8J9J

Cryo-EM structure of Euglena gracilis complex I, NADH state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 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
NDUFS1AA [auth 1A]385Euglena gracilisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFS1BB [auth 1B]527Euglena gracilisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ND2BC [auth 2B]142Euglena gracilisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ND4LD [auth 4L]171Euglena gracilisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA1E [auth A1]141Euglena gracilisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA2F [auth A2]193Euglena gracilisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA3G [auth A3]125Euglena gracilisMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA5H [auth A5]184Euglena gracilisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA6I [auth A6]437Euglena gracilisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA7J [auth A7]136Euglena gracilisMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA8K [auth A8]223Euglena gracilisMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA9L [auth A9]489Euglena gracilisMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFAB1-alphaM [auth AB]134Euglena gracilisMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFAB1-betaN [auth AC]134Euglena gracilisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA12O [auth AL]281Euglena gracilisMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA13P [auth AM]198Euglena gracilisMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA11Q [auth AN]287Euglena gracilisMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB2R [auth B2]145Euglena gracilisMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB3S [auth B3]62Euglena gracilisMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB4T [auth B4]171Euglena gracilisMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB5U [auth B5]140Euglena gracilisMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB6V [auth B6]91Euglena gracilisMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB7W [auth B7]97Euglena gracilisMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB8X [auth B8]176Euglena gracilisMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB9Y [auth B9]158Euglena gracilisMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB10Z [auth BL]144Euglena gracilisMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB11AA [auth BM]112Euglena gracilisMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFC2BA [auth C4]185Euglena gracilisMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NDUEG1CA [auth E1]483Euglena gracilisMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NDUEG2DA [auth E2]467Euglena gracilisMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NDUEG3EA [auth E3]434Euglena gracilisMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NDUEG4FA [auth E4]368Euglena gracilisMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NDUEG5GA [auth E5]290Euglena gracilisMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NDUEG6HA [auth E6]371Euglena gracilisMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NDUEG8IA [auth E8]205Euglena gracilisMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NDUEG10JA [auth EA]126Euglena gracilisMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NDUEG11KA [auth EB]101Euglena gracilisMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NDUEG12LA [auth EC]101Euglena gracilisMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NDUEG13MA [auth ED]151Euglena gracilisMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFXNA [auth FX]325Euglena gracilisMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NDUCA1OA [auth G1]436Euglena gracilisMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NDUCA2PA [auth G2]267Euglena gracilisMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
NDUCA3QA [auth G3]261Euglena gracilisMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
ND1RA [auth N1]670Euglena gracilisMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
ND2ASA [auth N2]300Euglena gracilisMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
ND3TA [auth N3],
WA [auth N6]
293Euglena gracilisMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4UA [auth N4]478Euglena gracilisMutation(s): 0 
UniProt
Find proteins for A0A0S2YRV6 (Euglena gracilis var. bacillaris)
Explore A0A0S2YRV6 
Go to UniProtKB:  A0A0S2YRV6
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UniProt GroupA0A0S2YRV6
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
ND5VA [auth N5]584Euglena gracilisMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFS2XA [auth S2]395Euglena gracilisMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFS3YA [auth S3]277Euglena gracilisMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFS4ZA [auth S4]208Euglena gracilisMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFS5AB [auth S5]122Euglena gracilisMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFS6BB [auth S6]147Euglena gracilisMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFS7CB [auth S7]207Euglena gracilisMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFS8DB [auth S8]212Euglena gracilisMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNKEB [auth U1],
FB [auth U2]
12Euglena gracilisMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFV1GB [auth V1]526Euglena gracilisMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFV2HB [auth V2]225Euglena gracilisMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
NDUEG7IB [auth E7]246Euglena 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 AM]
BC [auth AM]
BD [auth N4]
GC [auth B3]
HC [auth B5]
AC [auth AM],
BC [auth AM],
BD [auth N4],
GC [auth B3],
HC [auth B5],
HD [auth N5],
KC [auth C4],
LD [auth N5],
MC [auth C4],
OC [auth E6],
PB [auth A3],
TC [auth EA],
UC [auth EA],
UD [auth E7],
WB [auth AL],
XB [auth AL],
YB [auth AL],
ZB [auth AM]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
U10 (Subject of Investigation/LOI)
Query on U10

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FD [auth N4]UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PC1
Query on PC1

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AD [auth N3]
CC [auth AM]
CD [auth N4]
DC [auth AM]
DD [auth N4]
AD [auth N3],
CC [auth AM],
CD [auth N4],
DC [auth AM],
DD [auth N4],
EC [auth AN],
GD [auth N5],
IC [auth B5],
ID [auth N5],
JC [auth B5],
JD [auth N5],
LC [auth C4],
NB [auth A1],
NC [auth E4],
OB [auth A1],
PC [auth E8],
QC [auth E8],
RB [auth A9],
RC [auth E8],
SB [auth A9],
SC [auth E8],
VB [auth AL],
VC [auth ED],
XC [auth N1],
YC [auth N1],
ZC [auth N2]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
Query on 3PE

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ED [auth N4],
FC [auth AN],
KD [auth N5],
WC [auth G1]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP

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QB [auth A9]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
NAI
Query on NAI

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SD [auth V1]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
ZMP (Subject of Investigation/LOI)
Query on ZMP

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TB [auth AB],
UB [auth AC]
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
C25 H49 N2 O8 P S
HDTINWYIVVMRIN-HSZRJFAPSA-N
FMN
Query on FMN

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QD [auth V1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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KB [auth 1A]
LB [auth 1A]
ND [auth S7]
OD [auth S8]
PD [auth S8]
KB [auth 1A],
LB [auth 1A],
ND [auth S7],
OD [auth S8],
PD [auth S8],
RD [auth V1]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
JB [auth 1A],
TD [auth V2]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
MD [auth S6],
VD [auth E7]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
MB [auth 1A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
2MR
Query on 2MR
XA [auth S2]L-PEPTIDE LINKINGC8 H18 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv3.3.2
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

View Full Validation Report



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: 2024-03-13
    Changes: Database references