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- EMDB-4854: Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate ... -

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Basic information

Entry
Database: EMDB / ID: EMD-4854
TitleCryo-EM structure of Polytomella F-ATP synthase, Rotary substate 3B, focussed refinement of F1 head and rotor
Map data
Sample
  • Complex: Mitochondrial F-ATP synthase dimer from Polytomella sp. Pringsheim 198.80
    • Protein or peptide: Mitochondrial ATP synthase subunit c
    • Protein or peptide: Mitochondrial ATP synthase subunit OSCP
    • Protein or peptide: epsilon: Polytomella F-ATP synthase epsilon subunit
    • Protein or peptide: Mitochondrial ATP synthase subunit delta
    • Protein or peptide: ATP synthase gamma chain, mitochondrial
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsmitochondrial ATP synthase dimer flexible coupling cryoEM / PROTON TRANSPORT
Function / homology
Function and homology information


thylakoid / : / : / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / mitochondrial inner membrane ...thylakoid / : / : / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / mitochondrial inner membrane / hydrolase activity / lipid binding / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal ...ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
epsilon: Polytomella F-ATP synthase epsilon subunit / ATP synthase subunit alpha / ATP synthase subunit beta / Mitochondrial ATP synthase subunit c / Mitochondrial ATP synthase subunit delta / Mitochondrial ATP synthase subunit OSCP / ATP synthase subunit gamma, mitochondrial
Similarity search - Component
Biological speciesPolytomella sp. Pringsheim 198.80 (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMurphy BJ / Klusch N
Funding support Germany, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
European Molecular Biology OrganizationALTF 702 2016 Germany
CitationJournal: Science / Year: 2019
Title: Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F-F coupling.
Authors: Bonnie J Murphy / Niklas Klusch / Julian Langer / Deryck J Mills / Özkan Yildiz / Werner Kühlbrandt /
Abstract: FF-adenosine triphosphate (ATP) synthases make the energy of the proton-motive force available for energy-consuming processes in the cell. We determined the single-particle cryo-electron microscopy ...FF-adenosine triphosphate (ATP) synthases make the energy of the proton-motive force available for energy-consuming processes in the cell. We determined the single-particle cryo-electron microscopy structure of active dimeric ATP synthase from mitochondria of sp. at a resolution of 2.7 to 2.8 angstroms. Separation of 13 well-defined rotary substates by three-dimensional classification provides a detailed picture of the molecular motions that accompany -ring rotation and result in ATP synthesis. Crucially, the F head rotates along with the central stalk and -ring rotor for the first ~30° of each 120° primary rotary step to facilitate flexible coupling of the stoichiometrically mismatched F and F subcomplexes. Flexibility is mediated primarily by the interdomain hinge of the conserved OSCP subunit. A conserved metal ion in the proton access channel may synchronize -ring protonation with rotation.
History
DepositionApr 12, 2019-
Header (metadata) releaseJul 3, 2019-
Map releaseJul 3, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
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  • Surface view with fitted model
  • Atomic models: PDB-6rer
  • Surface level: 0.04
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rer
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4854.png

Downloads & links

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Map

FileDownload / File: emd_4854.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 480 pix.
= 505.44 Å		1.05 Å/pix.
x 480 pix.
= 505.44 Å		1.05 Å/pix.
x 480 pix.
= 505.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.053 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.10336926 - 0.21601257
Average (Standard dev.)-0.000020654224 (±0.005350477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 505.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0531.0531.053
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z505.440505.440505.440
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.1030.216-0.000

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Supplemental data

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Half map: #1

Fileemd_4854_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_4854_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Mitochondrial F-ATP synthase dimer from Polytomella sp. Pringshei...

EntireName: Mitochondrial F-ATP synthase dimer from Polytomella sp. Pringsheim 198.80
Components
  • Complex: Mitochondrial F-ATP synthase dimer from Polytomella sp. Pringsheim 198.80
    • Protein or peptide: Mitochondrial ATP synthase subunit c
    • Protein or peptide: Mitochondrial ATP synthase subunit OSCP
    • Protein or peptide: epsilon: Polytomella F-ATP synthase epsilon subunit
    • Protein or peptide: Mitochondrial ATP synthase subunit delta
    • Protein or peptide: ATP synthase gamma chain, mitochondrial
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Mitochondrial F-ATP synthase dimer from Polytomella sp. Pringshei...

