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- PDB-7ard: Cryo-EM structure of Polytomella Complex-I (complete composition) -

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Basic information

Entry
Database: PDB / ID: 7ard
TitleCryo-EM structure of Polytomella Complex-I (complete composition)
Components
  • (unknown) x 2
  • 13 kDa
  • 15 kDa
  • 18 kDa
  • 24 kDa
  • 39 kDa
  • 51 kDa
  • 75 kDa
  • AGGG
  • ASHI
  • B12
  • B13
  • B14
  • B14.5a
  • B14.5b
  • B14.7
  • B15
  • B16.6
  • B17.2
  • B18
  • B8
  • B9
  • C1-FDX
  • CA2
  • CA3
  • CAL
  • Complex I-B22
  • ESSS
  • KFYI
  • MNLL
  • MWFE
  • ND1
  • ND2
  • ND3
  • ND4
  • ND4L
  • ND5
  • ND6
  • ND7
  • ND9
  • NUOP4
  • NUOP5
  • NUOP7
  • NUOP8
  • PDSW
  • PGIV
  • PSST
  • SDAP1
  • SDAP2
  • TYKY
KeywordsELECTRON TRANSPORT / Complex-I
Function / homology
Function and homology information


mitochondrial electron transport, NADH to ubiquinone / respirasome / mitochondrial inner membrane
Similarity search - Function
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Complex 1 LYR protein domain / Complex 1 protein (LYR family)
Similarity search - Domain/homology
Chem-8Q1 / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / Chem-PC7 / PHOSPHATIDYLETHANOLAMINE / IRON/SULFUR CLUSTER / Complex I-B22
Similarity search - Component
Biological speciesPolytomella sp. Pringsheim 198.80 (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsKlusch, N. / Kuehlbrandt, W. / Yildiz, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society1 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 1.0Dec 8, 2021Provider: repository / Type: Initial release

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-11880
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Structure viewerMolecule:
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Assembly

Deposited unit
A: ND3
B: PSST
C: ND9
D: ND7
E: 24 kDa
F: 51 kDa
G: 75 kDa
H: ND1
I: TYKY
J: ND6
K: ND4L
L: ND5
M: ND4
N: ND2
O: C1-FDX
P: 39 kDa
Q: 18 kDa
R: 13 kDa
S: B8
T: SDAP1
U: SDAP2
V: B13
W: B14
X: PGIV
Y: B14.7
Z: B16.6
a: MWFE
b: B9
c: KFYI
d: B14.5b
e: 15 kDa
f: MNLL
g: ESSS
h: NUOP4
i: NUOP5
j: AGGG
k: B12
l: ASHI
m: B15
n: Complex I-B22
o: B18
p: PDSW
q: B17.2
r: B14.5a
s: NUOP7
t: NUOP8
u: unknown
w: unknown
x: CAL
y: CA2
z: CA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,095,46983
Polymers1,072,85951
Non-polymers22,61032
Water14,088782
1


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

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Components

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Protein , 49 types, 49 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#1: Protein ND3


Mass: 17828.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#2: Protein PSST /


Mass: 18158.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#3: Protein ND9


Mass: 25689.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#4: Protein ND7


Mass: 45263.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#5: Protein 24 kDa


Mass: 30186.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#6: Protein 51 kDa


Mass: 51593.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#7: Protein 75 kDa


Mass: 77364.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#8: Protein ND1


Mass: 31829.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#9: Protein TYKY


Mass: 26140.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#10: Protein ND6


Mass: 15938.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#11: Protein ND4L


Mass: 13836.075 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#12: Protein ND5


Mass: 58317.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#13: Protein ND4


Mass: 48407.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#14: Protein ND2


Mass: 41939.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#15: Protein C1-FDX


Mass: 23115.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#16: Protein 39 kDa


Mass: 41233.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#17: Protein 18 kDa


Mass: 20800.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#18: Protein 13 kDa


Mass: 14346.163 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#19: Protein B8


Mass: 10509.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#20: Protein SDAP1


Mass: 13409.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#21: Protein SDAP2


Mass: 13393.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#22: Protein B13


Mass: 17745.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#23: Protein B14


Mass: 16134.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#24: Protein PGIV


Mass: 11758.452 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#25: Protein B14.7


Mass: 22521.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#26: Protein B16.6


Mass: 16261.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#27: Protein MWFE


Mass: 8504.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#28: Protein B9


Mass: 4613.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#29: Protein KFYI


Mass: 12554.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#30: Protein B14.5b


Mass: 9574.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#31: Protein 15 kDa


Mass: 8915.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#32: Protein MNLL


Mass: 13507.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#33: Protein ESSS


Mass: 19333.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#34: Protein NUOP4


Mass: 9145.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#35: Protein NUOP5


Mass: 15118.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#36: Protein AGGG


Mass: 7422.140 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#37: Protein B12


Mass: 6332.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#38: Protein ASHI


Mass: 16986.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#39: Protein B15


Mass: 16276.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#40: Protein Complex I-B22 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH-ubiquinone oxidoreductase B22 subunit


Mass: 14418.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: A0A024FSS5
#41: Protein B18


Mass: 10292.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#42: Protein PDSW


Mass: 18434.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#43: Protein B17.2


Mass: 18178.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#44: Protein B14.5a


Mass: 13827.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#45: Protein NUOP7


Mass: 13476.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#46: Protein NUOP8


Mass: 15743.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#49: Protein CAL


Mass: 31348.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#50: Protein CA2 /


Mass: 33201.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#51: Protein CA3


Mass: 24150.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)

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Protein/peptide , 2 types, 2 molecules uw

#47: Protein/peptide unknown


Mass: 4273.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#48: Protein/peptide unknown


Mass: 3507.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)

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Non-polymers , 10 types, 814 molecules

#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.: 7 / Source method: obtained synthetically / Formula: C42H85NO8P / Comment: phospholipid*YM
#53: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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


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


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


Mass: 734.039 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#57: 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
#58: 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
#59: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#60: 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
#61: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 782 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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 Polytomella Complex-I (complete composition)
Type: COMPLEX / Entity ID: #1-#51 / Source: NATURAL
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Buffer solutionpH: 7.4
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: 64 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: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42350 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00471423
ELECTRON MICROSCOPYf_angle_d0.71596708
ELECTRON MICROSCOPYf_dihedral_angle_d11.00510425
ELECTRON MICROSCOPYf_chiral_restr0.04710601
ELECTRON MICROSCOPYf_plane_restr0.00612183

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