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- EMDB-10471: Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase,... -

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Entry
Database: EMDB / ID: EMD-10471
TitleCryo-EM structure of Euglena gracilis mitochondrial ATP synthase, OSCP/F1/cring in rotational state 1
Map datalocal resolution filtered map
Sample
  • Complex: Euglena gracilis mitochondrial ATP synthase dimer
    • Protein or peptide: x 11 types
  • Ligand: x 4 types
Keywordsmitochondria / ATP synthase / MEMBRANE PROTEIN
Biological speciesEuglena gracilis (euglena)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsMuhleip A / Amunts A
CitationJournal: Elife / Year: 2019
Title: Structure of a mitochondrial ATP synthase with bound native cardiolipin.
Authors: Alexander Mühleip / Sarah E McComas / Alexey Amunts /
Abstract: The mitochondrial ATP synthase fuels eukaryotic cells with chemical energy. Here we report the cryo-EM structure of a divergent ATP synthase dimer from mitochondria of , a member of the phylum ...The mitochondrial ATP synthase fuels eukaryotic cells with chemical energy. Here we report the cryo-EM structure of a divergent ATP synthase dimer from mitochondria of , a member of the phylum Euglenozoa that also includes human parasites. It features 29 different subunits, 8 of which are newly identified. The membrane region was determined to 2.8 Å resolution, enabling the identification of 37 associated lipids, including 25 cardiolipins, which provides insight into protein-lipid interactions and their functional roles. The rotor-stator interface comprises four membrane-embedded horizontal helices, including a distinct subunit . The dimer interface is formed entirely by phylum-specific components, and a peripherally associated subcomplex contributes to the membrane curvature. The central and peripheral stalks directly interact with each other. Last, the ATPase inhibitory factor 1 (IF) binds in a mode that is different from human, but conserved in Trypanosomatids.
History
DepositionNov 10, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseNov 27, 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: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tdy
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10471.png

Downloads & links

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Map

FileDownload / File: emd_10471.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal resolution filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 440 pix.
= 462. Å		1.05 Å/pix.
x 440 pix.
= 462. Å		1.05 Å/pix.
x 440 pix.
= 462. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.1514214 - 0.2668266
Average (Standard dev.)0.00061203114 (±0.004586906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 461.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z462.000462.000462.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-420-29
NX/NY/NZ887886
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.1510.2670.001

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Supplemental data

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Mask #1

Fileemd_10471_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_10471_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10471_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Euglena gracilis mitochondrial ATP synthase dimer

EntireName: Euglena gracilis mitochondrial ATP synthase dimer
Components
  • Complex: Euglena gracilis mitochondrial ATP synthase dimer
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase subunit gamma
    • Protein or peptide: ATP synthase subunit delta
    • Protein or peptide: ATP synthase subunit epsilon
    • Protein or peptide: p18
    • Protein or peptide: oligomycin sensitivity conferring protein (OSCP)
    • Protein or peptide: inhibitor of F1 (IF1)
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATP synthase subunit d
    • Protein or peptide: ATPTB4
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: FRAGMENT OF TRITON X-100

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Supramolecule #1: Euglena gracilis mitochondrial ATP synthase dimer

SupramoleculeName: Euglena gracilis mitochondrial ATP synthase dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 2 MDa

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Macromolecule #1: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 61.897199 KDa
SequenceString: MHYAEAATPA KSAGSAVAKK HLEAKQKIGF VHGIDGTIAT IAPAASKVTV PYNTVLEIAV SATNIANALV FNLEKDGSIG VILLDNISE VRSGQDVYAT GSLLKIPVGF HMLGKIINPL GKEIPTGLFT KAAPLLDDTK LGLVEEMAPN IVSRQPVNYN L LTGYKVID ...String:
MHYAEAATPA KSAGSAVAKK HLEAKQKIGF VHGIDGTIAT IAPAASKVTV PYNTVLEIAV SATNIANALV FNLEKDGSIG VILLDNISE VRSGQDVYAT GSLLKIPVGF HMLGKIINPL GKEIPTGLFT KAAPLLDDTK LGLVEEMAPN IVSRQPVNYN L LTGYKVID TLIPVGRGQR ELILGDRQTG KTSIALSTIL NQTKVNNEIL SKNNVLSVYV SIGQRCSNVA RIHRLLTEYD AM KYCTIVA ATAADPAGLQ YLAPYAGTTL GEEFRNSGRH ILLVYDDLSK QAVSYRQISL LLRRPPGREA YPGDVFYLHS RLL ERSAMM SPQKGSGSLT SLPIVETLSN DVTAYIVTNV ISITDGQIYL DAKLFTGGQR PAVNIGLSVS RVGSSAQNKA MKKV GGALK MLMGEYRKMA GEQTSGSQNV SPVMIRGARC LQLFNQKGPS YFMDAIVALY AVTNGYMDDV KLQYSKFYEF LLLNK DLPV LYGQVNNKYF YMYNKNLNYF IRYFGLNHEI LEPELKKYIE IHTNLFLDNY QSRMNELKSD EDLVQLKNLL YACKRT V

