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- PDB-7ar7: Cryo-EM structure of Arabidopsis thaliana complex-I (open conform... -

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Entry
Database: PDB / ID: 7ar7
TitleCryo-EM structure of Arabidopsis thaliana complex-I (open conformation)
Components
  • (Acyl carrier protein ...) x 2
  • (Gamma carbonic anhydrase ...) x 2
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 6
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 6
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 2
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 8
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • (Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 2
  • AT2G31490 protein
  • At1g67350
  • At2g46540/F11C10.23
  • At4g16450
  • B14.5a
  • ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein
  • Excitatory amino acid transporter
  • Gamma carbonic anhydrase-like 2, mitochondrial
  • Transmembrane protein
  • Uncharacterized protein At2g27730, mitochondrial
  • unknown
KeywordsELECTRON TRANSPORT / Complex-I Arabidopsis
Function / homology
Function and homology information


anther dehiscence / vegetative to reproductive phase transition of meristem / cold acclimation / NADH dehydrogenase complex / Lyases; Carbon-oxygen lyases; Hydro-lyases / photorespiration / embryo development ending in seed dormancy / response to abscisic acid / plant-type vacuole / NADH dehydrogenase activity ...anther dehiscence / vegetative to reproductive phase transition of meristem / cold acclimation / NADH dehydrogenase complex / Lyases; Carbon-oxygen lyases; Hydro-lyases / photorespiration / embryo development ending in seed dormancy / response to abscisic acid / plant-type vacuole / NADH dehydrogenase activity / respiratory chain complex I / ubiquinone binding / regulation of reactive oxygen species metabolic process / cobalt ion binding / electron transport coupled proton transport / response to osmotic stress / plastid / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / protein homotrimerization / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / respirasome / aerobic respiration / response to salt stress / respiratory electron transport chain / chloroplast / mitochondrial membrane / carbonate dehydratase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / peroxisome / fatty acid biosynthetic process / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / carbohydrate metabolic process / mitochondrial matrix / copper ion binding / nucleolus / mitochondrion / zinc ion binding / extracellular region / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Putative NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / At2g27730-like / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 ...Putative NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / At2g27730-like / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / Soluble ligand binding domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / SLBB domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / Zinc finger, CHCC-type / Zinc-finger domain / Hexapeptide repeat / GRIM-19 / GRIM-19 protein / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NDUFA6, LYR domain / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / 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] (complex I), alpha subcomplex, subunit 2 / NDUFB9, LYR domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Bacterial transferase hexapeptide (six repeats) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / 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:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH dehydrogenase, subunit C / NADH ubiquinone oxidoreductase, F subunit / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH-quinone oxidoreductase, chain M/4 / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / Trimeric LpxA-like superfamily / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / CHCH / NuoE domain / CHCH domain / NADH:ubiquinone oxidoreductase / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter
Similarity search - Domain/homology
Chem-8Q1 / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / Chem-PC7 / Chem-PGT / 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / PHOSPHATIDYLETHANOLAMINE / IRON/SULFUR CLUSTER / Phosphatidylinositol ...Chem-8Q1 / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / Chem-PC7 / Chem-PGT / 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / PHOSPHATIDYLETHANOLAMINE / IRON/SULFUR CLUSTER / Phosphatidylinositol / Ubiquinone-9 / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A / Acyl carrier protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-A / NADH-ubiquinone oxidoreductase chain 5 / Acyl carrier protein 1, mitochondrial / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial / At4g16450 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A / Transmembrane protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Excitatory amino acid transporter / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / Gamma carbonic anhydrase 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Gamma carbonic anhydrase 1, mitochondrial / At1g67350 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / At2g31490 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein / Gamma carbonic anhydrase-like 2, mitochondrial / At2g46540/F11C10.23 / Uncharacterized protein At2g27730, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsKlusch, N. / Kuelbrandt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Plant Cell / Year: 2021
Title: A ferredoxin bridge connects the two arms of plant mitochondrial complex I.
Authors: Niklas Klusch / Jennifer Senkler / Özkan Yildiz / Werner Kühlbrandt / Hans-Peter Braun /
Abstract: Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two ...Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two arms, which form a conserved L-shape. We report the structures of the intact, 47-subunit mitochondrial complex I from Arabidopsis thaliana and the 51-subunit complex I from the green alga Polytomella sp., both at around 2.9 Å resolution. In both complexes, a heterotrimeric γ-carbonic anhydrase domain is attached to the membrane arm on the matrix side. Two states are resolved in A. thaliana complex I, with different angles between the two arms and different conformations of the ND1 (NADH dehydrogenase subunit 1) loop near the quinol binding site. The angle appears to depend on a bridge domain, which links the peripheral arm to the membrane arm and includes an unusual ferredoxin. We propose that the bridge domain participates in regulating the activity of plant complex I.
History
DepositionOct 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: NADH-ubiquinone oxidoreductase chain 3
B: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
C: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3
D: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2
E: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
F: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
G: NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial
H: NADH-ubiquinone oxidoreductase chain 1
I: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial
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
P: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
Q: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
R: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
S: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
T: Acyl carrier protein 1, mitochondrial
U: Acyl carrier protein 2, mitochondrial
V: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial
W: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
X: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B
Z: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A
a: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
b: At2g46540/F11C10.23
c: Transmembrane protein
d: Excitatory amino acid transporter
e: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-A
f: At4g16450
g: ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein
i: At1g67350
j: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2
k: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A
l: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
m: AT2G31490 protein
n: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
o: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
p: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B
q: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
r: B14.5a
u: unknown
v: Uncharacterized protein At2g27730, mitochondrial
x: Gamma carbonic anhydrase-like 2, mitochondrial
y: Gamma carbonic anhydrase 2, mitochondrial
z: Gamma carbonic anhydrase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)879,15970
Polymers866,66246
Non-polymers12,49824
Water0
1


