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- PDB-5xtc: Cryo-EM structure of human respiratory complex I transmembrane arm -

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Entry
Database: PDB / ID: 5xtc
TitleCryo-EM structure of human respiratory complex I transmembrane arm
Components
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 6
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 11
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 2
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • Acyl carrier protein, mitochondrial
KeywordsELECTRON TRANSPORT / Homo sapiens / Oxidoreductase / Respiratory / Complex
Function / homology
Function and homology information


positive regulation of peptidase activity / response to light intensity / protein insertion into mitochondrial inner membrane / cellular response to oxygen levels / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Mitochondrial protein import / gliogenesis / Respiratory electron transport / neural precursor cell proliferation ...positive regulation of peptidase activity / response to light intensity / protein insertion into mitochondrial inner membrane / cellular response to oxygen levels / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Mitochondrial protein import / gliogenesis / Respiratory electron transport / neural precursor cell proliferation / NADH dehydrogenase activity / mitochondrial respirasome / NADH:ubiquinone reductase (H+-translocating) / oxygen sensor activity / protein lipoylation / Glyoxylate metabolism and glycine degradation / mitochondrial respiratory chain complex I / electron transport coupled proton transport / mitochondrial ATP synthesis coupled electron transport / acyl binding / cellular response to interferon-beta / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / acyl carrier activity / ATP synthesis coupled electron transport / response to hydroperoxide / ubiquinone binding / azurophil granule membrane / NADH dehydrogenase (ubiquinone) activity / cellular response to glucocorticoid stimulus / neurogenesis / quinone binding / ionotropic glutamate receptor binding / reactive oxygen species metabolic process / aerobic respiration / cellular response to retinoic acid / respirasome / extrinsic apoptotic signaling pathway / fatty acid binding / response to cocaine / negative regulation of intrinsic apoptotic signaling pathway / response to organonitrogen compound / cerebellum development / mitochondrial membrane / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / apoptotic signaling pathway / response to nicotine / sensory perception of sound / positive regulation of protein catabolic process / mitochondrial intermembrane space / response to organic cyclic compound / negative regulation of cell growth / fatty acid biosynthetic process / response to hydrogen peroxide / NAD binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / response to oxidative stress / in utero embryonic development / response to ethanol / postsynaptic density / response to hypoxia / electron transfer activity / aging / mitochondrial matrix / nuclear speck / neuron projection / negative regulation of transcription, DNA-templated / neuronal cell body / response to xenobiotic stimulus => GO:0009410 / dendrite / protein-containing complex binding / ubiquitin protein ligase binding / Neutrophil degranulation / calcium ion binding / protein kinase binding / endoplasmic reticulum / mitochondrion / integral component of membrane / nucleoplasm / ATP binding / plasma membrane / metal ion binding / cytoplasm
Similarity search - Function
NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / Helix Hairpins - #3510 / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH-ubiquinone oxidoreductase subunit 10 / NADH-ubiquinone oxidoreductase, subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-ubiquinone oxidoreductase MWFE subunit ...NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / Helix Hairpins - #3510 / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH-ubiquinone oxidoreductase subunit 10 / NADH-ubiquinone oxidoreductase, subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / GRIM-19 protein / GRIM-19 / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH:ubiquinone oxidoreductase, ESSS subunit / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase subunit 2 C-terminus / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase subunit 2, C-terminal / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH:ubiquinone oxidoreductase, chain 2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / Deoxynucleoside kinase / Deoxynucleoside kinase domain / NADH-quinone oxidoreductase, chain 5-like / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH:ubiquinone oxidoreductase / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH dehydrogenase / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / CHCH / CHCH domain / [NiFe]-hydrogenase, large subunit / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix Hairpins / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 ...NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Chem-8Q1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PLX / CARDIOLIPIN / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 1 / Acyl carrier protein, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH-ubiquinone oxidoreductase chain 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGu, J. / Wu, M. / Yang, M.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology2016YFA0501100 China
Ministry of Science and Technology2017YFA0504600 China
National Science Fund for Distinguished Young Scholars31625008 China
National Natural Science Foundation of China21532004 China
National Natural Science Foundation of China31570733 China
CitationJournal: Cell / Year: 2017
Title: Architecture of Human Mitochondrial Respiratory Megacomplex IIIIIV.
Authors: Runyu Guo / Shuai Zong / Meng Wu / Jinke Gu / Maojun Yang /
Abstract: The respiratory megacomplex represents the highest-order assembly of respiratory chain complexes, and it allows mitochondria to respond to energy-requiring conditions. To understand its architecture, ...The respiratory megacomplex represents the highest-order assembly of respiratory chain complexes, and it allows mitochondria to respond to energy-requiring conditions. To understand its architecture, we examined the human respiratory chain megacomplex-IIIIIV (MCIIIIIV) with 140 subunits and a subset of associated cofactors using cryo-electron microscopy. The MCIIIIIV forms a circular structure with the dimeric CIII located in the center, where it is surrounded by two copies each of CI and CIV. Two cytochrome c (Cyt.c) molecules are positioned to accept electrons on the surface of the c state CIII dimer. Analyses indicate that CII could insert into the gaps between CI and CIV to form a closed ring, which we termed the electron transport chain supercomplex. The structure not only reveals the precise assignment of individual subunits of human CI and CIII, but also enables future in-depth analysis of the electron transport chain as a whole.
History
DepositionJun 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 6, 2017Group: Data processing / Database references / Category: citation / em_software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_software.name
Revision 1.3Nov 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: cell / pdbx_validate_close_contact ...cell / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
Q: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
S: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
U: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
V: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
W: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
X: Acyl carrier protein, mitochondrial
Y: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial
Z: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
a: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
b: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
c: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
d: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
e: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
f: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
g: NADH dehydrogenase [ubiquinone] 1 subunit C2
h: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
i: NADH-ubiquinone oxidoreductase chain 2
j: NADH-ubiquinone oxidoreductase chain 3
k: NADH-ubiquinone oxidoreductase chain 4L
l: NADH-ubiquinone oxidoreductase chain 5
m: NADH-ubiquinone oxidoreductase chain 6
n: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
o: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
p: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
r: NADH-ubiquinone oxidoreductase chain 4
s: NADH-ubiquinone oxidoreductase chain 1
u: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
v: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
w: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)561,09648
Polymers543,33529
Non-polymers17,76119
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area182270 Å2
ΔGint-1332 kcal/mol
Surface area178170 Å2

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Components

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NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 2 types, 2 molecules Qh

#1: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / Complex I-49kD / CI-49kD / NADH-ubiquinone oxidoreductase 49 kDa subunit


Mass: 5380.995 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 34-79 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: O75306, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#16: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Complex I-15 kDa / CI-15 kDa / NADH-ubiquinone oxidoreductase 15 kDa subunit


Mass: 12314.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43920

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 6 types, 6 molecules SUVWuw

#2: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Complex I-MWFE / CI-MWFE / NADH-ubiquinone oxidoreductase MWFE subunit


Mass: 8084.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15239
#3: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Complex I-B9 / CI-B9 / NADH-ubiquinone oxidoreductase B9 subunit


Mass: 9156.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95167
#4: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / Complex I-B14.7 / CI-B14.7 / NADH-ubiquinone oxidoreductase subunit B14.7


Mass: 14736.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q86Y39
#5: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / Cell death regulatory protein GRIM-19 / Complex I-B16.6 / CI-B16.6 / Gene associated with retinoic ...Cell death regulatory protein GRIM-19 / Complex I-B16.6 / CI-B16.6 / Gene associated with retinoic and interferon-induced mortality 19 protein / Gene associated with retinoic and IFN-induced mortality 19 protein / NADH-ubiquinone oxidoreductase B16.6 subunit


Mass: 13589.633 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 29-144 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0J0
#27: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / Complex I-19kD / CI-19kD / Complex I-PGIV / CI-PGIV / NADH-ubiquinone oxidoreductase 19 kDa subunit


Mass: 19853.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P51970
#29: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Complex I-42kD / CI-42kD / NADH-ubiquinone oxidoreductase 42 kDa subunit


Mass: 37200.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95299

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Protein , 1 types, 1 molecules X

#6: Protein Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 9845.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14561

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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules YZabcdenopv

#7: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / Complex I-AGGG / CI-AGGG / NADH-ubiquinone oxidoreductase AGGG subunit


Mass: 7468.270 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 39-97 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95178
#8: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Complex I-B12 / CI-B12 / NADH-ubiquinone oxidoreductase B12 subunit


Mass: 9261.605 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 10-89 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43676
#9: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / Complex I-SGDH / CI-SGDH / NADH-ubiquinone oxidoreductase SGDH subunit


Mass: 16573.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43674
#10: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Complex I-B17 / CI-B17 / NADH-ubiquinone oxidoreductase B17 subunit


Mass: 15517.228 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95139
#11: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ASHI / CI-ASHI / NADH-ubiquinone oxidoreductase ASHI subunit


Mass: 18267.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95169
#12: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / Complex I-PDSW / CI-PDSW / NADH-ubiquinone oxidoreductase PDSW subunit


Mass: 20721.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O96000
#13: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / Complex I-ESSS / CI-ESSS / NADH-ubiquinone oxidoreductase ESSS subunit / Neuronal protein 17.3 / p17.3


Mass: 11494.942 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 54-150 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NX14
#22: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / Complex I-MNLL / CI-MNLL / NADH-ubiquinone oxidoreductase MNLL subunit


Mass: 6741.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75438
#23: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / Complex I-B15 / CI-B15 / NADH-ubiquinone oxidoreductase B15 subunit


Mass: 15100.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95168
#24: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Complex I-B22 / CI-B22 / LYR motif-containing protein 3 / NADH-ubiquinone oxidoreductase B22 subunit


Mass: 21189.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y6M9
#28: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Cell adhesion protein SQM1 / Complex I-B18 / CI-B18 / NADH-ubiquinone oxidoreductase B18 subunit


Mass: 14997.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P17568

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NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules fg

#14: Protein/peptide NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / Complex I-KFYI / CI-KFYI / NADH-ubiquinone oxidoreductase KFYI subunit


Mass: 5704.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43677
#15: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2 / Complex I-B14.5b / CI-B14.5b / Human lung cancer oncogene 1 protein / HLC-1 / NADH-ubiquinone ...Complex I-B14.5b / CI-B14.5b / Human lung cancer oncogene 1 protein / HLC-1 / NADH-ubiquinone oxidoreductase subunit B14.5b


Mass: 14209.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95298

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NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules ijklmrs

#17: Protein NADH-ubiquinone oxidoreductase chain 2


Mass: 39007.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q4GRX1, UniProt: P03891*PLUS, NADH:ubiquinone reductase (H+-translocating)
#18: Protein NADH-ubiquinone oxidoreductase chain 3


Mass: 13147.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: B9EE38, UniProt: P03897*PLUS, NADH:ubiquinone reductase (H+-translocating)
#19: Protein NADH-ubiquinone oxidoreductase chain 4L


Mass: 10702.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: V9JN72, UniProt: P03901*PLUS, NADH:ubiquinone reductase (H+-translocating)
#20: Protein NADH-ubiquinone oxidoreductase chain 5


Mass: 67096.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: X5BVZ3, UniProt: P03915*PLUS, NADH:ubiquinone reductase (H+-translocating)
#21: Protein NADH-ubiquinone oxidoreductase chain 6


Mass: 18660.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q8HAX7, UniProt: P03923*PLUS, NADH:ubiquinone reductase (H+-translocating)
#25: Protein NADH-ubiquinone oxidoreductase chain 4


Mass: 51689.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: B2XJG5, UniProt: P03905*PLUS, NADH:ubiquinone reductase (H+-translocating)
#26: Protein NADH-ubiquinone oxidoreductase chain 1


Mass: 35621.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: H9PGF0, UniProt: P03886*PLUS, NADH:ubiquinone reductase (H+-translocating)

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Non-polymers , 4 types, 19 molecules

#30: Chemical
ChemComp-PLX / (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL


Mass: 767.132 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C42H89NO8P / Comment: phospholipid*YM
#31: 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.: 5 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#32: Chemical
ChemComp-PEE / 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / Discrete optimized protein energy


Mass: 749.073 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H83NO8P / Comment: DOPE, phospholipid*YM
#33: Chemical ChemComp-8Q1 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate / S-dodecanoyl-4'-phosphopantetheine


Mass: 540.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N2O8PS

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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: Human respiratory complex I transmembrane arm / Type: COMPLEX / Entity ID: #1-#29 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1EMAN2.1particle selection
2AutoEMation2image acquisition
4CTFFIND3CTF correction
7Coot0.8.2model fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
13PHENIX1.11.1model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 167761 / Symmetry type: POINT

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