SupramoleculeName: Mitochondrial F-ATP synthase dimer from Polytomella sp. Pringsheim 198.80
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 1.6 MDa

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Macromolecule #1: Mitochondrial ATP synthase subunit c

MacromoleculeName: Mitochondrial ATP synthase subunit c / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 12.664013 KDa
SequenceString:
MSVQRLSLGA ARCLSAGVAR VQASQALVAQ KAVAVAPTRA QAAPAEVAQV RSMSVLAASK MVGAGCATIA LAGVGAGLGV MFGSLINGA ARNPNIAKQL VGYALLGFAL TESIALFSLL VVFLILFA

UniProtKB: Mitochondrial ATP synthase subunit c

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Macromolecule #2: Mitochondrial ATP synthase subunit OSCP

MacromoleculeName: Mitochondrial ATP synthase subunit OSCP / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 25.530793 KDa
SequenceString: MLARVASVAL RRAEGKIMPQ MVRALSVSAA SAAQAELKLP TAPLQLSGTS AQIATLLWQV AAKENQLDKV QDELYQFIEL FKQHSELRR LATDPFVPTL VRTKIISSVL KDSGASEITK KLFEALADEG ALSALLEVTV NYEELMLAHK KEVYCTVITA E PLDKLERV ...String:
MLARVASVAL RRAEGKIMPQ MVRALSVSAA SAAQAELKLP TAPLQLSGTS AQIATLLWQV AAKENQLDKV QDELYQFIEL FKQHSELRR LATDPFVPTL VRTKIISSVL KDSGASEITK KLFEALADEG ALSALLEVTV NYEELMLAHK KEVYCTVITA E PLDKLERV ELTKKAEKFV DAGFKLVMQE KIDKKLLGGF VIEFSDRRVD MSTAKKVEEF NNFVNKLVLS I

UniProtKB: Mitochondrial ATP synthase subunit OSCP

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Macromolecule #3: epsilon: Polytomella F-ATP synthase epsilon subunit

MacromoleculeName: epsilon: Polytomella F-ATP synthase epsilon subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 8.205479 KDa
SequenceString:
MCAPSGPFYR VAGMSYLRYS NICADLLRNV LKEPFKAKAQ ARQAIHFRQA PYVDGKAGAS KVYELENGIP KTAN

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Macromolecule #4: Mitochondrial ATP synthase subunit delta

MacromoleculeName: Mitochondrial ATP synthase subunit delta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 20.880533 KDa
SequenceString: MFGLKRAVTV GRRFISTSAA RMEAAAPAGP KEFTEVWNKK APSTLIVPEF PSNYTAVKAV GEGQVHGDAF PVNFYTPHSI LSQAQKDTV VLPGVDGYFG VKASHVPTIA QLKPGVVELH SGAESEKFFV SGGFAFVHPN GVTDICVLEA ATLDQVDPAA V KSALAAAS ...String:
MFGLKRAVTV GRRFISTSAA RMEAAAPAGP KEFTEVWNKK APSTLIVPEF PSNYTAVKAV GEGQVHGDAF PVNFYTPHSI LSQAQKDTV VLPGVDGYFG VKASHVPTIA QLKPGVVELH SGAESEKFFV SGGFAFVHPN GVTDICVLEA ATLDQVDPAA V KSALAAAS AAQPTDEFEQ AANRAAIELY SALESAVEAK A

UniProtKB: Mitochondrial ATP synthase subunit delta

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Macromolecule #5: ATP synthase gamma chain, mitochondrial

MacromoleculeName: ATP synthase gamma chain, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 34.639594 KDa
SequenceString: MALRKAVLSL GLSQGVAAEA VLGSGMFNAV QHESVRYASN QAVKQRIRAI KNIGKITKAM KMVAASKMKN AQIAVEQSRG LVDPFVRLF GDFPAVNSNK SVVVAVTSDK GLCGGLNSNI TKYTRATLAT TESEGKDVVV VSIGDKGRSQ LTRIESQRYQ L AIADTYKV ...String:
MALRKAVLSL GLSQGVAAEA VLGSGMFNAV QHESVRYASN QAVKQRIRAI KNIGKITKAM KMVAASKMKN AQIAVEQSRG LVDPFVRLF GDFPAVNSNK SVVVAVTSDK GLCGGLNSNI TKYTRATLAT TESEGKDVVV VSIGDKGRSQ LTRIESQRYQ L AIADTYKV RVTFGQASLI VEELIKHNPQ SYQILFNKFR SAISFKPTVA TILSPDLLEK QLEDVTGNSL DAYDIEASHE RS DVLRDLT EFHLGVTLYN AMLENNCSEH ASRMSAMENS TKSAGEMLGK LTLDYNRKRQ ATITTELIEI IAGASALMDE

