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- EMDB-0981: Structure of Mycobacterium smegmatis succinate dehydrogenase 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-0981
TitleStructure of Mycobacterium smegmatis succinate dehydrogenase 2
Map data
Sample
  • Complex: Mycobaterium smegmatis Succinate dehydrogenase 2
    • Protein or peptide: x 5 types
  • Ligand: x 10 types
Keywordselectron transfer chain / trimer / OXIDOREDUCTASE
Function / homology
Function and homology information


steroid dehydrogenase activity, acting on the CH-CH group of donors / : / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding / steroid metabolic process / tricarboxylic acid cycle / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding ...steroid dehydrogenase activity, acting on the CH-CH group of donors / : / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding / steroid metabolic process / tricarboxylic acid cycle / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / membrane / metal ion binding
Similarity search - Function
Succinate dehydrogenase membrane subunit SdhC, prokaryotes / 4Fe-4S dicluster domain / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site ...Succinate dehydrogenase membrane subunit SdhC, prokaryotes / 4Fe-4S dicluster domain / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / Alpha-helical ferredoxin / FAD binding domain / Beta-grasp domain superfamily / 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 / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Succinate dehydrogenase iron-sulfur subunit / Succinate dehydrogenase flavoprotein subunit / Succinate dehydrogenase hydrophobic membrane anchor protein SdhD / Succinate dehydrogenase, cytochrome b556 subunit / Uncharacterized protein
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 51 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsGao Y / Gong H
Funding support China, 3 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08020200 China
National Natural Science Foundation of China (NSFC)81520108019, 813300237 China
Chinese Academy of Sciences2017YFC0840300 China
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor SdhF.
Authors: Hongri Gong / Yan Gao / Xiaoting Zhou / Yu Xiao / Weiwei Wang / Yanting Tang / Shan Zhou / Yuying Zhang / Wenxin Ji / Lu Yu / Changlin Tian / Sin Man Lam / Guanghou Shui / Luke W Guddat / ...Authors: Hongri Gong / Yan Gao / Xiaoting Zhou / Yu Xiao / Weiwei Wang / Yanting Tang / Shan Zhou / Yuying Zhang / Wenxin Ji / Lu Yu / Changlin Tian / Sin Man Lam / Guanghou Shui / Luke W Guddat / Luet-Lok Wong / Quan Wang / Zihe Rao /
Abstract: Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic mechanisms they employ for succinate oxidation by ...Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic mechanisms they employ for succinate oxidation by menaquinone. Here, we present the 2.8 Å cryo-electron microscopy structure of a Mycobacterium smegmatis Sdh, which forms a trimer. We identified the membrane-anchored SdhF as a subunit of the complex. The 3 kDa SdhF forms a single transmembrane helix and this helix plays a role in blocking the canonically proximal quinone-binding site. We also identified two distal quinone-binding sites with bound quinones. One distal binding site is formed by neighboring subunits of the complex. Our structure further reveals the electron/proton transfer pathway for succinate oxidation by menaquinone. Moreover, this study provides further structural insights into the physiological significance of a trimeric respiratory complex II. The structure of the menaquinone binding site could provide a framework for the development of Sdh-selective anti-mycobacterial drugs.
History
DepositionJan 29, 2020-
Header (metadata) releaseMay 27, 2020-
Map releaseMay 27, 2020-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
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  • Surface view colored by cylindrical radius
  • Surface level: 0.2
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  • Surface view with fitted model
  • Atomic models: PDB-6lum
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0981.png

Downloads & links

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Map

FileDownload / File: emd_0981.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15 / Movie #1: 0.2
Minimum - Maximum-1.8452778 - 2.7443264
Average (Standard dev.)0.0005290698 (±0.056020573)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z314.880314.880314.880
α/β/γ90.00090.00090.000
start NX/NY/NZ-31-35-52
NX/NY/NZ11798209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-1.8452.7440.001

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Supplemental data

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Mask #1

Fileemd_0981_msk_1.map
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AxesZYX

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Half map: #2

Fileemd_0981_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

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Half map: #1

Fileemd_0981_half_map_2.map
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Sample components

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Entire : Mycobaterium smegmatis Succinate dehydrogenase 2

EntireName: Mycobaterium smegmatis Succinate dehydrogenase 2
Components
  • Complex: Mycobaterium smegmatis Succinate dehydrogenase 2
    • Protein or peptide: Succinate dehydrogenase subunit C
    • Protein or peptide: Succinate dehydrogenase subunit D
    • Protein or peptide: Succinate dehydrogenase subunit F
    • Protein or peptide: Succinate dehydrogenase subunit A
    • Protein or peptide: Succinate dehydrogenase subunit B
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: MENAQUINONE-9
  • Ligand: CARDIOLIPIN
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE3-S4 CLUSTER

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Supramolecule #1: Mycobaterium smegmatis Succinate dehydrogenase 2

SupramoleculeName: Mycobaterium smegmatis Succinate dehydrogenase 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Mycolicibacterium smegmatis MC2 51 (bacteria) / Strain: mc2 51
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: Succinate dehydrogenase subunit C

MacromoleculeName: Succinate dehydrogenase subunit C / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 51 (bacteria) / Strain: MC2 51
Molecular weightTheoretical: 15.644627 KDa
SequenceString:
MSTQTEVPAP QPKKTRRRTL YRGDPGMWSW VLHRITGATI FFFLFVHVLD TALVRVSPQA YNEVIETYKT PIVGLMEIGL VAAVLFHAL NGIRVILIDF WAKGPRYQRQ MLAVIAGLFL VIFIAAVGVI GMHMVERFL

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Macromolecule #2: Succinate dehydrogenase subunit D

