
98Euglena gracilisMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit i/jH [auth J],
Z [auth j]
104Euglena gracilisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit kAA [auth k],
I [auth K]
113Euglena gracilisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit 8BA [auth l],
J [auth L]
57Euglena gracilisMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG1CA [auth m],
K [auth M]
169Euglena gracilisMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG2DA [auth n],
L [auth N]
137Euglena gracilisMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG3EA [auth o],
M [auth O]
116Euglena gracilisMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG4FA [auth p],
N [auth P]
120Euglena gracilisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG5GA [auth q],
O [auth Q]
90Euglena gracilisMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG6HA [auth r],
P [auth R]
78Euglena gracilisMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG7IA [auth s],
Q [auth S]
74Euglena gracilisMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG8JA [auth t],
R [auth T]
66Euglena gracilisMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha561Euglena gracilisMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta501Euglena gracilisMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit gammaQA [auth AG],
QB [auth BG]
306Euglena gracilisMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit deltaRA [auth AH],
RB [auth BH]
176Euglena gracilisMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit epsilonSA [auth AI],
SB [auth BI]
76Euglena gracilisMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
p18192Euglena gracilisMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
oligomycin sensitivity conferring protein (OSCP)WA [auth AM],
WB [auth BM]
267Euglena gracilisMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
inhibitor of F1 (IF1)XA [auth AN],
XB [auth BN]
103Euglena gracilisMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit c104Euglena gracilisMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB3IB [auth B],
IC [auth b]
338Euglena gracilisMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB4JB [auth C],
JC [auth c]
169Euglena gracilisMutation(s): 0 
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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BD [auth M]
CD [auth M]
DE [auth m]
HD [auth O]
KC [auth A]
BD [auth M],
CD [auth M],
DE [auth m],
HD [auth O],
KC [auth A],
KD [auth P],
KE [auth o],
LC [auth A],
LD [auth P],
MC [auth A],
NC [auth A],
NE [auth p],
OC [auth A],
OD [auth R],
PC [auth D],
PD [auth a],
QD [auth a],
QE [auth r],
RC [auth E],
RD [auth a],
SD [auth a],
TD [auth a],
UD [auth d],
WD [auth e],
YC [auth M]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
LPP (Subject of Investigation/LOI)
Query on LPP

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BE [auth i]
CE [auth k]
FD [auth N]
GE [auth n]
ID [auth O]
BE [auth i],
CE [auth k],
FD [auth N],
GE [auth n],
ID [auth O],
JD [auth O],
LE [auth o],
ME [auth o],
SC [auth F],
WC [auth I],
XC [auth K],
XD [auth f]
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
C35 H69 O8 P
PORPENFLTBBHSG-MGBGTMOVSA-N
LMT
Query on LMT

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GD [auth N]
HE [auth n]
ND [auth Q]
PE [auth q]
QC [auth D]
GD [auth N],
HE [auth n],
ND [auth Q],
PE [auth q],
QC [auth D],
TC [auth F],
VD [auth d],
YD [auth g]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
ATP (Subject of Investigation/LOI)
Query on ATP

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AF
DF [auth BA]
FF [auth BB]
HF [auth BC]
MF [auth BF]
AF,
DF [auth BA],
FF [auth BB],
HF [auth BC],
MF [auth BF],
RE [auth AA],
TE [auth AB],
VE [auth AC]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

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JF [auth BD],
XE [auth AD]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
TRT
Query on TRT

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AD [auth M]
AE [auth g]
CF [auth AR]
DD [auth N]
ED [auth N]
AD [auth M],
AE [auth g],
CF [auth AR],
DD [auth N],
ED [auth N],
EE [auth m],
FE [auth m],
IE [auth n],
JE [auth n],
LF [auth BE],
MD [auth P],
OE [auth p],
OF [auth BR],
UC [auth G],
VC [auth G],
ZC [auth M],
ZD [auth g],
ZE [auth AE]
FRAGMENT OF TRITON X-100
C21 H36 O4
HEUDUECKTWTQQR-UHFFFAOYSA-N
MG
Query on MG

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BF [auth AF]
EF [auth BA]
GF [auth BB]
IF [auth BC]
KF [auth BD]
BF [auth AF],
EF [auth BA],
GF [auth BB],
IF [auth BC],
KF [auth BD],
NF [auth BF],
SE [auth AA],
UE [auth AB],
WE [auth AC],
YE [auth AD]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.32 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