UniProtKB: ATP synthase subunit gamma, mitochondrial

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Macromolecule #6: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 60.766152 KDa
SequenceString: MRSPAAFVAR SGLFKASLGQ SNWAQKAEQM MASVTRTFAA DAKALDELRK PKFSSKYLIQ HVSQKLIPAV KEWEKSYQPP VIHLGRVLS VGDGIARVYG LKSVQAGELV CFDSGVKGMA LNLQADHVGV VVFGNDSVIH QGDLVYRTGQ IVNVPIGPGT L GRVTDGLG ...String:
MRSPAAFVAR SGLFKASLGQ SNWAQKAEQM MASVTRTFAA DAKALDELRK PKFSSKYLIQ HVSQKLIPAV KEWEKSYQPP VIHLGRVLS VGDGIARVYG LKSVQAGELV CFDSGVKGMA LNLQADHVGV VVFGNDSVIH QGDLVYRTGQ IVNVPIGPGT L GRVTDGLG QPIDGKGPLT NVRSSLVEVK APGIIARQSV REPLFTGVKA VDALVPIGRG QRELIIGDRQ TGKTAVAIDA II HQKNCNE QVPKAQRVYC VYVAVGQKRS TVAQLVKLFT QTGAMRYTIM VSATASDAAP LQFLAPYSGC AMAEYFRDTG KHG LIIYDD LSKQSVAYRQ MSLLLRRPPG REAFPGDVFY LHSRLLERAA KLSKELGGGS LTAFPVIETQ AGDVSAYIAT NVIS ITDGQ IFLETELFYK GIRPALNVGL SVSRVGSAAQ FPGMKQVAGT LKLELAQYRE VAAFAQFGSD LDAATQYVLE RGARL TEML KQKQFAPIPI ERQTVAVYAA TKGFLDKVRV QDIVAAEEAV ISQVNPAVFK ILKANGKITP ALDAHLKAEL RKVKLP GA

UniProtKB: ATP synthase subunit alpha

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Macromolecule #7: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 61.93907 KDa
SequenceString: MALRYAAGLA KNVVQRQGAS LNIARAFAAE PAPAIDAGYV SQVIGPVVDV RFDGELPSIL SSLEVEGHSV RLVLEVAQHM GDNTVRCIA MDSTDGLVRG QKVVDTGSPI KVPVGRGTLG RIMNVIGEPV DEQGPIDAAD IWSIHREAPE FTEQSTEQEI L VTGIKVVD ...String:
MALRYAAGLA KNVVQRQGAS LNIARAFAAE PAPAIDAGYV SQVIGPVVDV RFDGELPSIL SSLEVEGHSV RLVLEVAQHM GDNTVRCIA MDSTDGLVRG QKVVDTGSPI KVPVGRGTLG RIMNVIGEPV DEQGPIDAAD IWSIHREAPE FTEQSTEQEI L VTGIKVVD LLAPYQRGGK IGLFGGAGVG KTVLIMELIN NVAKAHGGFS VFAGVGERTR EGNDLYREMI ESGVIKLGAE RG NSKCTLV YGQMNEPPGA RARVALTGLT VAEYFRDIEG QDVLLFVDNI FRFTQANSEV SALLGRIPSA VGYQPTLATD LGG LQERIT TTTKGSITSV QAVYVPADDL TDPAPATTFA HLDATTVLSR SIAELGIYPA VDPLDSTSRM LNPNVIGAEH YNVA RGVQK VLQDYKNLQD IIAILGMDEL SEEDKLTVAR ARKIQRFLSQ PFQVAEVFTG TPGKYVDLAD TISGFQGVLT GKYDD LPEM AFYMVGDIKE VKEKADKMAK DIASRKEADN KKVSEELKDI PSLDKLVSEI KEVVIEEDDG LEEDFKAEAL SSETVV LNE EGKSVPLPKK N

UniProtKB: ATP synthase subunit beta

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Macromolecule #8: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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

Concentration3.5 mg/mL
BufferpH: 7.8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3840 pixel / Digitization - Dimensions - Height: 3712 pixel / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -5.0 µm / Nominal defocus min: -0.4 µm / Nominal magnification: 75000
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

Particle selectionNumber selected: 735197
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 88303
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6rer:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 3B, focussed refinement of F1 head and rotor

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