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- PDB-8j9j: Cryo-EM structure of Euglena gracilis complex I, NADH state -

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Basic information

Entry
Database: PDB / ID: 8j9j
TitleCryo-EM structure of Euglena gracilis complex I, NADH state
Components
  • NADH-ubiquinone oxidoreductase chain 4
  • ND1
  • ND2A
  • ND2B
  • ND3
  • ND4L
  • ND5
  • NDUCA1
  • NDUCA2
  • NDUCA3
  • NDUEG1
  • NDUEG10
  • NDUEG11
  • NDUEG12
  • NDUEG13
  • NDUEG2
  • NDUEG3
  • NDUEG4
  • NDUEG5
  • NDUEG6
  • NDUEG7
  • NDUEG8
  • NDUFA11
  • NDUFA12
  • NDUFA13
  • NDUFA1NADH dehydrogenase (ubiquinone), alpha 1
  • 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
  • UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK
KeywordsELECTRON TRANSPORT / Electron transport chain / respiratory complex / membrane protein / Euglena gracilis
Function / homology
Function and homology information


NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / respirasome / mitochondrial membrane
Similarity search - Function
NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / : / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / UBIQUINONE-10 ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / : / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / UBIQUINONE-10 / Chem-ZMP / NADH-ubiquinone oxidoreductase chain 4
Similarity search - Component
Biological speciesEuglena gracilis (euglena)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsWu, M.C. / He, Z.X. / Tian, H.T. / Hu, Y.Q. / Han, F.Z. / 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
DepositionMay 3, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1A: NDUFS1A
1B: NDUFS1B
2B: ND2B
4L: ND4L
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
C4: NDUFC2
E1: NDUEG1
E2: NDUEG2
E3: NDUEG3
E4: NDUEG4
E5: NDUEG5
E6: NDUEG6
E8: NDUEG8
EA: NDUEG10
EB: NDUEG11
EC: NDUEG12
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
S2: NDUFS2
S3: NDUFS3
S4: NDUFS4
S5: NDUFS5
S6: NDUFS6
S7: NDUFS7
S8: NDUFS8
U1: UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK
U2: UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK
V1: NDUFV1
V2: NDUFV2
E7: NDUEG7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,793,987126
Polymers1,737,59961
Non-polymers56,38865
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 58 types, 59 molecules 1A1B2B4LA1A2A3A5A6A7A8A9ABACALAMANB2B3B4B5B6B7B8B9BLBMC4E1E2...

#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 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.
#5: Protein NDUFA1 / NADH dehydrogenase (ubiquinone), alpha 1


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.
#6: 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.
#7: 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.
#8: 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.
#9: 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.
#10: 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.
#11: 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.
#12: 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.
#13: 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.
#14: 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.
#15: 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.
#16: 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.
#17: 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.
#18: 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.
#19: 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.
#20: 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.
#21: 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.
#22: 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.
#23: 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.
#24: 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.
#25: 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.
#26: 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.
#27: 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.
#28: 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.
#29: 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.
#30: Protein NDUEG2


Mass: 50515.348 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 NDUEG3


Mass: 46409.844 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 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.
#33: 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.
#34: 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.
#35: 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.
#36: 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.
#37: 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.
#38: Protein NDUEG12


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.
#39: 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.
#40: 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.
#41: 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.
#42: 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.
#43: 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.
#44: 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.
#45: 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.
#46: 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.
#47: 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
#48: 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.
#49: 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.
#50: 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.
#51: 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.
#52: 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.
#53: 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.
#54: 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.
#55: 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.
#57: 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.
#58: 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.
#59: 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.

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Protein/peptide , 1 types, 2 molecules U1U2

#56: Protein/peptide UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK


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

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Non-polymers , 12 types, 65 molecules

#60: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#61: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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


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


Mass: 790.145 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#64: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#65: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#66: 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
#67: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#68: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#69: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#70: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#71: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Euglena gracilis respiratory complex I, NADH state / Type: COMPLEX / Entity ID: #1-#55, #57-#59 / Source: NATURAL
Molecular weightValue: 1.5 MDa / Experimental value: NO
Source (natural)Organism: Euglena gracilis (euglena)
Buffer solutionpH: 7.4
Details: SEC-Q buffer (30 mM Tris pH 7.4, 200 mM NaCl, 1mM EDTA, 0.002% PMSF (w/v), 0.001% CHS (w/v), 0.007% LMNG (w/v))
Buffer component
IDConc.NameFormulaBuffer-ID
130 mMTrimethylsilylTris1
2200 mMSodium chlorideNaClSodium chloride1
31 mMEthylene diamine tetraacetic acidEDTAEthylenediaminetetraacetic acid1
40.002 %Phenylmethylsulfonyl fluoridePMSFPMSF1
50.001 %Cholesteryl hemisuccinateCHS1
60.007 %Lauryl maltose neopentyl glycolLMNG1
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 25mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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 FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 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 sec. / Electron dose: 61.5 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2949
Image scansWidth: 4096 / Height: 4096

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Processing

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
13cryoSPARCv3.3.23D reconstruction
14PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 468732
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76643 / 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: 49.47 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0031116516
ELECTRON MICROSCOPYf_angle_d0.509157802
ELECTRON MICROSCOPYf_chiral_restr0.040516947
ELECTRON MICROSCOPYf_plane_restr0.003919969
ELECTRON MICROSCOPYf_dihedral_angle_d12.275343938

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