8IUJ

Cryo-EM structure of Euglena gracilis super-complex III2+IV2, composite


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 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

Euglena's atypical respiratory chain adapts to the discoidal cristae and flexible metabolism.

He, Z.Wu, M.Tian, H.Wang, L.Hu, Y.Han, F.Zhou, J.Wang, Y.Zhou, L.

(2024) Nat Commun 15: 1628-1628

  • DOI: https://doi.org/10.1038/s41467-024-46018-z
  • Primary Citation of Related Structures:  
    8IUF, 8IUJ, 8J9H, 8J9I, 8J9J

  • PubMed Abstract: 

    Euglena gracilis, a model organism of the eukaryotic supergroup Discoba harbouring also clinically important parasitic species, possesses diverse metabolic strategies and an atypical electron transport chain. While structures of the electron transport chain complexes and supercomplexes of most other eukaryotic clades have been reported, no similar structure is currently available for Discoba, limiting the understandings of its core metabolism and leaving a gap in the evolutionary tree of eukaryotic bioenergetics. Here, we report high-resolution cryo-EM structures of Euglena's respirasome I + III 2  + IV and supercomplex III 2  + IV 2 . A previously unreported fatty acid synthesis domain locates on the tip of complex I's peripheral arm, providing a clear picture of its atypical subunit composition identified previously. Individual complexes are re-arranged in the respirasome to adapt to the non-uniform membrane curvature of the discoidal cristae. Furthermore, Euglena's conformationally rigid complex I is deactivated by restricting ubiquinone's access to its substrate tunnel. Our findings provide structural insights for therapeutic developments against euglenozoan parasite infections.


  • Organizational Affiliation

    Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MPP-betaA [auth QA],
G [auth Qa]
479Euglena gracilisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bB [auth QC],
H [auth Qc]
368Euglena gracilisMutation(s): 0 
UniProt
Find proteins for A0A0S2YRT7 (Euglena gracilis var. bacillaris)
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UniProt GroupA0A0S2YRT7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme proteinC [auth QD],
I [auth Qd]
243Euglena gracilisMutation(s): 0 
EC: 7.1.1.8
UniProt
Find proteins for P20114 (Euglena gracilis)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
UQCRQD [auth QH],
J [auth Qh]
86Euglena gracilisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
UQCR10E [auth QJ],
K [auth Qj]
154Euglena gracilisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrialF [auth QK],
L [auth Qk]
100Euglena gracilisMutation(s): 0 
UniProt
Find proteins for P43266 (Euglena gracilis)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
COXEG1M [auth 4a],
Z [auth 4A]
246Euglena gracilisMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
COXEG3AA [auth 4C],
N [auth 4c]
139Euglena gracilisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
COXEG5BA [auth 4E],
O [auth 4e]
165Euglena gracilisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
COXEG8CA [auth 4H],
P [auth 4h]
221Euglena gracilisMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
COXEG10DA [auth 4J],
Q [auth 4j]
88Euglena gracilisMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
COX5cEA [auth 5C],
R [auth 5c]
208Euglena gracilisMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
COX6aLA [auth 6A],
S [auth 6a]
112Euglena gracilisMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
COX6b-1FA [auth 6B],
T [auth 6b]
287Euglena gracilisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
COX7cGA [auth 7C],
U [auth 7c]
171Euglena gracilisMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1HA [auth C1],
V [auth c1]
495Euglena gracilisMutation(s): 0 
EC: 7.1.1.9
UniProt
Find proteins for Q34463 (Euglena gracilis)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2IA [auth C2],
W [auth c2]
196Euglena gracilisMutation(s): 0 
UniProt
Find proteins for Q9XN19 (Euglena gracilis)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Putative NADH dehydrogenase subunit 6JA [auth C3],
X [auth c3]
161Euglena gracilisMutation(s): 0 
UniProt
Find proteins for Q9XN18 (Euglena gracilis)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
COX4KA [auth DC],
Y [auth dc]
179Euglena gracilisMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
UQCRFS1MA [auth QE],
NA [auth Qe]
252Euglena gracilisMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
UQCRHOA [auth QF],
SA [auth Qf]
72Euglena gracilisMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
UQCRBPA [auth QG],
TA [auth Qg]
228Euglena gracilisMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
UQCR9QA [auth QI],
UA [auth Qi]
70Euglena gracilisMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrialRA [auth Qb],
VA [auth QB]
474Euglena gracilisMutation(s): 0 
UniProt
Find proteins for P43265 (Euglena gracilis)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
COX5b-2GB [auth 5b],
WA [auth 5B]
174Euglena gracilisMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
COXEG4CB [auth 4d],
XA [auth 4D]
174Euglena gracilisMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
COXEG6DB [auth 4f],
YA [auth 4F]
75Euglena gracilisMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
COXEG7EB [auth 4g],
ZA [auth 4G]
315Euglena gracilisMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
COXEG9AB [auth 4I],
FB [auth 4i]
274Euglena gracilisMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
COX7aBB [auth 7a],
HB [auth 7A]
178Euglena gracilisMutation(s): 0 
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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AC [auth Qh]
CC [auth Qj]
FC [auth 4c]
FD [auth C1]
HC [auth 4e]
AC [auth Qh],
CC [auth Qj],
FC [auth 4c],
FD [auth C1],
HC [auth 4e],
IC [auth 7c],
KB [auth QC],
MB [auth QD],
OD [auth QE],
PB [auth QH],
RB [auth QJ],
VB [auth Qc],
XB [auth Qd],
ZB [auth Qh],
ZC [auth 4E]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HEA
Query on HEA

