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- EMDB-42129: Komagataella pastoris Cytochrome c oxidase (9 subunits) in comple... -

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Entry
Database: EMDB / ID: EMD-42129
TitleKomagataella pastoris Cytochrome c oxidase (9 subunits) in complex with human VMAT2
Map data3.26A DEEPEMhancer cryoEM map of Komagataella pastoris Cytochrome c oxidase (9 subunits) in complex with human VMAT2
Sample
  • Complex: Komagataella pastoris Cytochrome c oxidase (9 subunits) in complex with human VMAT2
    • Protein or peptide: x 10 types
  • Ligand: x 5 types
KeywordsVMAT / SLC18 / vascular monoamine transporter / Cytochrome c oxidase-VMAT2 complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


serotonin secretion by mast cell / sequestering of neurotransmitter / somato-dendritic dopamine secretion / histamine uptake / neurotransmitter loading into synaptic vesicle / monoamine:proton antiporter activity / aminergic neurotransmitter loading into synaptic vesicle / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / serotonin:sodium:chloride symporter activity ...serotonin secretion by mast cell / sequestering of neurotransmitter / somato-dendritic dopamine secretion / histamine uptake / neurotransmitter loading into synaptic vesicle / monoamine:proton antiporter activity / aminergic neurotransmitter loading into synaptic vesicle / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / serotonin:sodium:chloride symporter activity / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / serotonin uptake / dopamine transport / dopaminergic synapse / monoamine transmembrane transporter activity / histamine secretion by mast cell / monoamine transport / Na+/Cl- dependent neurotransmitter transporters / : / cytochrome-c oxidase / neurotransmitter transport / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / electron transport coupled proton transport / negative regulation of reactive oxygen species biosynthetic process / response to amphetamine / post-embryonic development / secretory granule membrane / locomotory behavior / terminal bouton / response to toxic substance / synaptic vesicle membrane / synaptic vesicle / chemical synaptic transmission / mitochondrial inner membrane / axon / intracellular membrane-bounded organelle / centrosome / dendrite / heme binding / mitochondrion / membrane / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome c oxidase, subunit VIIa, fungal / : / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily ...Cytochrome c oxidase, subunit VIIa, fungal / : / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Major facilitator superfamily / Major Facilitator Superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Cytochrome c oxidase subunit 9, mitochondrial / Cytochrome c oxidase subunit 8, mitochondrial / Cytochrome c oxidase subunit 7 / Cytochrome c oxidase subunit / Cytochrome c oxidase subunit 6, mitochondrial / Cytochrome c oxidase subunit 5B / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 1 / Synaptic vesicular amine transporter
Similarity search - Component
Biological speciesHomo sapiens (human) / Komagataella pastoris (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsYe J / Liu B / Li W
Funding support United States, 1 items
OrganizationGrant numberCountry
American Heart AssociationEstablished Investigator Award United States
CitationJournal: To Be Published
Title: Komagataella pastoris Cytochrome c oxidase (9 subunits) in complex with human VMAT2
Authors: Ye J / Liu B / Li W
History
DepositionSep 26, 2023-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42129.png

Downloads & links

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Map

FileDownload / File: emd_42129.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3.26A DEEPEMhancer cryoEM map of Komagataella pastoris Cytochrome c oxidase (9 subunits) in complex with human VMAT2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.00174309 - 1.7638394
Average (Standard dev.)0.0016673063 (±0.030697698)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A of VMAT2-CCO complex

Fileemd_42129_half_map_1.map
AnnotationHalf map A of VMAT2-CCO complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of VMAT2-CCO complex

Fileemd_42129_half_map_2.map
AnnotationHalf map B of VMAT2-CCO complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Komagataella pastoris Cytochrome c oxidase (9 subunits) in comple...

EntireName: Komagataella pastoris Cytochrome c oxidase (9 subunits) in complex with human VMAT2
Components
  • Complex: Komagataella pastoris Cytochrome c oxidase (9 subunits) in complex with human VMAT2
    • Protein or peptide: Synaptic vesicular amine transporter
    • Protein or peptide: Cytochrome c oxidase subunit 1
    • Protein or peptide: Cytochrome c oxidase subunit 2
    • Protein or peptide: Cytochrome c oxidase subunit 3
    • Protein or peptide: Cytochrome c oxidase subunit 4
    • Protein or peptide: Cytochrome c oxidase subunit 5
    • Protein or peptide: Cytochrome c oxidase subunit 6
    • Protein or peptide: Cytochrome c oxidase subunit 7
    • Protein or peptide: Cytochrome c oxidase subunit 8
    • Protein or peptide: Cytochrome c oxidase subunit 9
  • Ligand: COPPER (II) ION
  • Ligand: HEME-A
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: DINUCLEAR COPPER ION
  • Ligand: ZINC ION

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Supramolecule #1: Komagataella pastoris Cytochrome c oxidase (9 subunits) in comple...

