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- EMDB-28637: Cryo EM structure of Vibrio cholerae NQR -

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Basic information

Entry
Database: EMDB / ID: EMD-28637
TitleCryo EM structure of Vibrio cholerae NQR
Map dataRelion Refine3D full map
Sample
  • Complex: Na(+)-translocating NADH-quinone reductase
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit A
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit B
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit C
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit D
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit E
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit F
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: RIBOFLAVIN
  • Ligand: UBIQUINONE-1
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
Function / homology
Function and homology information


NADH:ubiquinone reductase (Na+-transporting) / Gram-negative-bacterium-type cell wall / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / respiratory electron transport chain / transmembrane transport / 2 iron, 2 sulfur cluster binding / FMN binding / flavin adenine dinucleotide binding / electron transfer activity ...NADH:ubiquinone reductase (Na+-transporting) / Gram-negative-bacterium-type cell wall / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / respiratory electron transport chain / transmembrane transport / 2 iron, 2 sulfur cluster binding / FMN binding / flavin adenine dinucleotide binding / electron transfer activity / metal ion binding / plasma membrane
Similarity search - Function
Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-translocating NADH-quinone reductase subunit D / Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NADH-quinone reductase subunit A, C-terminal domain / Na(+)-translocating NADH-quinone reductase subunit A (NQRA) / NQRA C-terminal domain / Na(+)-translocating NADH-quinone reductase subunit C / NqrDE/RnfAE / Ion-translocating oxidoreductase NqrB/RnfD ...Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-translocating NADH-quinone reductase subunit D / Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NADH-quinone reductase subunit A, C-terminal domain / Na(+)-translocating NADH-quinone reductase subunit A (NQRA) / NQRA C-terminal domain / Na(+)-translocating NADH-quinone reductase subunit C / NqrDE/RnfAE / Ion-translocating oxidoreductase NqrB/RnfD / Na(+)-translocating NADH-quinone reductase subunit F / Rnf-Nqr subunit, membrane protein / NQR2, RnfD, RnfE family / FMN-binding / FMN-binding domain / FMN_bind / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
Na(+)-translocating NADH-quinone reductase subunit C / Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-translocating NADH-quinone reductase subunit D / Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-translocating NADH-quinone reductase subunit F
Similarity search - Component
Biological speciesVibrio cholerae O395 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5804 Å
AuthorsFuller JR / Juarez O
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI151152 United States
CitationJournal: To Be Published
Title: Novel cofactor binding motifs, electron transfer and ion pumping mechanisms of the respiratory complex NQR
Authors: Juarez O / Fuller JR
History
DepositionOct 20, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateNov 16, 2022-
Current statusNov 16, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28637.png

Downloads & links

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Map

FileDownload / File: emd_28637.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRelion Refine3D full map
Voxel sizeX=Y=Z: 1.068 Å
Density
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.0147757 - 0.051789135
Average (Standard dev.)-7.833622e-06 (±0.001230014)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 384.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28637_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map sharpened by fitted Bfactor (-31.1772) and filtered...

Fileemd_28637_additional_1.map
AnnotationMap sharpened by fitted Bfactor (-31.1772) and filtered to local resolution via the Relion LocalRes method. Model was built and refined primarily into this map, including model ADPs.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Relion Refine3D half-map 2

Fileemd_28637_half_map_1.map
AnnotationRelion Refine3D half-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Relion Refine3D half-map 1

Fileemd_28637_half_map_2.map
AnnotationRelion Refine3D half-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Na(+)-translocating NADH-quinone reductase

EntireName: Na(+)-translocating NADH-quinone reductase
Components
  • Complex: Na(+)-translocating NADH-quinone reductase
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit A
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit B
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit C
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit D
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit E
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit F
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: RIBOFLAVIN
  • Ligand: UBIQUINONE-1
  • Ligand: FE2/S2 (INORGANIC) CLUSTER

