[English] 日本語
Yorodumi
- PDB-8iuf: Cryo-EM structure of Euglena gracilis super-complex I+III2+IV, co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8iuf
TitleCryo-EM structure of Euglena gracilis super-complex I+III2+IV, composite
Components
  • (Cytochrome c oxidase subunit ...) x 2
  • (NDUEG11) x 2
  • (Ubiquinol-cytochrome- ...) x 2
  • COX4
  • COX5b-2
  • COX5c
  • COX6a
  • COX6b-1
  • COX7a
  • COX7c
  • COXEG1
  • COXEG10
  • COXEG3
  • COXEG4
  • COXEG5
  • COXEG6
  • COXEG7
  • COXEG8
  • COXEG9
  • Cytochrome b
  • Cytochrome c1, heme protein
  • MPP-beta
  • NADH-ubiquinone oxidoreductase chain 4
  • ND1
  • ND2a
  • ND2b
  • ND3
  • ND4L
  • ND5
  • NDUCA1
  • NDUCA2
  • NDUCA3
  • NDUEG1
  • NDUEG10
  • NDUEG13
  • NDUEG2
  • NDUEG3
  • NDUEG4
  • NDUEG5
  • NDUEG6
  • NDUEG7
  • NDUEG8
  • NDUEG9
  • NDUFA1
  • NDUFA11
  • NDUFA12
  • NDUFA13
  • NDUFA2
  • NDUFA3
  • NDUFA5
  • NDUFA6
  • NDUFA7
  • NDUFA8
  • NDUFA9
  • NDUFAB1-alpha
  • NDUFAB1-beta
  • NDUFB10
  • NDUFB11
  • NDUFB2
  • NDUFB3
  • NDUFB4
  • NDUFB5
  • NDUFB6
  • NDUFB7
  • NDUFB8
  • NDUFB9
  • NDUFC2
  • NDUFS1a
  • NDUFS1b
  • NDUFS2
  • NDUFS3
  • NDUFS4
  • NDUFS5
  • NDUFS6
  • NDUFS7
  • NDUFS8
  • NDUFV1
  • NDUFV2
  • NDUFX
  • Putative NADH dehydrogenase subunit 6
  • UQCR10
  • UQCR9
  • UQCRB
  • UQCRFS1
  • UQCRH
  • UQCRQ
  • poly(UNK)
KeywordsELECTRON TRANSPORT / Electron transport chain / supercomplex / membrane protein / Euglena gracilis
Function / homology
Function and homology information


: / : / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / NADH:ubiquinone reductase (H+-translocating) / electron transport coupled proton transport ...: / : / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / NADH:ubiquinone reductase (H+-translocating) / electron transport coupled proton transport / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / : / respiratory electron transport chain / mitochondrial membrane / electron transport chain / mitochondrial inner membrane / electron transfer activity / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / membrane / metal ion binding
Similarity search - Function
Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome c/quinol oxidase subunit II / : / Cytochrome c1 / Cytochrome C1 family / Copper centre Cu(A) ...Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome c/quinol oxidase subunit II / : / Cytochrome c1 / Cytochrome C1 family / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / Cytochrome c-like domain superfamily / Cupredoxin
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / : / Chem-NDP ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / : / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / Chem-S12 / IRON/SULFUR CLUSTER / UBIQUINONE-10 / Chem-ZMP / Cytochrome b / NADH-ubiquinone oxidoreductase chain 4 / Cytochrome c1, heme protein / Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial / Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrial / Cytochrome c oxidase subunit 1 / Putative NADH dehydrogenase subunit 6 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesEuglena gracilis (euglena)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsWu, M.C. / Tian, H.T. / He, Z.X. / Hu, Y.Q. / Zhou, L.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentZJU100 Young Professor China
CitationJournal: Nat Commun / Year: 2024
Title: Euglena's atypical respiratory chain adapts to the discoidal cristae and flexible metabolism.
Authors: Zhaoxiang He / Mengchen Wu / Hongtao Tian / Liangdong Wang / Yiqi Hu / Fangzhu Han / Jiancang Zhou / Yong Wang / Long Zhou /
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 ...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 + IV and supercomplex III + IV. 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.
History
DepositionMar 24, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1A: NDUFS1a
1B: NDUFS1b
2B: ND2b
4A: COXEG1
4C: COXEG3
4D: COXEG4
4E: COXEG5
4F: COXEG6
4G: COXEG7
4H: COXEG8
4I: COXEG9
4J: COXEG10
4L: ND4L
5B: COX5b-2
5C: COX5c
6A: COX6a
6B: COX6b-1
7A: COX7a
7C: COX7c
A1: NDUFA1
A2: NDUFA2
A3: NDUFA3
A5: NDUFA5
A6: NDUFA6
A7: NDUFA7
A8: NDUFA8
A9: NDUFA9
AB: NDUFAB1-alpha
AC: NDUFAB1-beta
AL: NDUFA12
AM: NDUFA13
AN: NDUFA11
B2: NDUFB2
B3: NDUFB3
B4: NDUFB4
B5: NDUFB5
B6: NDUFB6
B7: NDUFB7
B8: NDUFB8
B9: NDUFB9
BL: NDUFB10
BM: NDUFB11
C1: Cytochrome c oxidase subunit 1
C2: Cytochrome c oxidase subunit 2
C3: Putative NADH dehydrogenase subunit 6
C4: NDUFC2
DC: COX4
E1: NDUEG1
E2: NDUEG2
E3: NDUEG3
E4: NDUEG4
E5: NDUEG5
E6: NDUEG6
E7: NDUEG7
E8: NDUEG8
E9: NDUEG9
EA: NDUEG10
EB: NDUEG11
EC: NDUEG11
ED: NDUEG13
FX: NDUFX
G1: NDUCA1
G2: NDUCA2
G3: NDUCA3
N1: ND1
N2: ND2a
N3: ND3
N4: NADH-ubiquinone oxidoreductase chain 4
N5: ND5
N6: ND3
QA: MPP-beta
QB: Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial
QC: Cytochrome b
QD: Cytochrome c1, heme protein
QE: UQCRFS1
QF: UQCRH
QG: UQCRB
QH: UQCRQ
QI: UQCR9
QJ: UQCR10
QK: Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrial
Qa: MPP-beta
Qb: Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial
Qc: Cytochrome b
Qd: Cytochrome c1, heme protein
Qe: UQCRFS1
Qf: UQCRH
Qg: UQCRB
Qh: UQCRQ
Qi: UQCR9
Qj: UQCR10
Qk: Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrial
S2: NDUFS2
S3: NDUFS3
S4: NDUFS4
S5: NDUFS5
S6: NDUFS6
S7: NDUFS7
S8: NDUFS8
V1: NDUFV1
V2: NDUFV2
A: poly(UNK)
B: poly(UNK)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,880,813219
Polymers2,782,294103
Non-polymers98,519116
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
Protein , 85 types, 95 molecules 1A1B2B4A4C4D4E4F4G4H4I4J4L5B5C6A6B7A7CA1A2A3A5A6A7A8A9ABACAL...