SupramoleculeName: Komagataella pastoris Cytochrome c oxidase (9 subunits) in complex with human VMAT2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 225 KDa

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Macromolecule #1: Synaptic vesicular amine transporter

MacromoleculeName: Synaptic vesicular amine transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.749352 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MALSELALVR WLQESRRSRK LILFIVFLAL LLDNMLLTVV VPIIPSYLYS IKHEKNATEI QTARPVHTAS ISDSFQSIFS YYDNSTMVT GNATRDLTLH QTATQHMVTN ASAVPSDCPS EDKDLLNENV QVGLLFASKA TVQLITNPFI GLLTNRIGYP I PIFAGFCI ...String:
MALSELALVR WLQESRRSRK LILFIVFLAL LLDNMLLTVV VPIIPSYLYS IKHEKNATEI QTARPVHTAS ISDSFQSIFS YYDNSTMVT GNATRDLTLH QTATQHMVTN ASAVPSDCPS EDKDLLNENV QVGLLFASKA TVQLITNPFI GLLTNRIGYP I PIFAGFCI MFVSTIMFAF SSSYAFLLIA RSLQGIGSSC SSVAGMGMLA SVYTDDEERG NVMGIALGGL AMGVLVGPPF GS VLYEFVG KTAPFLVLAA LVLLDGAIQL FVLQPSRVQP ESQKGTPLTT LLKDPYILIA AGSICFANMG IAMLEPALPI WMM ETMCSR KWQLGVAFLP ASISYLIGTN IFGILAHKMG RWLCALLGMI IVGVSILCIP FAKNIYGLIA PNFGVGFAIG MVDS SMMPI MGYLVDLRHV SVYGSVYAIA DVAFCMGYAI GPSAGGAIAK AIGFPWLMTI IGIIDILFAP LCFFLRSPPA KEEKM AILM DHNCPIKTKM YTQNNIQSYP IGEDEESESD

UniProtKB: Synaptic vesicular amine transporter

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Macromolecule #2: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella pastoris (fungus)
Molecular weightTheoretical: 58.857352 KDa
SequenceString: MNYINRWLFS TNAKDIAVLY FIFALFCGLL GSIMSLILRL ELSAPGNQIL MGNHQLFNVV ATAHAVLMVF FLVMPAAIGF FGNYLLPLM IGASDMSFAR LNNISFWLLP PALVSLLASA LIENGAGTGW TVYPPLAGVQ SHSGPSVDLA IFALHLTSIS S LLGAINFI ...String:
MNYINRWLFS TNAKDIAVLY FIFALFCGLL GSIMSLILRL ELSAPGNQIL MGNHQLFNVV ATAHAVLMVF FLVMPAAIGF FGNYLLPLM IGASDMSFAR LNNISFWLLP PALVSLLASA LIENGAGTGW TVYPPLAGVQ SHSGPSVDLA IFALHLTSIS S LLGAINFI TTTLNMRTIG MTMSKLPLFV WAVVFTSILL LLSLPVLSAG VTLLLLDRNF NTSFFEPAGG GDPILYQHLF WF FGHPEVY ILIIPGFGII SHIVSTYSKK PVFGAIGMVY AMGSIGFLGL LVWSHHMYTV GLDVDSRAYF TSATMVIAVP TGI KIFSWL ATLYGGSIRY TTPMLYAFAF LFLFTVGGLS GVVLSNASLD IAFHDTYYVI GHFHYVLSLG AVFSLFAGYY YWSP LITGL YYNNNLANIQ FWLLFIGTNV TFFPMHFLGL NGMPRRIPDY PDAFAGWNAI SSFGSLISII SVILFAYVIY DQLVN GLTN KQLSTNSLFK NPDFIESNII FNDNSIKSSS IDFLLTSPPL PHTFNTPAIQ S

UniProtKB: Cytochrome c oxidase subunit 1

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Macromolecule #3: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella pastoris (fungus)
Molecular weightTheoretical: 26.886889 KDa
SequenceString: DVPTPWGIFF QDSATPNMEG IIELHNNIMF YLVLILTFVS YILYTIIYNY SNATIVHKYM NHGQLIEIVW TTLPAVILLI IAFPSFILL YLCDEVISPA MTIKAIGLQW YWKYEYSDFI NDDGEIVEFE SYVIPEELLE DGQLRLLDVD ASVVVPVDTH I RFIVSSAD ...String:
DVPTPWGIFF QDSATPNMEG IIELHNNIMF YLVLILTFVS YILYTIIYNY SNATIVHKYM NHGQLIEIVW TTLPAVILLI IAFPSFILL YLCDEVISPA MTIKAIGLQW YWKYEYSDFI NDDGEIVEFE SYVIPEELLE DGQLRLLDVD ASVVVPVDTH I RFIVSSAD VIHDFCVPAL GVKVDASPGR LNQTSALIQR EGVYYGQCSE LCGVMHSAMP IKIEAVSLYE FINWLDEQ

