8J9H | pdb_00008j9h

Cryo-EM structure of Euglena gracilis respiratory complex I, deactive state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8J9H

This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 1,793.32 kDa 
  • Atom Count: 113,591 
  • Modeled Residue Count: 13,825 
  • Deposited Residue Count: 15,261 
  • Unique protein chains: 59

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUS1AA [auth 1A]385Euglena gracilisMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUS1BB [auth 1B]527Euglena gracilisMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 5C [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
NDUFA12N [auth AL]281Euglena gracilisMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFA13O [auth AM]198Euglena gracilisMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFA11P [auth AN]287Euglena gracilisMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFB2Q [auth B2]145Euglena gracilisMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFB3R [auth B3]62Euglena gracilisMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFB4S [auth B4]171Euglena gracilisMutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFB5T [auth B5]140Euglena gracilisMutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFB6U [auth B6]91Euglena gracilisMutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFB7V [auth B7]97Euglena gracilisMutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFB8W [auth B8]176Euglena gracilisMutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFB9X [auth B9]158Euglena gracilisMutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFB10Y [auth BL]144Euglena gracilisMutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFB11Z [auth BM]112Euglena gracilisMutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFC2AA [auth C4]185Euglena gracilisMutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUEG1BA [auth E1]483Euglena gracilisMutation(s): 0 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUEG2CA [auth E2]467Euglena gracilisMutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUEG3DA [auth E3]434Euglena gracilisMutation(s): 0 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUEG4EA [auth E4]368Euglena gracilisMutation(s): 0 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUEG5FA [auth E5]290Euglena gracilisMutation(s): 0 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUEG6GA [auth E6]371Euglena gracilisMutation(s): 0 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUEG8HA [auth E8]205Euglena gracilisMutation(s): 0 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUEG10IA [auth EA]126Euglena gracilisMutation(s): 0 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUEG11JA [auth EB]101Euglena gracilisMutation(s): 0 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUEG12KA [auth EC]101Euglena gracilisMutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUEG13LA [auth ED]151Euglena gracilisMutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFXMA [auth FX]325Euglena gracilisMutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUCA1NA [auth G1]436Euglena gracilisMutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUCA2OA [auth G2]267Euglena gracilisMutation(s): 0 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUCA3PA [auth G3]261Euglena gracilisMutation(s): 0 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
ND1QA [auth N1]670Euglena gracilisMutation(s): 0 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
ND2ARA [auth N2]300Euglena gracilisMutation(s): 0 
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
ND3SA [auth N3],
VA [auth N6]
293Euglena gracilisMutation(s): 0 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4TA [auth N4]478Euglena gracilisMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for A0A0S2YRV6 (Euglena gracilis var. bacillaris)
Explore A0A0S2YRV6 
Go to UniProtKB:  A0A0S2YRV6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0S2YRV6
Sequence Annotations
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Reference Sequence
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
ND5UA [auth N5]584Euglena gracilisMutation(s): 0 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFS2WA [auth S2]395Euglena gracilisMutation(s): 0 
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFS3XA [auth S3]277Euglena gracilisMutation(s): 0 
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFS4YA [auth S4]208Euglena gracilisMutation(s): 0 
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFS5ZA [auth S5]122Euglena gracilisMutation(s): 0 
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFS6AB [auth S6]147Euglena gracilisMutation(s): 0 
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFS7BB [auth S7]207Euglena gracilisMutation(s): 0 
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFS8CB [auth S8]212Euglena gracilisMutation(s): 0 
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Entity ID: 55
MoleculeChains  Sequence LengthOrganismDetailsImage
UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNKDB [auth U1],
EB [auth U2]
12Euglena gracilisMutation(s): 0 
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Entity ID: 56
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFV1FB [auth V1]526Euglena gracilisMutation(s): 0 
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Entity ID: 57
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFV2GB [auth V2]225Euglena gracilisMutation(s): 0 
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Entity ID: 58
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUEG7HB [auth E7]246Euglena gracilisMutation(s): 0 
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Entity ID: 59
MoleculeChains  Sequence LengthOrganismDetailsImage
NDUFAB1-betaIB [auth AC]134Euglena gracilisMutation(s): 0 

Small Molecules

Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
AC [auth AM]
AD [auth N4]
FC [auth B3]
GC [auth B5]
GD [auth N5]
AC [auth AM],
AD [auth N4],
FC [auth B3],
GC [auth B5],
GD [auth N5],
JC [auth C4],
KD [auth N5],
LC [auth C4],
NC [auth E6],
PB [auth A3],
SC [auth EA],
SD [auth E7],
TC [auth EA],
VB [auth AL],
WB [auth AL],
XB [auth AL],
YB [auth AM],
ZB [auth AM]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
U10
(Subject of Investigation/LOI)

Query on U10



Download:Ideal Coordinates CCD File
ED [auth N4]UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PC1

Query on PC1



Download:Ideal Coordinates CCD File
BC [auth AM]
BD [auth N4]
CC [auth AM]
CD [auth N4]
DC [auth AN]
BC [auth AM],
BD [auth N4],
CC [auth AM],
CD [auth N4],
DC [auth AN],
FD [auth N5],
HC [auth B5],
HD [auth N5],
IC [auth B5],
ID [auth N5],
KC [auth C4],
MC [auth E4],
NB [auth A1],
OB [auth A1],
OC [auth E8],
PC [auth E8],
QC [auth E8],
RB [auth A9],
RC [auth E8],
SB [auth A9],
UB [auth AL],
UC [auth ED],
WC [auth N1],
XC [auth N1],
YC [auth N2],
ZC [auth N3]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE

Query on 3PE



Download:Ideal Coordinates CCD File
DD [auth N4],
EC [auth AN],
JD [auth N5],
VC [auth G1]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP

Query on NDP



Download:Ideal Coordinates CCD File
QB [auth A9]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
ZMP
(Subject of Investigation/LOI)

Query on ZMP



Download:Ideal Coordinates CCD File
TB [auth AB],
UD [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



Download:Ideal Coordinates CCD File
PD [auth V1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
(Subject of Investigation/LOI)

Query on SF4



Download:Ideal Coordinates CCD File
KB [auth 1A]
LB [auth 1A]
MD [auth S7]
ND [auth S8]
OD [auth S8]
KB [auth 1A],
LB [auth 1A],
MD [auth S7],
ND [auth S8],
OD [auth S8],
QD [auth V1]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES

Query on FES



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

Query on ZN



Download:Ideal Coordinates CCD File
LD [auth S6],
TD [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
UNK
Query on UNK
C [auth 2B]L-PEPTIDE LINKINGC4 H9 N O2

--

2MR
Query on 2MR
WA [auth S2]L-PEPTIDE LINKINGC8 H18 N4 O2ARG

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 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
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary