[English] 日本語
Yorodumi
- PDB-6y79: Cryo-EM structure of a respiratory complex I F89A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y79
TitleCryo-EM structure of a respiratory complex I F89A mutant
Components
  • (Acyl carrier protein ...) x 2
  • Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)
KeywordsOXIDOREDUCTASE / Complex I / NADH dehydrogenase / Mitochondrion proton pumping / Ubiquinone
Function / homology
Function and homology information


NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / ubiquinone-6 biosynthetic process / protein import into mitochondrial matrix / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / acyl binding / acyl carrier activity ...NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / ubiquinone-6 biosynthetic process / protein import into mitochondrial matrix / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / acyl binding / acyl carrier activity / electron transport coupled proton transport / mitochondrial respiratory chain complex I assembly / integral component of mitochondrial inner membrane / mitochondrial electron transport, NADH to ubiquinone / ATP synthesis coupled electron transport / ubiquinone binding / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding / aerobic respiration / respirasome / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / catalytic activity / fatty acid biosynthetic process / mitochondrial intermembrane space / NAD binding / 4 iron, 4 sulfur cluster binding / FMN binding / mitochondrial inner membrane / response to oxidative stress / oxidation-reduction process / electron transfer activity / oxidoreductase activity / mitochondrion / membrane / integral component of membrane / metal ion binding
NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / [NiFe]-hydrogenase, large subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / 2Fe-2S ferredoxin-like superfamily / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily / ACP-like superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NAD(P)H-quinone oxidoreductase subunit D/H ...NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / [NiFe]-hydrogenase, large subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / 2Fe-2S ferredoxin-like superfamily / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily / ACP-like superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH-quinone oxidoreductase, subunit D superfamily / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone oxidoreductase 9.5kDa subunit / NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NADH-quinone oxidoreductase subunit E, N-terminal / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH dehydrogenase [ubiquinone] (complex I), 21kDa subunit, fungi / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH-ubiquinone oxidoreductase, subunit 10 / Zinc finger, CHCC-type / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NuoE domain / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / CHCH domain / 4Fe-4S dicluster domain / NADH ubiquinone oxidoreductase, 20 Kd subunit / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Zinc-finger domain / Phosphopantetheine attachment site / Complex1_LYR-like / GRIM-19 protein / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit / ETC complex I subunit conserved region / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH-ubiquinone oxidoreductase B12 subunit family / NADH-ubiquinone oxidoreductase subunit 10 / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Thioredoxin-like [2Fe-2S] ferredoxin / ETC complex I subunit conserved region / NADH dehydrogenase / Molybdopterin oxidoreductase / Proton-conducting membrane transporter / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NAD dependent epimerase/dehydratase family / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit / SLBB domain / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH-ubiquinone oxidoreductase MWFE subunit / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH-plastoquinone oxidoreductase, chain 5 / NADH:ubiquinone oxidoreductase / Acyl carrier protein (ACP) / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NAD-dependent epimerase/dehydratase / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH-quinone oxidoreductase, subunit D / NADH-ubiquinone oxidoreductase chain 4L/K / 2Fe-2S ferredoxin-type iron-sulfur binding domain / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Phosphopantetheine attachment site / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / Phosphopantetheine binding ACP domain / NADH ubiquinone oxidoreductase, F subunit / CHCH / NADH:ubiquinone oxidoreductase, subunit G
Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I) / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 6 / Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I) / NUCM protein ...Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I) / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 6 / Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I) / NUCM protein / Subunit NUHM of protein NADH:Ubiquinone Oxidoreductase (Complex I) / NUGM protein / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NUAM protein / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 2 / NUVM protein / YALI0A01419p / NUWM protein / Uncharacterized protein / Complex I-B14.7 / ETC complex I subunit conserved region-domain-containing protein / NADH-ubiquinone oxidoreductase / NADH dehydrogenase 1 beta subcomplex subunit 3 / Epimerase domain-containing protein / zf-CHCC domain-containing protein / Uncharacterized protein / Acyl carrier protein / GRIM-19 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Thioredoxin-like protein / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Uncharacterized protein / Uncharacterized protein / Acyl carrier protein / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / YALI0D10274p / YALI0A02651p / YALI0E23089p / NADH-ubiquinone oxidoreductase / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit N7BM / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / YALI0C03201p / YALI0D04939p / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Acyl carrier protein / YALI0D19030p / YALI0D24585p / Acyl carrier protein / Complex I-B14.7 / YALI0E28424p / YALI0E23749p / YALI0F14003p / YALI0D05467p / YALI0F02123p / YALI0D00737p / YALI0E29095p / YALI0F17248p / YALI0F00924p / YALI0F18359p / YALI0F06061p / YALI0A17946p / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / YALI0E28930p / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
Biological speciesYarrowia lipolytica (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsParey, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)ZI 552/4-2 Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of a respiratory complex I F89A mutant
Authors: Parey, K.
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10711
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)
B: Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)
C: Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I)
D: Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)
E: Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)
F: Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)
G: Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)
H: Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
I: Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)
J: Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)
K: Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)
L: Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I)
M: Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
O: Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I)
P: Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
Q: Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I)
R: Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)
S: Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)
U: Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
W: Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)
X: Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)
Y: Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)
Z: Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)
a: Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)
b: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
c: Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)
d: Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)
e: Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)
f: Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)
g: Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I)
h: Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)
i: Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)
j: Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)
n: Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)
1: Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I)
2: Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I)
3: Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I)
4: Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)
5: Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)
6: Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I)
8: Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)
9: Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,010,74286
Polymers978,47242
Non-polymers32,27044
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area301440 Å2
ΔGint-2025 kcal/mol
Surface area251070 Å2
MethodPISA

-
Components

+
Protein , 40 types, 40 molecules ABCDEFGHIJKLMPRSUWXYZabcdefghi...

#1: Protein Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 79088.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9UUU3, UniProt: F2Z6F1*PLUS, NADH dehydrogenase
#2: Protein Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 53829.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9UUU2, UniProt: F2Z660*PLUS, NADH:ubiquinone reductase (H+-translocating)
#3: Protein Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 52494.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9UUU1, UniProt: F2Z626*PLUS, NADH dehydrogenase
#4: Protein Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 9806.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NC63, UniProt: B5FVD3*PLUS
#5: Protein Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 42765.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371BY45, UniProt: Q6C7X4*PLUS
#6: Protein Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 16657.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371C5F3, UniProt: Q6C4W9*PLUS
#7: Protein Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 32389.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9UUU0, UniProt: F2Z6D7*PLUS, NADH dehydrogenase
#8: Protein Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 27247.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9UUT9, UniProt: F2Z6C0*PLUS, NADH dehydrogenase
#9: Protein Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 25682.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9UUT8, UniProt: F2Z619*PLUS, NADH dehydrogenase
#10: Protein Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 20849.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371CB65, UniProt: Q6C674*PLUS
#11: Protein Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 23455.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUT7, NADH dehydrogenase
#12: Protein Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I) / NADH dehydrogenase subunit 4L / subunit ND4L