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Macromolecule #4: Cytochrome c oxidase subunit 3

MacromoleculeName: Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella pastoris (fungus)
Molecular weightTheoretical: 30.561145 KDa
SequenceString: MRIQNRENLQ LFPFHLVTNS PWPLTTSLAL MSLALTLGLT MHGYIGNHLW LFLAISLVLS SIFLWVRDVV IEGTYLGDHT IAVRKGLNI GFMLFVLSEI LIFAALFWSY FHSAMGPTIE IGCQWPPVGI TSIKPTELPL LNTIILLASG ATVTWAHHSI L YKDRQGTL ...String:
MRIQNRENLQ LFPFHLVTNS PWPLTTSLAL MSLALTLGLT MHGYIGNHLW LFLAISLVLS SIFLWVRDVV IEGTYLGDHT IAVRKGLNI GFMLFVLSEI LIFAALFWSY FHSAMGPTIE IGCQWPPVGI TSIKPTELPL LNTIILLASG ATVTWAHHSI L YKDRQGTL VGLFITTLLI ILFVGCQVLE YTWATFTIAD SVFGSIFYAG TGLHFIHMVM LIVMLAICYA RMYFYHFTSN HH LGLETTI LYLHVLDIIW LFLYIVFYWW G

UniProtKB: Cytochrome c oxidase subunit 3

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Macromolecule #5: Cytochrome c oxidase subunit 4

MacromoleculeName: Cytochrome c oxidase subunit 4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella pastoris (fungus)
Molecular weightTheoretical: 12.970557 KDa
SequenceString:
QFKTATSIAE VEGLENLVGP GAKTGTVPTD LEQATGLERY ELLGKLEGIE VFDETPLEAV RKGTMKDPIL IDSYDDYRYV GCTGVPADS HNIEWLKPTT EKNARCWECG SVYKLNFL

UniProtKB: Cytochrome c oxidase subunit

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Macromolecule #6: Cytochrome c oxidase subunit 5

MacromoleculeName: Cytochrome c oxidase subunit 5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella pastoris (fungus)
Molecular weightTheoretical: 14.51934 KDa
SequenceString:
NATVTNLEKR WEDLPETDQK DIISQLSERQ KLPWKDLTLS EKKAAWYISF GEWGPRRPVH TKEDKLYIFW GTVIGIVISA TIFGAFRYN RNVPKTMNRE WQAASDEYLK SKNAEPFTGY SQIQS

UniProtKB: Cytochrome c oxidase subunit 5B

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Macromolecule #7: Cytochrome c oxidase subunit 6

MacromoleculeName: Cytochrome c oxidase subunit 6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella pastoris (fungus)
Molecular weightTheoretical: 11.851136 KDa
SequenceString:
EETYEEFSQR YEKEFDEAYD LFEVQRVLNN CFSYDIVPSP AVIGKALNAC RRVNDYATAV RVFEGLKHKV ETKEQYDAYL EELKDVREE LGIDLKEELF P

UniProtKB: Cytochrome c oxidase subunit 6, mitochondrial

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Macromolecule #8: Cytochrome c oxidase subunit 7

MacromoleculeName: Cytochrome c oxidase subunit 7 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella pastoris (fungus)
Molecular weightTheoretical: 6.573613 KDa
SequenceString:
TATEKIIELQ KFYQSTNKPI YAAHPRSKYY LIPYFGLLGV SVAATLFYTG RACFGIKD

UniProtKB: Cytochrome c oxidase subunit 7

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Macromolecule #9: Cytochrome c oxidase subunit 8

MacromoleculeName: Cytochrome c oxidase subunit 8 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella pastoris (fungus)
Molecular weightTheoretical: 5.456455 KDa
SequenceString:
DVGPYSNLPF KVKNRRVPYA VPHFLFFAIG MGIPFFACYV QLKRSGSI

UniProtKB: Cytochrome c oxidase subunit 8, mitochondrial

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Macromolecule #10: Cytochrome c oxidase subunit 9

MacromoleculeName: Cytochrome c oxidase subunit 9 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella pastoris (fungus)
Molecular weightTheoretical: 6.490561 KDa
SequenceString:
SLTRIQGSVK RRILTDISVG LTLGFGFASY WWWGVHKPTV AHRENYYIEL AKKKKA

UniProtKB: Cytochrome c oxidase subunit 9, mitochondrial

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Macromolecule #11: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #12: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 12 / Number of copies: 2 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

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Macromolecule #13: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 13 / Number of copies: 4 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #14: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 14 / Number of copies: 1 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

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Macromolecule #15: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 15 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 281 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 63.0 K / Max: 77.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
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 / Average exposure time: 3.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 105062
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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