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- PDB-8qby: Respiratory complex I from Paracoccus denitrificans in MSP2N2 nan... -

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Basic information

Entry
Database: PDB / ID: 8qby
TitleRespiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs
Components
  • (NADH dehydrogenase subunit ...) x 3
  • (NADH-quinone ...) x 11
  • ETC complex I subunit conserved region
  • NADH:ubiquinone oxidoreductase 17.2 kD subunit
  • Protein-L-isoaspartate O-methyltransferase
  • Zinc finger CHCC-type domain-containing protein
KeywordsOXIDOREDUCTASE / Respiratory complex I / NADH:ubiquinone oxidoreductase / Nanodiscs
Function / homology
Function and homology information


NADH:ubiquinone reductase (H+-translocating) / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / : / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / respiratory chain complex I / NADH dehydrogenase activity / NADH dehydrogenase (ubiquinone) activity ...NADH:ubiquinone reductase (H+-translocating) / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / : / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / respiratory chain complex I / NADH dehydrogenase activity / NADH dehydrogenase (ubiquinone) activity / quinone binding / : / ATP synthesis coupled electron transport / electron transport chain / protein modification process / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / methylation / oxidoreductase activity / iron ion binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) / Protein-L-isoaspartate(D-aspartate) O-methyltransferase / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / SLBB domain / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Zinc finger, CHCC-type / Zinc-finger domain ...Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) / Protein-L-isoaspartate(D-aspartate) O-methyltransferase / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / SLBB domain / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Zinc finger, CHCC-type / Zinc-finger domain / 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 / 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 / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / 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 ubiquinone oxidoreductase, F subunit / NADH dehydrogenase, subunit C / 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 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / 2Fe-2S iron-sulfur cluster binding domain / 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 chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / 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 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / NADH:ubiquinone oxidoreductase / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Thioredoxin-like superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-P5S / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / UBIQUINONE-10 / NADH:ubiquinone oxidoreductase 17.2 kD subunit ...1,2-Distearoyl-sn-glycerophosphoethanolamine / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-P5S / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / UBIQUINONE-10 / NADH:ubiquinone oxidoreductase 17.2 kD subunit / ETC complex I subunit conserved region / Zinc finger CHCC-type domain-containing protein / NADH-quinone oxidoreductase subunit N / NADH dehydrogenase subunit M / NADH dehydrogenase subunit L / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase / NADH-quinone oxidoreductase subunit F / NADH dehydrogenase subunit E / NADH-quinone oxidoreductase subunit D / NADH-quinone oxidoreductase subunit C / NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit A / Protein-L-isoaspartate O-methyltransferase / NADH-quinone oxidoreductase chain 10
Similarity search - Component
Biological speciesParacoccus denitrificans PD1222 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsIvanov, B.S. / Bridges, H.R. / Hirst, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_00028/1 United Kingdom
CitationJournal: To Be Published
Title: Respiratory complex I from Paracoccus denitrificans
Authors: Ivanov, B.S. / Bridges, H.R. / Hirst, J. / Jarman, O.D.
History
DepositionAug 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
K: NADH-quinone oxidoreductase subunit K
G: NADH-quinone oxidoreductase
t: Protein-L-isoaspartate O-methyltransferase
I: NADH-quinone oxidoreductase subunit I
E: NADH dehydrogenase subunit E
N: NADH-quinone oxidoreductase subunit N
H: NADH-quinone oxidoreductase subunit H
F: NADH-quinone oxidoreductase subunit F
D: NADH-quinone oxidoreductase subunit D
q: NADH:ubiquinone oxidoreductase 17.2 kD subunit
A: NADH-quinone oxidoreductase subunit A
J: NADH-quinone oxidoreductase chain 10
R: Zinc finger CHCC-type domain-containing protein
Q: ETC complex I subunit conserved region
C: NADH-quinone oxidoreductase subunit C
B: NADH-quinone oxidoreductase subunit B
L: NADH dehydrogenase subunit L
M: NADH dehydrogenase subunit M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)614,70967
Polymers585,12118
Non-polymers29,58849
Water19,4561080
1


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

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Components

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NADH-quinone ... , 11 types, 11 molecules KGINHFDAJCB

#1: Protein NADH-quinone oxidoreductase subunit K / NADH dehydrogenase I subunit K / NADH dehydrogenase I / subunit 11 / NADH-quinone oxidoreductase ...NADH dehydrogenase I subunit K / NADH dehydrogenase I / subunit 11 / NADH-quinone oxidoreductase subunit 11 / NQO11 / NDH-1 subunit K / NDH-1


Mass: 10863.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B482, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#2: Protein NADH-quinone oxidoreductase


Mass: 73289.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B489, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#4: Protein NADH-quinone oxidoreductase subunit I


Mass: 18925.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B486
#6: Protein NADH-quinone oxidoreductase subunit N


Mass: 52564.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B479
#7: Protein NADH-quinone oxidoreductase subunit H


Mass: 38861.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B487
#8: Protein NADH-quinone oxidoreductase subunit F


Mass: 47281.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B491
#9: Protein NADH-quinone oxidoreductase subunit D


Mass: 46811.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B495
#11: Protein NADH-quinone oxidoreductase subunit A


Mass: 13686.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B498
#12: Protein NADH-quinone oxidoreductase chain 10


Mass: 21835.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: P29922
#15: Protein NADH-quinone oxidoreductase subunit C


Mass: 23920.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B496
#16: Protein NADH-quinone oxidoreductase subunit B


Mass: 19525.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B497

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Protein , 4 types, 4 molecules tqRQ

#3: Protein Protein-L-isoaspartate O-methyltransferase


Mass: 23528.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B5L6
#10: Protein NADH:ubiquinone oxidoreductase 17.2 kD subunit


Mass: 14432.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B1H8
#13: Protein Zinc finger CHCC-type domain-containing protein


Mass: 7069.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B357
#14: Protein ETC complex I subunit conserved region


Mass: 12048.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B1M0

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NADH dehydrogenase subunit ... , 3 types, 3 molecules ELM

#5: Protein NADH dehydrogenase subunit E


Mass: 26145.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B494
#17: Protein NADH dehydrogenase subunit L


Mass: 77811.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B481
#18: Protein NADH dehydrogenase subunit M


Mass: 56519.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B480

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Non-polymers , 13 types, 1129 molecules

#19: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#21: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#22: Chemical
ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C39H77O8P
#23: Chemical ChemComp-P5S / O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / phosphatidyl serine


Mass: 792.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H82NO10P
#24: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#25: 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.: 10 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#26: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C81H156O17P2 / Comment: phospholipid*YM
#27: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#28: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#29: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#30: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4
#31: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1080 / 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: Respiratory complex I / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Buffer solutionpH: 6.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: The grids were glow discharged at 20 mA for 90 s to clean and increase the hydrophilicity of the grid surface and then incubated in 5 mM 11-mercaptoundecyl hexaethyleneglycol in ethanol for ...Details: The grids were glow discharged at 20 mA for 90 s to clean and increase the hydrophilicity of the grid surface and then incubated in 5 mM 11-mercaptoundecyl hexaethyleneglycol in ethanol for two days under anaerobic conditions. The grids were then washed in 100% ethanol and dried three times prior to sample application.
Grid material: GOLD / Grid type: UltrAuFoil R0./1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.4 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 16814
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2EPU2.7image acquisition
4CTFFIND4CTF correction
10RELION3.1.0final Euler assignment
11RELION3.1.0classification
12RELION3.1.03D reconstruction
13PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146603 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingDetails: Model Angelo / Source name: Other / Type: in silico model

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