ISDA: 8IUF

Deposition Date 2023-03-24

Release Date 2024-02-28

Last Version Date 2024-11-13

Entry Detail

PDB ID:

8IUF

Keywords:

ELECTRON TRANSPORT

Title:

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

Biological Source:

Source Organism:

Euglena gracilis (Taxon ID: 3039)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.81 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polypeptide(L)
Molecule:NDUFS1a
Chain IDs:A (auth: 1A)
Chain Length:385
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFS1b
Chain IDs:B (auth: 1B)
Chain Length:527
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:ND2b
Chain IDs:C (auth: 2B)
Chain Length:142
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:COXEG1
Chain IDs:D (auth: 4A)
Chain Length:246
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:COXEG3
Chain IDs:E (auth: 4C)
Chain Length:139
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:COXEG4
Chain IDs:F (auth: 4D)
Chain Length:174
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:COXEG5
Chain IDs:G (auth: 4E)
Chain Length:165
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:COXEG6
Chain IDs:H (auth: 4F)
Chain Length:75
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:COXEG7
Chain IDs:I (auth: 4G)
Chain Length:315
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:COXEG8
Chain IDs:J (auth: 4H)
Chain Length:221
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:COXEG9
Chain IDs:K (auth: 4I)
Chain Length:274
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:COXEG10
Chain IDs:L (auth: 4J)
Chain Length:88
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:ND4L
Chain IDs:M (auth: 4L)
Chain Length:171
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:COX5b-2
Chain IDs:N (auth: 5B)
Chain Length:174
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:COX5c
Chain IDs:O (auth: 5C)
Chain Length:208
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:COX6a
Chain IDs:P (auth: 6A)
Chain Length:112
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:COX6b-1
Chain IDs:Q (auth: 6B)
Chain Length:287
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:COX7a
Chain IDs:R (auth: 7A)
Chain Length:178
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:COX7c
Chain IDs:S (auth: 7C)
Chain Length:171
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:poly(UNK)
Chain IDs:XC (auth: A), YC (auth: B)
Chain Length:12
Number of Molecules:2
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFA1
Chain IDs:T (auth: A1)
Chain Length:141
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFA2
Chain IDs:U (auth: A2)
Chain Length:193
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFA3
Chain IDs:V (auth: A3)
Chain Length:125
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFA5
Chain IDs:W (auth: A5)
Chain Length:184
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFA6
Chain IDs:X (auth: A6)
Chain Length:437
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFA7
Chain IDs:Y (auth: A7)
Chain Length:136
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFA8
Chain IDs:Z (auth: A8)
Chain Length:223
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFA9
Chain IDs:AA (auth: A9)
Chain Length:489
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFAB1-alpha
Chain IDs:BA (auth: AB)
Chain Length:134
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFAB1-beta
Chain IDs:CA (auth: AC)
Chain Length:134
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFA12
Chain IDs:DA (auth: AL)
Chain Length:281
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFA13
Chain IDs:EA (auth: AM)
Chain Length:198
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFA11
Chain IDs:FA (auth: AN)
Chain Length:287
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFB2
Chain IDs:GA (auth: B2)
Chain Length:145
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFB3
Chain IDs:HA (auth: B3)
Chain Length:62
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFB4
Chain IDs:IA (auth: B4)
Chain Length:171
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFB5
Chain IDs:JA (auth: B5)
Chain Length:140
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFB6
Chain IDs:KA (auth: B6)
Chain Length:91
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFB7
Chain IDs:LA (auth: B7)
Chain Length:97
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFB8
Chain IDs:MA (auth: B8)
Chain Length:176
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFB9
Chain IDs:NA (auth: B9)
Chain Length:158
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFB10
Chain IDs:OA (auth: BL)
Chain Length:144
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFB11
Chain IDs:PA (auth: BM)
Chain Length:112
Number of Molecules:1
Biological Source:Euglena gracilis

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 1
Gene (Uniprot):CoI
Chain IDs:QA (auth: C1)
Chain Length:495
Number of Molecules:1
Biological Source:Euglena gracilis

UniProt ID:Q34463 Pfam ID:PF00115

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 2
Gene (Uniprot):COXII
Chain IDs:RA (auth: C2)
Chain Length:196
Number of Molecules:1
Biological Source:Euglena gracilis

UniProt ID:Q9XN19 Pfam ID:PF02790, PF00116

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative NADH dehydrogenase subunit 6
Gene (Uniprot):ND6
Chain IDs:SA (auth: C3)
Chain Length:161
Number of Molecules:1
Biological Source:Euglena gracilis