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Supramolecule #1: Na(+)-translocating NADH-quinone reductase

SupramoleculeName: Na(+)-translocating NADH-quinone reductase / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Vibrio cholerae O395 (bacteria)
Recombinant expressionOrganism: Vibrio cholerae O395 (bacteria)

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Macromolecule #1: Na(+)-translocating NADH-quinone reductase subunit A

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae O395 (bacteria) / Strain: O395N1
Molecular weightTheoretical: 48.680734 KDa
Recombinant expressionOrganism: Vibrio cholerae O395 (bacteria)
SequenceString: MITIKKGLDL PIAGTPSQVI SDGKAIKKVA LLGEEYVGMR PTMHVRVGDE VKKAQILFED KKNPGVKFTS PVSGKVVEIN RGAKRVLQS VVIEVAGDDQ VTFDKFEANQ LASLNRDAIK TQLVESGLWT AFRTRPFSKV PAIDSTSEAI FVTAMDTNPL A AEPTVVIN ...String:
MITIKKGLDL PIAGTPSQVI SDGKAIKKVA LLGEEYVGMR PTMHVRVGDE VKKAQILFED KKNPGVKFTS PVSGKVVEIN RGAKRVLQS VVIEVAGDDQ VTFDKFEANQ LASLNRDAIK TQLVESGLWT AFRTRPFSKV PAIDSTSEAI FVTAMDTNPL A AEPTVVIN EQSEAFVAGL DVLSALTTGK VYVCKKGTSL PRSQQPNVEE HVFDGPHPAG LAGTHMHFLY PVSADHVAWS IN YQDVIAV GQLFLTGELY TQRVVSLAGP VVNKPRLVRT VMGASLEQLV DSEIMPGEVR IISGSVLSGT KATGPHAYLG RYH LQVSVL REGRDKELFG WAMPGKNKFS VTRSFLGHLF KGQVYNMTTT TNGSDRSMVP IGNYEKVMPL DMEPTLLLRD LCAG DSDSA VRLGALELDE EDLALCTFVC PGKYEYGQLL RECLDKIEKE G

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Macromolecule #2: Na(+)-translocating NADH-quinone reductase subunit B

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae O395 (bacteria) / Strain: O395N1
Molecular weightTheoretical: 45.390883 KDa
Recombinant expressionOrganism: Vibrio cholerae O395 (bacteria)
SequenceString: MGLKKFLEDI EHHFEPGGKH EKWFALYEAA ATLFYTPGLV TKRSSHVRDS VDLKRIMIMV WLAVFPAMFW GMYNAGGQAI AALNHLYSG DQLAAIVAGN WHYWLTEMLG GTMSSDAGWG SKMLLGATYF LPIYATVFIV GGFWEVLFCM VRKHEVNEGF F VTSILFAL ...String:
MGLKKFLEDI EHHFEPGGKH EKWFALYEAA ATLFYTPGLV TKRSSHVRDS VDLKRIMIMV WLAVFPAMFW GMYNAGGQAI AALNHLYSG DQLAAIVAGN WHYWLTEMLG GTMSSDAGWG SKMLLGATYF LPIYATVFIV GGFWEVLFCM VRKHEVNEGF F VTSILFAL IVPPTLPLWQ AALGITFGVV VAKEVFGGTG RNFLNPALAG RAFLFFAYPA QISGDLVWTA ADGYSGATAL SQ WAQGGAG ALINNATGQT ITWMDAFIGN IPGSIGEVST LALMIGAAFI VYMGIASWRI IGGVMIGMIL LSTLFNVIGS DTN AMFNMP WHWHLVLGGF AFGMFFMATD PVSASFTNSG KWAYGILIGV MCVLIRVVNP AYPEGMMLAI LFANLFAPLF DHVV VERNI KRRLARYGKQ

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Macromolecule #3: Na(+)-translocating NADH-quinone reductase subunit C