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

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Components

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

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


Mass: 13941.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P92533, NADH:ubiquinone reductase (H+-translocating)
#8: Protein NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 35888.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P92558, NADH:ubiquinone reductase (H+-translocating)
#10: Protein NADH-ubiquinone oxidoreductase chain 6


Mass: 23690.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: A0A2P2CLG1, NADH:ubiquinone reductase (H+-translocating)
#11: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 9892.114 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q04614, NADH:ubiquinone reductase (H+-translocating)
#12: Protein NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 68214.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P29388, NADH:ubiquinone reductase (H+-translocating)
#13: Protein NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 55001.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P93313, NADH:ubiquinone reductase (H+-translocating)
#14: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 54161.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: O05000, NADH:ubiquinone reductase (H+-translocating)

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NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 8 types, 8 molecules BCDGIQRe

#2: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial


Mass: 17794.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q42577, NADH:ubiquinone reductase (H+-translocating)
#3: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / NADH dehydrogenase subunit 9


Mass: 22366.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q95748, NADH:ubiquinone reductase (H+-translocating)
#4: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 / NADH dehydrogenase subunit 7


Mass: 43889.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P93306, NADH:ubiquinone reductase (H+-translocating)
#7: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial / Protein EMBRYO DEFECTIVE 1467


Mass: 75100.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q9FGI6, NADH:ubiquinone reductase (H+-translocating)
#9: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial


Mass: 19723.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q42599, NADH:ubiquinone reductase (H+-translocating)
#16: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Protein FROSTBITE1


Mass: 13290.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FJW4
#17: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial


Mass: 6928.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9M9M6
#29: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-A


Mass: 7847.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O82238

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NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules EF

#5: Protein NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial


Mass: 21411.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: O22769, NADH:ubiquinone reductase (H+-translocating)
#6: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial


Mass: 48087.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q9FNN5, NADH:ubiquinone reductase (H+-translocating)

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

#15: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial


Mass: 36400.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SK66
#18: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 10433.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FIJ2
#22: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6


Mass: 15102.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LHI0
#23: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B


Mass: 11036.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LGE7
#24: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A / Protein MATERNAL EFFECT EMBRYO ARREST 4


Mass: 14150.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8RWA7
#25: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1


Mass: 6717.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9C9Z5

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Acyl carrier protein ... , 2 types, 2 molecules TU

#19: Protein Acyl carrier protein 1, mitochondrial / MtACP-1 / ACP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 9526.669 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P53665
#20: Protein Acyl carrier protein 2, mitochondrial / MtACP-2 / ACP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 9232.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O80800

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Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 2 types, 2 molecules Vq