MacromoleculeName: Succinate dehydrogenase subunit D / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 51 (bacteria) / Strain: MC2 51
Molecular weightTheoretical: 19.2804 KDa
SequenceString:
MSAPGAGESR LGRPAPVMER EHDRPAALDH PRAPRKPRGI PYFEKYAWLF MRFSGIALVF LALGHLFIML MWQDGVYRID FNYVAERWA SPFWQIWDMA LLWLAMIHGA NGMRTIIGDY ARKNVTKFWL NSLLLLATGF TLVLGSYVLV TFDANISHHH H HHHHHH

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Macromolecule #3: Succinate dehydrogenase subunit F

MacromoleculeName: Succinate dehydrogenase subunit F / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 51 (bacteria) / Strain: MC2 51
Molecular weightTheoretical: 3.707443 KDa
SequenceString:
MVLFFEILLV AAVLVITWFA VYALYRLVTD ES

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Macromolecule #4: Succinate dehydrogenase subunit A

MacromoleculeName: Succinate dehydrogenase subunit A / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 51 (bacteria) / Strain: MC2 51
Molecular weightTheoretical: 64.476754 KDa
SequenceString: MIQEHRYDVV IVGAGGAGMR AAVEAGPRAR TAVLTKLYPT RSHTGAAQGG MCAALANVEE DNWEWHTFDT VKGGDYLADQ DAVEIMCKE AIDAVLDLEK MGMPFNRTPE GRIDQRRFGG HTRDHGKAPV RRACYAADRT GHMILQTLYQ NCVKHDVEFF N EFYALDIA ...String:
MIQEHRYDVV IVGAGGAGMR AAVEAGPRAR TAVLTKLYPT RSHTGAAQGG MCAALANVEE DNWEWHTFDT VKGGDYLADQ DAVEIMCKE AIDAVLDLEK MGMPFNRTPE GRIDQRRFGG HTRDHGKAPV RRACYAADRT GHMILQTLYQ NCVKHDVEFF N EFYALDIA LTETPAGPVA TGVIAYELAT GDIHVFHAKA IVFATGGSGR MYKTTSNAHT LTGDGLGIVF RKGLPLEDME FH QFHPTGL AGLGILISEA VRGEGGRLLN GEGERFMERY APTIVDLAPR DIVARSMVLE VLEGRGAGPN KDYVYIDVRH LGE DVLEAK LPDITEFART YLGVDPVKEL VPVYPTCHYV MGGIPTTVNG QVLRDNTNVI PGLYAAGECA CVSVHGANRL GTNS LLDIN VFGRRAGIAA AEYAQNHNFV DMPENPAEMV VGWVGDILSE HGNERVADIR GALQQSMDNN AAVFRTEETL KQALT DIHA LKERYSRITV HDKGKRYNSD LLEAIELGFL LELAEVTVVG ALNRKESRGG HAREDYPNRD DTNYMRHTMA YKQGTD LLS DIRLDYKPVV QTRYEPMERK Y

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Macromolecule #5: Succinate dehydrogenase subunit B

MacromoleculeName: Succinate dehydrogenase subunit B / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 51 (bacteria) / Strain: MC2 51
Molecular weightTheoretical: 29.24576 KDa
SequenceString: MSAPVIDKPE AGDPELPPVP EGAVMVTLKI ARFNPENPDA AGWQSFRVPC LPSDRLLNLL HYVKWYLDGT LTFRRSCAHG VCGSDAMRI NGVNRLACKV LMRDMLPKNP NKQLTITIEP IRGLPVEKDL VVNMEPFFDA YRAVKPFLVT SGNPPTKERI Q SPTDRARY ...String:
MSAPVIDKPE AGDPELPPVP EGAVMVTLKI ARFNPENPDA AGWQSFRVPC LPSDRLLNLL HYVKWYLDGT LTFRRSCAHG VCGSDAMRI NGVNRLACKV LMRDMLPKNP NKQLTITIEP IRGLPVEKDL VVNMEPFFDA YRAVKPFLVT SGNPPTKERI Q SPTDRARY DDTTKCILCA CCTTSCPVYW SEGSYFGPAA IVNAHRFIFD SRDEAAAERL DILNEVDGVW RCRTTFNCTE AC PRGIQVT QAIQEVKRAL MFAR

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Macromolecule #6: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY...

MacromoleculeName: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 6 / Number of copies: 6 / Formula: PEV
Molecular weightTheoretical: 720.012 Da
Chemical component information

ChemComp-PEV:
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / POPE, phospholipid*YM

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Macromolecule #7: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 7 / Number of copies: 6 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #8: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 8 / Number of copies: 6 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9

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Macromolecule #9: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 9 / Number of copies: 3 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #10: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE

MacromoleculeName: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
type: ligand / ID: 10 / Number of copies: 3 / Formula: LPP
Molecular weightTheoretical: 648.891 Da
Chemical component information

ChemComp-LPP:
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / phospholipid*YM

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Macromolecule #11: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL / type: ligand / ID: 11 / Number of copies: 3 / Formula: PIE
Molecular weightTheoretical: 836.061 Da
Chemical component information

ChemComp-PIE:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL

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Macromolecule #12: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 12 / Number of copies: 3 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #13: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 13 / Number of copies: 3 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #14: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 14 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #15: FE3-S4 CLUSTER

MacromoleculeName: FE3-S4 CLUSTER / type: ligand / ID: 15 / Number of copies: 3 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMMOPSDVLFYONBTKHTER-UHFFFAOYSA-N
0.1 %(v/w)digitonin

Details: Solutions were made fresh
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK II
DetailsThis sample was mono disperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: cryoSPARC software was used for the reconstruction.
Number images used: 461385
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC
Final angle assignmentType: COMMON LINE / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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