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae O395 (bacteria) / Strain: O395N1
Molecular weightTheoretical: 27.65227 KDa
Recombinant expressionOrganism: Vibrio cholerae O395 (bacteria)
SequenceString: MASNNDSIKK TLFVVIALSL VCSIIVSAAA VGLRDKQKEN AALDKQSKIL QVAGIEAKGS KQIVELFNKS IEPRLVDFNT GDFVEGDAA NYDQRKAAKE ASESIKLTAE QDKAKIQRRA NVGVVYLVKD GDKTSKVILP VHGNGLWSMM YAFVAVETDG N TVSGLTYY ...String:
MASNNDSIKK TLFVVIALSL VCSIIVSAAA VGLRDKQKEN AALDKQSKIL QVAGIEAKGS KQIVELFNKS IEPRLVDFNT GDFVEGDAA NYDQRKAAKE ASESIKLTAE QDKAKIQRRA NVGVVYLVKD GDKTSKVILP VHGNGLWSMM YAFVAVETDG N TVSGLTYY EQGETPGLGG EVENPAWRAQ WVGKKLFDEN HKPAIKIVKG GAPQGSEHGV DGLSGATLTS NGVQNTFDFW LG DMGFGPF LTKVRDGGLN

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Macromolecule #4: Na(+)-translocating NADH-quinone reductase subunit D

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae O395 (bacteria) / Strain: O395N1
Molecular weightTheoretical: 22.853217 KDa
Recombinant expressionOrganism: Vibrio cholerae O395 (bacteria)
SequenceString: MSSAKELKKS VLAPVLDNNP IALQVLGVCS ALAVTTKLET AFVMTLAVMF VTALSNFFVS LIRNHIPNSV RIIVQMAIIA SLVIVVDQI LKAYLYDISK QLSVFVGLII TNCIVMGRAE AFAMKSEPIP SFIDGIGNGL GYGFVLMTVG FFRELLGSGK L FGLEVLPL ...String:
MSSAKELKKS VLAPVLDNNP IALQVLGVCS ALAVTTKLET AFVMTLAVMF VTALSNFFVS LIRNHIPNSV RIIVQMAIIA SLVIVVDQI LKAYLYDISK QLSVFVGLII TNCIVMGRAE AFAMKSEPIP SFIDGIGNGL GYGFVLMTVG FFRELLGSGK L FGLEVLPL ISNGGWYQPN GLMLLAPSAF FLIGFMIWAI RTFKPEQVEA KE

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Macromolecule #5: Na(+)-translocating NADH-quinone reductase subunit E

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit E / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae O395 (bacteria) / Strain: O395N1
Molecular weightTheoretical: 21.481678 KDa
Recombinant expressionOrganism: Vibrio cholerae O395 (bacteria)
SequenceString: MEHYISLLVK SIFIENMALS FFLGMCTFLA VSKKVKTSFG LGIAVIVVLT ISVPVNNLVY NLVLKPDALV EGVDLSFLNF ITFIGVIAA LVQILEMILD RFFPPLYNAL GIFLPLITVN CAIFGGVSFM VQRDYSFAES VVYGFGSGVG WMLAIVALAG I REKMKYSD ...String:
MEHYISLLVK SIFIENMALS FFLGMCTFLA VSKKVKTSFG LGIAVIVVLT ISVPVNNLVY NLVLKPDALV EGVDLSFLNF ITFIGVIAA LVQILEMILD RFFPPLYNAL GIFLPLITVN CAIFGGVSFM VQRDYSFAES VVYGFGSGVG WMLAIVALAG I REKMKYSD VPPGLRGLGI TFITAGLMAL GFMSFSGVQL

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Macromolecule #6: Na(+)-translocating NADH-quinone reductase subunit F