#1: Protein NDUFS1a


Mass: 43888.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#2: Protein NDUFS1b


Mass: 59671.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#3: Protein ND2b


Mass: 15756.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#4: Protein COXEG1


Mass: 27278.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#5: Protein COXEG3


Mass: 16394.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#6: Protein COXEG4


Mass: 19359.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#7: Protein COXEG5


Mass: 19464.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#8: Protein COXEG6


Mass: 8728.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#9: Protein COXEG7


Mass: 35651.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#10: Protein COXEG8


Mass: 24495.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#11: Protein COXEG9


Mass: 31754.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#12: Protein COXEG10


Mass: 10043.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#13: Protein ND4L


Mass: 19673.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#14: Protein COX5b-2


Mass: 19736.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#15: Protein COX5c


Mass: 23788.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#16: Protein COX6a


Mass: 13079.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#17: Protein COX6b-1


Mass: 32995.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#18: Protein COX7a


Mass: 20078.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#19: Protein COX7c


Mass: 19897.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#20: Protein NDUFA1


Mass: 15659.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#21: Protein NDUFA2


Mass: 21331.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#22: Protein NDUFA3


Mass: 14950.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#23: Protein NDUFA5


Mass: 20961.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#24: Protein NDUFA6


Mass: 48786.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#25: Protein NDUFA7


Mass: 16358.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#26: Protein NDUFA8


Mass: 25916.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#27: Protein NDUFA9


Mass: 54983.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#28: Protein NDUFAB1-alpha


Mass: 14936.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#29: Protein NDUFAB1-beta


Mass: 14899.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#30: Protein NDUFA12


Mass: 33338.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#31: Protein NDUFA13


Mass: 22683.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#32: Protein NDUFA11


Mass: 32617.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#33: Protein NDUFB2


Mass: 17202.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#34: Protein NDUFB3


Mass: 6831.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#35: Protein NDUFB4


Mass: 19511.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#36: Protein NDUFB5


Mass: 15815.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#37: Protein NDUFB6


Mass: 10926.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#38: Protein NDUFB7


Mass: 12247.089 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#39: Protein NDUFB8


Mass: 20488.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#40: Protein NDUFB9


Mass: 18347.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#41: Protein NDUFB10


Mass: 17471.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#42: Protein NDUFB11


Mass: 13048.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#45: Protein Putative NADH dehydrogenase subunit 6


Mass: 19414.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
References: UniProt: Q9XN18
#46: Protein NDUFC2


Mass: 22010.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#47: Protein COX4


Mass: 20427.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#48: Protein NDUEG1


Mass: 53351.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#49: Protein NDUEG2


Mass: 51015.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#50: Protein NDUEG3


Mass: 63096.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#51: Protein NDUEG4


Mass: 41313.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#52: Protein NDUEG5


Mass: 29182.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#53: Protein NDUEG6


Mass: 43669.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#54: Protein NDUEG7


Mass: 26818.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#55: Protein NDUEG8


Mass: 23994.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#56: Protein NDUEG9


Mass: 18272.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#57: Protein NDUEG10