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AD [auth C1],
BD [auth C1],
KC [auth c1],
LC [auth c1]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PC1
Query on PC1

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BC [auth Qj]
DC [auth 4a]
ED [auth C1]
GC [auth 4e]
ID [auth C1]
BC [auth Qj],
DC [auth 4a],
ED [auth C1],
GC [auth 4e],
ID [auth C1],
JC [auth 7c],
LD [auth C3],
MD [auth DC],
NB [auth QD],
OC [auth c1],
PD [auth QE],
QD [auth Qe],
RC [auth c1],
RD [auth Qe],
TD [auth Qe],
UB [auth Qc],
UC [auth c3],
UD [auth Qg],
VC [auth 4A],
WC [auth 4A],
YB [auth Qd],
YC [auth 4E]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
Query on 3PE

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AE [auth 4d]
BE [auth 4d]
EC [auth 4a]
EE [auth 7A]
GD [auth C1]
AE [auth 4d],
BE [auth 4d],
EC [auth 4a],
EE [auth 7A],
GD [auth C1],
HD [auth C1],
PC [auth c1],
QC [auth c1],
WD [auth 4D],
XD [auth 4F],
ZD [auth 7a]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
HEC (Subject of Investigation/LOI)
Query on HEC

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LB [auth QD],
WB [auth Qd]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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IB [auth QC],
JB [auth QC],
SB [auth Qc],
TB [auth Qc]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PX2
Query on PX2

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OB [auth QD],
QB [auth QJ],
XC [auth 4C]
1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
C27 H52 O8 P
OKLASJZQBDJAPH-RUZDIDTESA-M
S12
Query on S12

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CE [auth 4d],
YD [auth 4F]
O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine
C24 H46 N O9 P
JZWNYZVVZXZRRH-VXKWHMMOSA-N
FES (Subject of Investigation/LOI)
Query on FES

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ND [auth QE],
SD [auth Qe]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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DE [auth 5b],
VD [auth 5B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)
Query on CU

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CD [auth C1]
JD [auth C2]
KD [auth C2]
MC [auth c1]
SC [auth c2]
CD [auth C1],
JD [auth C2],
KD [auth C2],
MC [auth c1],
SC [auth c2],
TC [auth c2]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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DD [auth C1],
NC [auth c1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv.3.3.2
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChinaZJU100 Young Professor

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Database references