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae O395 (bacteria) / Strain: O395N1
Molecular weightTheoretical: 45.113492 KDa
Recombinant expressionOrganism: Vibrio cholerae O395 (bacteria)
SequenceString: MSTIIFGVVM FTLIILALVL VILFAKSKLV PTGDITISIN GDPEKAIVTQ PGGKLLTALA GAGVFVSSAC GGGGSCGQCR VKIKSGGGD ILPTELDHIS KGEAREGERL ACQVAVKADM DLELPEEIFG VKKWECTVIS NDNKATFIKE LKLAIPDGES V PFRAGGYI ...String:
MSTIIFGVVM FTLIILALVL VILFAKSKLV PTGDITISIN GDPEKAIVTQ PGGKLLTALA GAGVFVSSAC GGGGSCGQCR VKIKSGGGD ILPTELDHIS KGEAREGERL ACQVAVKADM DLELPEEIFG VKKWECTVIS NDNKATFIKE LKLAIPDGES V PFRAGGYI QIEAPAHHVK YADFDVPEKY RGDWDKFNLF RYESKVDEPI IRAYSMANYP EEFGIIMLNV RIATPPPNNP NV PPGQMSS YIWSLKAGDK CTISGPFGEF FAKDTDAEMV FIGGGAGMAP MRSHIFDQLK RLKSKRKMSY WYGARSKREM FYV EDFDGL AAENDNFVWH CALSDPQPED NWTGYTGFIH NVLYENYLKD HEAPEDCEYY MCGPPMMNAA VINMLKNLGV EEEN ILLDD FGG

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Macromolecule #7: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 7 / Number of copies: 2 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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Macromolecule #8: RIBOFLAVIN

MacromoleculeName: RIBOFLAVIN / type: ligand / ID: 8 / Number of copies: 1 / Formula: RBF
Molecular weightTheoretical: 376.364 Da
Chemical component information

ChemComp-RBF:
RIBOFLAVIN

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Macromolecule #9: UBIQUINONE-1

MacromoleculeName: UBIQUINONE-1 / type: ligand / ID: 9 / Number of copies: 1 / Formula: UQ1
Molecular weightTheoretical: 250.29 Da
Chemical component information

ChemComp-UQ1:
UBIQUINONE-1

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Macromolecule #10: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 10 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) 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

Concentration2 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
100.0 mMKClpotassium chloride
1.0 mMC10H16N2O8EDTA
50.0 mMC8H18N2O4SHEPES

Details: 100 mM KCl, 1 mM EDTA, 50 mM HEPES, pH 7.0
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
Details: Gatan Solarus plasma cleaner operated at 20W and using ambient/room air
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
Details: A 3.5 uL droplet of sample was applied to the grid surface and blotted for 4 s before plunging into liquid ethane..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: EPU (ver. 2.9)
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 3159 / Average exposure time: 4.66 sec. / Average electron dose: 50.0 e/Å2 / Details: 50 e-/A2 fractionated over 40 movie frames
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.6 µm / Calibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsMicrograph movies were summed and dose-weighted using the motion correction algorithm implemented in RELION.
Particle selectionNumber selected: 304335
CTF correctionSoftware: (Name: CTFFIND (ver. 4.1.14), RELION (ver. 4.0beta2))
Startup modelType of model: OTHER
Details: 3D initial model generated from a subset of the data itself using RELION 4.0beta2
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.5804 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0beta2) / Number images used: 106466
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0beta2)
Final 3D classificationNumber classes: 2 / Avg.num./class: 90115 / Software - Name: RELION (ver. 4.0beta2)
Details: A final fixed-posed 3D classification was used to separate the two conformations of the NqrE subunit
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: UCSF Chimera
DetailsThe model was refined by iterating between manual edits in Coot, molecular dynamics-guided edits using the ISOLDE ChimeraX package, and automated real-space refinement in Phenix. Models that had been automatically rebuilt using Rosetta were used as guides during manual refinement.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation
Output model

PDB-8evu:
Cryo EM structure of Vibrio cholerae NQR

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