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Macromolecule #2: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 53.213035 KDa
SequenceString: TAPATAADVK QVGYVQQIIG AVVDVTFTDS VPPVLTALTV DAKETGTLLT MEIVQHLDTK TARCICMSST DMLRLRTPVV NTGSQITVP VGEATLGRIF NVMGDAIDQR GPVKNKVRWP IHRKAPTLAE QSGKDEVLVT GIKVIDLILP YCKGGKIGLF G GAGVGKTV ...String:
TAPATAADVK QVGYVQQIIG AVVDVTFTDS VPPVLTALTV DAKETGTLLT MEIVQHLDTK TARCICMSST DMLRLRTPVV NTGSQITVP VGEATLGRIF NVMGDAIDQR GPVKNKVRWP IHRKAPTLAE QSGKDEVLVT GIKVIDLILP YCKGGKIGLF G GAGVGKTV IIMELINNVA KGHGGYSVFA GVGERTREGT DLYLEMMGSK VIDLQGDSKC VLVYGQMNEP PGARARVAQT AL TMAEYFR DEAGQDVLLF VDNVFRFTQA NSEVSALLGR IPAAVGYQPT LAEDLGMLQE RITSTVKGSI TSVQAVYVPA DDI TDPAPA TTFSHLDATT VLSRSVAEAG IYPAVEPLEC ASRIMDPDAI DVNHYNVAMD IVEMLTKYKE LQDIIAVLGI DELS EEDKL IVDRARKVAK FMSQPFAVAE VFTGMKGYYV QLEDCVSDFG SLLMGQCDNI PEMAFYMVGG LDSVKEKAAK MAAEA AAMR ERARKAAEAK

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Macromolecule #3: ATP synthase subunit gamma

MacromoleculeName: ATP synthase subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 35.110375 KDa
SequenceString: MPGGGTIRFW REKLEGYKKY HQIVKTIKMV TLAKYRQTVV RTRVRDQTLR YTRKALDAKT QDDQEVIEKS ECLLYVPITT NRGSCGALN TNMVRYLQEV ENPKMTIISV GKKALDAMTK VFQDTYRRTI LNDMKQAMSF QFAAYVLEHM NTVPWDRAQI V YNRYHGAA ...String:
MPGGGTIRFW REKLEGYKKY HQIVKTIKMV TLAKYRQTVV RTRVRDQTLR YTRKALDAKT QDDQEVIEKS ECLLYVPITT NRGSCGALN TNMVRYLQEV ENPKMTIISV GKKALDAMTK VFQDTYRRTI LNDMKQAMSF QFAAYVLEHM NTVPWDRAQI V YNRYHGAA SQKLAIFNLP KFEDWKQKLE EDSAGDGKIE EDGLLQSLPM KTALGELEET AVEDFYNFHS CLAVLNAVSE NE LSEYAAR IVAVENQLGN ITGLMQLADY TYNKTRKELI TAELLEIIGT MTAMHAGKKV GLKKTEFWK

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Macromolecule #4: ATP synthase subunit delta

MacromoleculeName: ATP synthase subunit delta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 19.559953 KDa
SequenceString:
MRASRTLLLS VSRFMRQDPR KFFPDNGFRF FDGPEDSFGD GNIPAQIILT LTRQDEFILK QEPVAAITIR TNEGEMGVLA GHEYTVQQL APGILEVEYE GGKKDQYVIS GGFAHVNDTG VVDINTVEAV PLEEIDHEKL AKALEEARAK SQSPDEAVRI Q GEIALEIF EPLEAALH

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Macromolecule #5: ATP synthase subunit epsilon

MacromoleculeName: ATP synthase subunit epsilon / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 8.751981 KDa
SequenceString:
MSWRDAGISY LRYLSIVTRC IHEVQKEGPL LTKNVRFSTI GWKSLYLDHG ATKEYTAIPA ELEKIPENQV AQQHHA

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Macromolecule #6: p18

MacromoleculeName: p18 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 20.995094 KDa
SequenceString: MQKLSRVVCN RLVRFHGTVA ASAGGKRYDL FGYEVSVATG PFIEEIKKAQ FYDDAGEVIV KMNLANTPPD LQTYNAVLER ILNCKSKRS QPVKGENKFA AMMDILEEMD ARSGIKPNAE SWGYVLKELV QAGDFRLGWV CIAGMKSLGI TPDQALVDAN E ANAAKAKA ...String:
MQKLSRVVCN RLVRFHGTVA ASAGGKRYDL FGYEVSVATG PFIEEIKKAQ FYDDAGEVIV KMNLANTPPD LQTYNAVLER ILNCKSKRS QPVKGENKFA AMMDILEEMD ARSGIKPNAE SWGYVLKELV QAGDFRLGWV CIAGMKSLGI TPDQALVDAN E ANAAKAKA AGTDFPAYLK KAAPESFDTK AWGI