Mass: 9815.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6D4, NADH:ubiquinone reductase (H+-translocating)
#13: Protein Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 15148.970 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6Q8Z5, UniProt: Q6C8J9*PLUS
#15: Protein Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I) / Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 14702.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N3C8, UniProt: Q6CI60*PLUS
#17: Protein Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 12902.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NDL1, UniProt: Q6C9Z1*PLUS
#18: Protein Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 28479.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q6ZY23, UniProt: F2Z673*PLUS, NADH dehydrogenase
#19: Protein Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 19355.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371C2D0, UniProt: Q6CGB4*PLUS
#20: Protein Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 14112.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PPE5, UniProt: B5FVF8*PLUS
#21: Protein Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 18588.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NKB4, UniProt: Q6C4A6*PLUS
#22: Protein Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 18656.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N7X0, UniProt: Q6CEK9*PLUS
#23: Protein Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 19772.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N3H5, UniProt: Q6CI10*PLUS
#24: Protein Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 17328.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8ND94, UniProt: Q6CA88*PLUS
#25: Protein Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 8059.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NGI5
#26: Protein Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 6948.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371C0F2, UniProt: B5FVE5*PLUS
#27: Protein Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 11039.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N596, UniProt: B5RSK3*PLUS
#28: Protein Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 7807.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NFX6
#29: Protein Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 9621.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PJS3, UniProt: Q6CD73*PLUS
#30: Protein Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 8921.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NJR0, UniProt: B5FVF3*PLUS
#31: Protein Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 16175.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N5V2, UniProt: Q6CG53*PLUS
#32: Protein Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 9793.966 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6Q311
#33: Protein Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 10494.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q6ZY24, UniProt: B5RSK9*PLUS, NADH dehydrogenase
#34: Protein Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 13523.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371CFV9, UniProt: Q6C1R9*PLUS
#35: Protein Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 38361.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5U3V2, UniProt: Q9B6E8*PLUS, NADH:ubiquinone reductase (H+-translocating)
#36: Protein Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 53353.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5U4R9, UniProt: Q9B6C8*PLUS, NADH:ubiquinone reductase (H+-translocating)
#37: Protein Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 14478.329 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5TMS4, UniProt: Q9B6C7*PLUS, NADH:ubiquinone reductase (H+-translocating)
#38: Protein Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 54506.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5TMP9, UniProt: Q9B6D6*PLUS, NADH:ubiquinone reductase (H+-translocating)
#39: Protein Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 73740.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5TF58, UniProt: Q9B6D3*PLUS, NADH:ubiquinone reductase (H+-translocating)
#40: Protein Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I) / NADH dehydrogenase subunit 6 / Subunit ND6


Mass: 20765.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6E9, NADH:ubiquinone reductase (H+-translocating)
#41: Protein Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 11219.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PKH9, UniProt: B5FVG1*PLUS
#42: Protein Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 10035.651 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NNZ0, UniProt: B5RSL7*PLUS

-
Acyl carrier protein ... , 2 types, 2 molecules OQ

#14: Protein Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 12053.585 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PXT9, UniProt: Q6C926*PLUS
#16: Protein Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 14444.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NG21, UniProt: Q6C7X2*PLUS

-
Non-polymers , 13 types, 44 molecules

#43: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#44: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#45: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#46: 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
#47: Chemical
ChemComp-3PE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / 3-SN-PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#48: Chemical ChemComp-LMN / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside


Mass: 1005.188 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C47H88O22 / Comment: detergent*YM
#49: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#50: 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
#51: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#52: 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
#53: Chemical ChemComp-UQ9 / Ubiquinone-9 / 2,3-dimethoxy-5-methyl-6-[(2E,6E,10E,14Z,18E,22E,26E,30Z)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,6,10,14,18 ,22,26,30,34-nonaen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 795.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H82O4
#54: Chemical
ChemComp-T7X / Phosphatidylinositol / Phosphatidylinositol


Mass: 887.128 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C47H83O13P
#55: Chemical ChemComp-PSC / (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE / PHOSPHATIDYLCHOLINE / 2-LINOLEOYL-1-PALMITOYL-SN-GYCEROL-3-PHOSPHOCHOLINE / Phosphatidylcholine


Mass: 759.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H81NO8P / Comment: phospholipid*YM

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Mitochondrial NADH:ubiquinone oxidoreductase / Type: COMPLEX / Entity ID: #1-#42 / Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Organism: Yarrowia lipolytica (yeast) / Strain: GB30
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris1
2100 mMsodium clorideNaClSodium chloride1
31 mMEDTAEthylenediaminetetraacetic acid1
40.025 %LMNG1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 283 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 FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: -2500 nm / Nominal defocus min: -1500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 51.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 2016
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 30 eV
Image scansMovie frames/image: 40

-
Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 479372
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143203 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 30 / Protocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 6RFR
RefinementHighest resolution: 3.2 Å
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0167573
ELECTRON MICROSCOPYf_angle_d1.3291341
ELECTRON MICROSCOPYf_dihedral_angle_d14.05140639
ELECTRON MICROSCOPYf_chiral_restr0.06510083
ELECTRON MICROSCOPYf_plane_restr0.00911398

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
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.

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