UniProt ID:Q9XN18

Polymer Type:polypeptide(L)
Molecule:NDUFC2
Chain IDs:TA (auth: C4)
Chain Length:185
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:COX4
Chain IDs:UA (auth: DC)
Chain Length:179
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUEG1
Chain IDs:VA (auth: E1)
Chain Length:483
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUEG2
Chain IDs:WA (auth: E2)
Chain Length:472
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUEG3
Chain IDs:XA (auth: E3)
Chain Length:594
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUEG4
Chain IDs:YA (auth: E4)
Chain Length:368
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUEG5
Chain IDs:ZA (auth: E5)
Chain Length:290
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUEG6
Chain IDs:AB (auth: E6)
Chain Length:371
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUEG7
Chain IDs:BB (auth: E7)
Chain Length:246
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUEG8
Chain IDs:CB (auth: E8)
Chain Length:205
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUEG9
Chain IDs:DB (auth: E9)
Chain Length:178
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUEG10
Chain IDs:EB (auth: EA)
Chain Length:126
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUEG11
Chain IDs:FB (auth: EB)
Chain Length:101
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUEG11
Chain IDs:GB (auth: EC)
Chain Length:101
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUEG13
Chain IDs:HB (auth: ED)
Chain Length:151
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFX
Chain IDs:IB (auth: FX)
Chain Length:325
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUCA1
Chain IDs:JB (auth: G1)
Chain Length:436
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUCA2
Chain IDs:KB (auth: G2)
Chain Length:267
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUCA3
Chain IDs:LB (auth: G3)
Chain Length:261
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:ND1
Chain IDs:MB (auth: N1)
Chain Length:670
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:ND2a
Chain IDs:NB (auth: N2)
Chain Length:300
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:ND3
Chain IDs:OB (auth: N3), RB (auth: N6)
Chain Length:293
Number of Molecules:2
Biological Source:Euglena gracilis

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 4
Gene (Uniprot):nad4
Chain IDs:PB (auth: N4)
Chain Length:478
Number of Molecules:1
Biological Source:Euglena gracilis

UniProt ID:A0A0S2YRV6 Pfam ID:PF00361

Polymer Type:polypeptide(L)
Molecule:ND5
Chain IDs:QB (auth: N5)
Chain Length:584
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:MPP-beta
Chain IDs:SB (auth: QA), DC (auth: Qa)
Chain Length:479
Number of Molecules:2
Biological Source:Euglena gracilis

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial
Chain IDs:TB (auth: QB), EC (auth: Qb)
Chain Length:474
Number of Molecules:2
Biological Source:Euglena gracilis

UniProt ID:P43265 Pfam ID:PF00675

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome b
Gene (Uniprot):cob
Chain IDs:UB (auth: QC), FC (auth: Qc)
Chain Length:368
Number of Molecules:2
Biological Source:Euglena gracilis

UniProt ID:A0A0S2YRT7 Pfam ID:PF00033, PF00032

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c1, heme protein
Chain IDs:VB (auth: QD), GC (auth: Qd)
Chain Length:243
Number of Molecules:2
Biological Source:Euglena gracilis

UniProt ID:P20114 Pfam ID:PF02167

Polymer Type:polypeptide(L)
Molecule:UQCRFS1
Chain IDs:WB (auth: QE), HC (auth: Qe)
Chain Length:252
Number of Molecules:2
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:UQCRH
Chain IDs:XB (auth: QF), IC (auth: Qf)
Chain Length:72
Number of Molecules:2
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:UQCRB
Chain IDs:YB (auth: QG), JC (auth: Qg)
Chain Length:228
Number of Molecules:2
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:UQCRQ
Chain IDs:ZB (auth: QH), KC (auth: Qh)
Chain Length:85
Number of Molecules:2
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:UQCR9
Chain IDs:AC (auth: QI), LC (auth: Qi)
Chain Length:70
Number of Molecules:2
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:UQCR10
Chain IDs:BC (auth: QJ), MC (auth: Qj)
Chain Length:154
Number of Molecules:2
Biological Source:Euglena gracilis

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrial
Chain IDs:CC (auth: QK), NC (auth: Qk)
Chain Length:100
Number of Molecules:2
Biological Source:Euglena gracilis

UniProt ID:P43266

Polymer Type:polypeptide(L)
Molecule:NDUFS2
Chain IDs:OC (auth: S2)
Chain Length:395
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFS3
Chain IDs:PC (auth: S3)
Chain Length:277
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFS4
Chain IDs:QC (auth: S4)
Chain Length:208
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFS5
Chain IDs:RC (auth: S5)
Chain Length:122
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFS6
Chain IDs:SC (auth: S6)
Chain Length:147
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFS7
Chain IDs:TC (auth: S7)
Chain Length:207
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFS8
Chain IDs:UC (auth: S8)
Chain Length:212
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFV1
Chain IDs:VC (auth: V1)
Chain Length:526
Number of Molecules:1
Biological Source:Euglena gracilis

Polymer Type:polypeptide(L)
Molecule:NDUFV2
Chain IDs:WC (auth: V2)
Chain Length:225
Number of Molecules:1
Biological Source:Euglena gracilis

Ligand Molecules

3PE

CDL

FES

FMN

HEA

HEC

HEM

NDP

PC1

PX2

S12

SF4

U10

ZMP

Primary Citation

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.Show

Nat Commun 15 1628 1628 (2024)

PMID: 38388527 DOI: 10.1038/s41467-024-46018-z

Abstact

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 + III2 + IV and supercomplex III2 + IV2. 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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures