[English] 日本語
Yorodumi
- PDB-9r01: Complex I from Ovis aries in presence of D1 inhibitor, Closed state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9r01
TitleComplex I from Ovis aries in presence of D1 inhibitor, Closed state
Components
  • (Mitochondrial complex I, ...) x 2
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 11
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 9
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 2
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 5
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • (NADH:ubiquinone oxidoreductase subunit ...) x 2
  • Acyl carrier protein
  • Complex I-23kD
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
  • NADH:ubiquinone oxidoreductase core subunit S3
KeywordsPROTON TRANSPORT / Complex I / inhibitor / respiration / proton pump / NADH:ubiquinone oxidoreductase / membrane protein / mitochondria
Function / homology
Function and homology information


myoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / positive regulation of macrophage chemotaxis / NADH:ubiquinone reductase (H+-translocating) / ubiquinone binding / mitochondrial ATP synthesis coupled electron transport / mitochondrial electron transport, NADH to ubiquinone / electron transport coupled proton transport / acyl binding / mitochondrial respiratory chain complex I assembly ...myoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / positive regulation of macrophage chemotaxis / NADH:ubiquinone reductase (H+-translocating) / ubiquinone binding / mitochondrial ATP synthesis coupled electron transport / mitochondrial electron transport, NADH to ubiquinone / electron transport coupled proton transport / acyl binding / mitochondrial respiratory chain complex I assembly / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / positive regulation of myoblast differentiation / acyl carrier activity / quinone binding / ATP synthesis coupled electron transport / positive regulation of lamellipodium assembly / reactive oxygen species metabolic process / aerobic respiration / transcription coregulator activity / electron transport chain / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / mitochondrial membrane / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / chromatin / positive regulation of transcription by RNA polymerase II / mitochondrion / membrane / metal ion binding / nucleus
Similarity search - Function
Akirin / 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 flavoprotein 3 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial ...Akirin / 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 flavoprotein 3 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH:ubiquinone oxidoreductase, chain 2 / NADH dehydrogenase subunit 2, C-terminal / : / : / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH dehydrogenase subunit 2 C-terminus / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / Zinc finger, CHCC-type / Zinc-finger domain / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / GRIM-19 / GRIM-19 protein / NDUFA6, LYR domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / : / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / : / SLBB domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain I / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NAD(P)H-quinone oxidoreductase subunit D/H / Complex 1 LYR protein domain / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH ubiquinone oxidoreductase, F subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / Complex 1 protein (LYR family) / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH-quinone oxidoreductase, chain 5-like / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / : / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / : / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / : / MYRISTIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE ...1,2-Distearoyl-sn-glycerophosphoethanolamine / : / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / : / MYRISTIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / Chem-ZMP / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / Complex I-15 kDa / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / : / : / : / : / : / : / : / : / : / : / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / : / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 6 / Acyl carrier protein / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsSazanov, L. / Petrova, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)5549-06, RO1 AG 062135, UG3/UH3NS 113776-2 United States
Citation
Journal: To Be Published
Title: Complex I from Ovis aries in presence of D1 inhibitor
Authors: Sazanov, L. / Petrova, O.
#1: Journal: To Be Published
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Sazanov, L.
History
DepositionApr 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADH-ubiquinone oxidoreductase chain 3
H: NADH-ubiquinone oxidoreductase chain 1
J: NADH-ubiquinone oxidoreductase chain 6
K: NADH-ubiquinone oxidoreductase chain 4L
L: NADH-ubiquinone oxidoreductase chain 5
M: NADH-ubiquinone oxidoreductase chain 4
N: NADH-ubiquinone oxidoreductase chain 2
V: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
W: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
X: Acyl carrier protein
Y: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Z: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
k: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
l: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
m: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
n: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
o: NADH dehydrogenase [ubiquinone] 1 subunit C2
p: NADH:ubiquinone oxidoreductase subunit B4
q: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
r: Mitochondrial complex I, B17 subunit
s: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
t: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
u: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial
v: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
w: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
x: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
y: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
z: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
1: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
2: Mitochondrial complex I, 24 kDa subunit
3: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
5: NADH:ubiquinone oxidoreductase core subunit S3
6: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
9: Complex I-23kD
a: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
b: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
c: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
d: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
e: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
f: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
g: NADH:ubiquinone oxidoreductase subunit A6
h: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
i: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
j: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,053,32982
Polymers1,032,93045
Non-polymers20,39937
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