#21: Protein Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial


Mass: 16006.163 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FLX7
#40: Protein Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 7325.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9M9M9

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Protein/peptide , 4 types, 4 molecules bruv

#26: Protein/peptide At2g46540/F11C10.23 / Expressed protein / F11C10.23/F11C10.23 / Fiber


Mass: 4240.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9ZPY5
#41: Protein/peptide B14.5a


Mass: 1245.536 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#42: Protein/peptide unknown


Mass: 2571.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#43: Protein/peptide Uncharacterized protein At2g27730, mitochondrial


Mass: 3208.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9ZUX4

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Protein , 7 types, 7 molecules cdfgimx

#27: Protein Transmembrane protein /


Mass: 8811.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8VZT9
#28: Protein Excitatory amino acid transporter / Uncharacterized protein At4g20150


Mass: 8457.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q94AL6
#30: Protein At4g16450 / NADH-ubiquinone oxidoreductase / Uncharacterized protein At4g16450


Mass: 10720.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q84W12
#31: Protein ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein


Mass: 8319.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SLC8
#32: Protein At1g67350 / F1N21.17 / NADH-ubiquinone oxidoreductase


Mass: 10493.911 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FYF8
#36: Protein AT2G31490 protein / At2g31490 / Expressed protein / Neuronal acetylcholine receptor subunit alpha-5 / Uncharacterized ...At2g31490 / Expressed protein / Neuronal acetylcholine receptor subunit alpha-5 / Uncharacterized protein At2g31490


Mass: 8003.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SIQ8
#44: Protein Gamma carbonic anhydrase-like 2, mitochondrial / AtCAL2 / GAMMA CAL2


Mass: 23542.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SMN1

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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 6 types, 6 molecules jklnop

#33: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2


Mass: 5878.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LDK3
#34: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A


Mass: 5337.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O64725
#35: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial


Mass: 5074.872 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FGK0
#37: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / B22 subunit of eukaryotic mitochondrial complex I / Complex I-B22 / AtCIB22 / CI-B22 / NADH- ...B22 subunit of eukaryotic mitochondrial complex I / Complex I-B22 / AtCIB22 / CI-B22 / NADH-ubiquinone oxidoreductase B22 subunit


Mass: 12864.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q945M1
#38: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7


Mass: 9509.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SKC9
#39: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B


Mass: 11070.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q94C12

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Gamma carbonic anhydrase ... , 2 types, 2 molecules yz

#45: Protein Gamma carbonic anhydrase 2, mitochondrial / AtCA2 / GAMMA CA2 / Transcription factor APFI


Mass: 28947.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q9C6B3, Lyases; Carbon-oxygen lyases; Hydro-lyases
#46: Protein Gamma carbonic anhydrase 1, mitochondrial / AtCA1 / GAMMA CA1


Mass: 25202.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q9FWR5, Lyases; Carbon-oxygen lyases; Hydro-lyases

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Non-polymers , 13 types, 24 molecules

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


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


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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#50: 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
#51: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 734.039 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#52: Chemical ChemComp-PC7 / (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / PHOSPHATIDYLCHOLINE / 1-PALMITOYL-2-STEAROYL-PC / Phosphatidylcholine


Mass: 763.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H85NO8P / Comment: phospholipid*YM
#53: Chemical ChemComp-LMN / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside


Mass: 1005.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H88O22 / Comment: detergent*YM
#54: 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
#55: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#56: 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.: 2 / Source method: obtained synthetically / Formula: C23H45N2O8PS
#57: Chemical ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT) / Phosphatidylglycerol


Mass: 751.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
#58: Chemical ChemComp-PSF / 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / PHOSPHATIDYLSERINE / Phosphatidylserine


Mass: 455.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34NO10P
#59: Chemical ChemComp-T7X / Phosphatidylinositol / Phosphatidylinositol


Mass: 887.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H83O13P

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Cryo-EM structure of Arabidopsis thaliana complex-I (open conformation)
Type: COMPLEX / Entity ID: #1-#46 / Source: NATURAL
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.8
SpecimenEmbedding 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 43 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48933 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00362114
ELECTRON MICROSCOPYf_angle_d0.61984110
ELECTRON MICROSCOPYf_dihedral_angle_d7.0658574
ELECTRON MICROSCOPYf_chiral_restr0.0429322
ELECTRON MICROSCOPYf_plane_restr0.00510583

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