Mass: 14140.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#58: Protein NDUEG11


Mass: 11472.202 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#59: Protein NDUEG11


Mass: 11323.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#60: Protein NDUEG13


Mass: 17731.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#61: Protein NDUFX


Mass: 37196.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#62: Protein NDUCA1


Mass: 48726.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#63: Protein NDUCA2


Mass: 28857.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#64: Protein NDUCA3


Mass: 28016.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#65: Protein ND1


Mass: 79682.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#66: Protein ND2a


Mass: 35864.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#67: Protein ND3


Mass: 34504.223 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#68: Protein NADH-ubiquinone oxidoreductase chain 4


Mass: 56417.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
References: UniProt: A0A0S2YRV6
#69: Protein ND5


Mass: 68375.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#70: Protein MPP-beta


Mass: 53520.293 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#72: Protein Cytochrome b


Mass: 42476.266 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
References: UniProt: A0A0S2YRT7
#73: Protein Cytochrome c1, heme protein / Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol- ...Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol-cytochrome-c reductase complex cytochrome c1 subunit / Cytochrome c-1


Mass: 27889.436 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
References: UniProt: P20114, quinol-cytochrome-c reductase
#74: Protein UQCRFS1


Mass: 27825.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#75: Protein UQCRH


Mass: 8207.571 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#76: Protein UQCRB


Mass: 27404.115 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#77: Protein UQCRQ


Mass: 9948.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#78: Protein UQCR9


Mass: 6939.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#79: Protein UQCR10


Mass: 17577.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#81: Protein NDUFS2


Mass: 45251.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#82: Protein NDUFS3


Mass: 32466.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#83: Protein NDUFS4


Mass: 23736.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#84: Protein NDUFS5


Mass: 14244.042 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#85: Protein NDUFS6


Mass: 17101.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#86: Protein NDUFS7


Mass: 22837.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#87: Protein NDUFS8


Mass: 24370.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#88: Protein NDUFV1


Mass: 57940.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#89: Protein NDUFV2


Mass: 25189.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.

-
Cytochrome c oxidase subunit ... , 2 types, 2 molecules C1C2

#43: Protein Cytochrome c oxidase subunit 1


Mass: 55759.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
References: UniProt: Q34463, cytochrome-c oxidase
#44: Protein Cytochrome c oxidase subunit 2


Mass: 22443.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
References: UniProt: Q9XN19

-
Ubiquinol-cytochrome- ... , 2 types, 4 molecules QBQbQKQk

#71: Protein Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial


Mass: 51132.660 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
References: UniProt: P43265
#80: Protein Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrial


Mass: 11300.364 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
References: UniProt: P43266

-
Protein/peptide , 1 types, 2 molecules AB

#90: Protein/peptide poly(UNK)


Mass: 1039.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)

-
Non-polymers , 18 types, 116 molecules

#91: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#92: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#93: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#94: Chemical...
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#95: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#96: Chemical ChemComp-S12 / O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine / 1-oleoyl-2-hydroxy-sn-glycero-3-phospho-L-serine


Type: L-peptide linking / Mass: 523.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46NO9P
#97: Chemical...
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#98: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#99: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#100: Chemical ChemComp-ZMP / S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate


Mass: 568.704 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49N2O8PS / Feature type: SUBJECT OF INVESTIGATION
#101: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#102: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#103: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#104: Chemical ChemComp-PX2 / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE


Mass: 535.671 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H52O8P
#105: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#106: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#107: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#108: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Euglena gracilis respirasome supercomplex I+III2+IVCOMPLEX#1-#890NATURAL
2Euglena gracilis respirasome supercomplex I+III2+IVCOMPLEX#1-#891NATURAL
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Euglena gracilis (euglena)3039
32Euglena gracilis (euglena)3039
Buffer solutionpH: 7.4
Details: SEC buffer (30 mM Tris pH 7.4, 100 mM NaCl, 0.002% PMSF, 0.1% GDN (w/v), 1mM EDTA)
Buffer component
IDConc.NameFormulaBuffer-ID
130 mMTrimethylsilylTris1
2100 mMSodium chlorideNaCl1
30.002 %Phenylmethylsulfonyl fluoridePMSF1
40.1 %Glyco-diosgeninGDN1
51 mMEthylene diamine tetraacetic acidEDTA1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7.8 sec. / Electron dose: 51.5 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9807
Image scansWidth: 4096 / Height: 4096

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM software
IDNameVersionCategory
1crYOLO1.6.0particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7PHENIX1.20.1model fitting
8Coot0.9.6model fitting
10cryoSPARCv3.3.2initial Euler assignment
11cryoSPARCv3.3.2final Euler assignment
12cryoSPARCv3.3.2classification
13v3.3.23D reconstruction
14PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3232325
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 345048 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 50.38 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0056189880
ELECTRON MICROSCOPYf_angle_d0.5714257268
ELECTRON MICROSCOPYf_chiral_restr0.043427637
ELECTRON MICROSCOPYf_plane_restr0.004932427
ELECTRON MICROSCOPYf_dihedral_angle_d12.407171423

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more