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Macromolecule #7: oligomycin sensitivity conferring protein (OSCP)

MacromoleculeName: oligomycin sensitivity conferring protein (OSCP) / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 29.56452 KDa
SequenceString: MHMRRAVSVF GRCRSLNGLR NYAVPSPKYI EIYQSDFSRN AYPLELLGGS HVDFAKLLYS FADQVENKKF EVYVEDFKKL DSIIAEKGP FWAEEKIFQS PTFQGLSEGF KFILGWIQSE GAIDRLENVR LAYKELVNEA RKETTATVIV AKEPSGNDLA E IRKQVEEL ...String:
MHMRRAVSVF GRCRSLNGLR NYAVPSPKYI EIYQSDFSRN AYPLELLGGS HVDFAKLLYS FADQVENKKF EVYVEDFKKL DSIIAEKGP FWAEEKIFQS PTFQGLSEGF KFILGWIQSE GAIDRLENVR LAYKELVNEA RKETTATVIV AKEPSGNDLA E IRKQVEEL HKESPLKDYK LVLETKVDPS IGGGYILEVC NQVVNRSAAA AAAETAALAK ASAAQVDWTS LPAAPPRPSP SA PDTLIRL LGSVVDDLAD ADKVEQKYGA

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Macromolecule #8: inhibitor of F1 (IF1)

MacromoleculeName: inhibitor of F1 (IF1) / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 11.687415 KDa
SequenceString:
MAAACAVRGF TTARPMLTPN KVKVPGRKPQ DEEDLTWAEA DRKLTPEERY ARDKQMALLD KMTSQVEELE KSHTEQKKSN KGVKAQIEA ISRQLEALKA QLKE

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Macromolecule #9: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 9 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 10.820831 KDa
SequenceString:
MQRGSSITKV VRRAALARST RNAAIAYEVT VNGANLIGAG MAASGVGVPA IGVAMCFSSY MLAAARQPNM SAKLLPYCIL GFALSEALA LFTLLIALLE LFVFS

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Macromolecule #10: ATP synthase subunit d

MacromoleculeName: ATP synthase subunit d / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 53.928289 KDa
SequenceString: MMRRACRIIR PSHVRGVSGV APTIYLRSKA ALPATSTTDV RPQLYALQRF AKAQLKTATE AERAAIEADI ARYQEYLDSD LEKLKQDVA EDTAKKQKLI PLLDRYPDVP IEKIPEHANV LLKKIDACLE ILSKDIGEVT DAEAHEMYFE TSKFQILHIY T GCVASFPE ...String:
MMRRACRIIR PSHVRGVSGV APTIYLRSKA ALPATSTTDV RPQLYALQRF AKAQLKTATE AERAAIEADI ARYQEYLDSD LEKLKQDVA EDTAKKQKLI PLLDRYPDVP IEKIPEHANV LLKKIDACLE ILSKDIGEVT DAEAHEMYFE TSKFQILHIY T GCVASFPE GDVPPGAVEC LPGQVIRTKV NGEDVMLEID EVDPGYQVCW FKPDVPLPEN AEILWSYPYE PTAALPTGTT WE EGQANVL IPAEPTPEAA VWPPTPVTNV YAPMAEKLAL KSNPELKVLF KEALLQPAKL LPLDVDYQCS HDREVVEAKR DRY LTALVE AEQAPPLPFT PDVLQLQLEH NVLKGELIDR LRALEYTIVT EQLQARLHER RLRGDVIDEW EELDYHPLVR DDTY LAIDF GDPTFGRYIW KLFPHTDGDE ECMFKDTRLD VLPPQVNPLN AILAQHTAQT PVHRSLEKRL WTEVRATAVS E

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Macromolecule #11: ATPTB4

MacromoleculeName: ATPTB4 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 18.83351 KDa
SequenceString:
MFRGFRPVLA ADAVKFQTLY NVLTGKQHLK DQVPVKDCNL TAIFGASWKA DLNKWFDSEY APKLPAAERD SAKKSLDLYL KRVDLTRYT REELTTYGIL ACGPGKVDAL TEKHLLETGK ARLEELTAGL GNKDEGVNAF RKEVEQEGKY ANWPAEKSKA L ADKVIAAS P

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Macromolecule #12: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 12 / Number of copies: 4 / 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 #13: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 13 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #14: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 14 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #15: FRAGMENT OF TRITON X-100

MacromoleculeName: FRAGMENT OF TRITON X-100 / type: ligand / ID: 15 / Number of copies: 1 / Formula: TRT
Molecular weightTheoretical: 352.508 Da
Chemical component information

ChemComp-TRT:
FRAGMENT OF TRITON X-100 / detergent*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

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3 seconds blot.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number real images: 9045 / Average exposure time: 10.0 sec. / Average electron dose: 36.3 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 magnification: 130000
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: 555269
Startup modelType of model: EMDB MAP
EMDB ID:

3559

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 150744
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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