+
NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules AHJKLMN

#1: Protein NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 13106.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: O78753, NADH:ubiquinone reductase (H+-translocating)
#2: Protein NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 35884.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: O78747, NADH:ubiquinone reductase (H+-translocating)
#3: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 19126.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: O78757, NADH:ubiquinone reductase (H+-translocating)
#4: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 10868.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: O78754, NADH:ubiquinone reductase (H+-translocating)
#5: Protein NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 68438.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: O78756, NADH:ubiquinone reductase (H+-translocating)
#6: Protein NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 52086.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: O78755, NADH:ubiquinone reductase (H+-translocating)
#7: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 39149.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: O78748, NADH:ubiquinone reductase (H+-translocating)

+
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 11 types, 11 molecules VYkmqzdefhi

#8: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / Complex I-B14.7 / NADH-ubiquinone oxidoreductase subunit B14.7


Mass: 14636.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A8V6VBD6
#11: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8


Mass: 20008.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A8V6W0E9
#13: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial


Mass: 40557.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A8V6WD49
#15: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Complex I-B9 / NADH-ubiquinone oxidoreductase B9 subunit


Mass: 9325.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A8V6UZQ8
#19: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13


Mass: 16766.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P3E975
#28: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Complex I-MWFE / NADH-ubiquinone oxidoreductase MWFE subunit


Mass: 8211.519 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P9FRJ5
#39: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / Complex I-39kD / NADH-ubiquinone oxidoreductase 39 kDa subunit


Mass: 43025.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A8V6VJX1
#40: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 11097.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A8V6WE19
#41: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / Complex I subunit B13 / Complex I-13kD-B / NADH-ubiquinone oxidoreductase 13 kDa-B subunit


Mass: 13287.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A8V6VT05
#43: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / Complex I-B14.5a / NADH-ubiquinone oxidoreductase subunit B14.5a


Mass: 12425.239 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P3E9B7
#44: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 17115.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A8N7XJ18

+
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 9 types, 9 molecules WZnstuvwy

#9: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / Complex I-SGDH / NADH-ubiquinone oxidoreductase SGDH subunit


Mass: 21614.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A8V6WJW2
#12: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / Complex I-PDSW / NADH-ubiquinone oxidoreductase PDSW subunit


Mass: 20880.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A7M4DUF5
#16: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Complex I-B12 / NADH-ubiquinone oxidoreductase B12 subunit


Mass: 11146.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P7DQB1
#21: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Complex I-B18 / NADH-ubiquinone oxidoreductase B18 subunit


Mass: 16413.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A8V6V740
#22: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Complex I-B22 / NADH-ubiquinone oxidoreductase B22 subunit


Mass: 21779.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A8V6VHV8
#23: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / Complex I-AGGG / NADH-ubiquinone oxidoreductase AGGG subunit


Mass: 12226.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A8N7XJB4
#24: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ASHI / NADH-ubiquinone oxidoreductase ASHI subunit


Mass: 21752.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5Q1B0
#25: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / Complex I-ESSS / NADH-ubiquinone oxidoreductase ESSS subunit


Mass: 17410.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A8V6VZU3
#27: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / Complex I-MNLL / NADH-ubiquinone oxidoreductase MNLL subunit


Mass: 7075.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A7M4DUG1

+
Protein , 4 types, 5 molecules Xj359

#10: Protein Acyl carrier protein


Mass: 10032.462 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5NQT7
#31: Protein NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial


Mass: 79519.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A8V6WEB9
#33: Protein NADH:ubiquinone oxidoreductase core subunit S3


Mass: 30384.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PB27
#35: Protein Complex I-23kD / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8 / mitochondrial / NADH-ubiquinone ...NADH dehydrogenase [ubiquinone] iron-sulfur protein 8 / mitochondrial / NADH-ubiquinone oxidoreductase 23 kDa subunit


Mass: 24496.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P3TFB2

+
NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 5 types, 5 molecules l46bc

#14: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Complex I-15 kDa / NADH-ubiquinone oxidoreductase 15 kDa subunit


Mass: 12605.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A836D7R1
#32: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / Complex I-49kD / NADH-ubiquinone oxidoreductase 49 kDa subunit


Mass: 52661.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P3DZ89
#34: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / Complex I-20kD / NADH-ubiquinone oxidoreductase 20 kDa subunit


Mass: 24622.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P7E5N1
#37: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial


Mass: 13457.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P7EX23
#38: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-18 kDa / NADH-ubiquinone oxidoreductase 18 kDa subunit


Mass: 19381.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PE07

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

#17: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2


Mass: 14431.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P9Q8
#26: Protein NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / Complex I-KFYI / NADH-ubiquinone oxidoreductase KFYI subunit


Mass: 8802.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P3EDV0

+
NADH:ubiquinone oxidoreductase subunit ... , 2 types, 2 molecules pg

#18: Protein NADH:ubiquinone oxidoreductase subunit B4


Mass: 15236.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QF73
#42: Protein NADH:ubiquinone oxidoreductase subunit A6


Mass: 16302.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QC06

+
Mitochondrial complex I, ... , 2 types, 2 molecules r2

#20: Protein Mitochondrial complex I, B17 subunit


Mass: 15565.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PZE3
#30: Protein Mitochondrial complex I, 24 kDa subunit


Mass: 27373.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5NRY1

+
NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules 1a

#29: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial


Mass: 50687.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: W5PUX0, NADH:ubiquinone reductase (H+-translocating)
#36: Protein NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / Complex I-9kD / NADH-ubiquinone oxidoreductase 9 kDa subunit


Mass: 11916.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P3E7B5

+
Non-polymers , 14 types, 37 molecules

#45: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#46: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#47: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#48: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#49: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#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-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#52: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#54: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#55: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#56: Chemical ChemComp-A1JBT / (7~{S})-7-[(2~{S})-1-(6-azanylpurin-3-yl)propan-2-yl]-3-methyl-6,7,8,9-tetrahydro-5~{a}~{H}-pyrano[4,3-b]chromen-1-one


Mass: 393.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23N5O3 / Feature type: SUBJECT OF INVESTIGATION
#57: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#58: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3

+
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Composite map of Complex I from Ovis aries in presence of D1 inhibitor, Closed state
Type: COMPLEX / Entity ID: #1-#44 / Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: YES
Source (natural)Organism: Ovis aries (sheep)
Buffer solutionpH: 7.4 / Details: 50mM NaCl, 1mM EDTA, 0.02% LMNG
Buffer componentConc.: 20 mM / Name: Hepes / Formula: C8H18N2O4S
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

-
Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 3.39 sec. / Electron dose: 90 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4167

-
Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
4CTFFINDCTF correction
13PHENIX1.19_4092:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 448410
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50108 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6ZKK

6zkk


Accession code: 6ZKK / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00568955
ELECTRON MICROSCOPYf_angle_d0.72593381
ELECTRON MICROSCOPYf_dihedral_angle_d9.5249944
ELECTRON MICROSCOPYf_chiral_restr0.04910181
ELECTRON MICROSCOPYf_plane_restr0.00611819

+
About Yorodumi

-
News

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

New format data for meta-information of EMDB entries

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

Related info.:EMDB header

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

-
Aug 12, 2020. Covid-19 info

Covid-19 info

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

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

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

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

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

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

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

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

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

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

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

+
Jul 12, 2017. Major update of PDB

Major update of PDB

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

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

-
Yorodumi

Thousand views of thousand structures

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

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

Read more