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- EMDB-42476: PLCb3-Gbg-Gaq complex on membranes -

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Basic information

Entry
Database: EMDB / ID: EMD-42476
TitlePLCb3-Gbg-Gaq complex on membranes
Map data
Sample
  • Complex: PLCb3-Gbg-Gaq complex
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein subunit gamma
    • Protein or peptide: Guanine nucleotide-binding protein G(q) subunit alpha
    • Protein or peptide: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TETRAFLUOROALUMINATE ION
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION
  • Ligand: water
KeywordsPLCb3 / Gbg / Gaq / SIGNALING PROTEIN
Function / homology
Function and homology information


phosphoinositide phospholipase C / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / phosphatidylinositol metabolic process / PLC beta mediated events / phospholipase C-activating dopamine receptor signaling pathway / entrainment of circadian clock / regulation of systemic arterial blood pressure / regulation of platelet activation / phospholipase C activity ...phosphoinositide phospholipase C / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / phosphatidylinositol metabolic process / PLC beta mediated events / phospholipase C-activating dopamine receptor signaling pathway / entrainment of circadian clock / regulation of systemic arterial blood pressure / regulation of platelet activation / phospholipase C activity / phototransduction, visible light / phosphatidylinositol phospholipase C activity / regulation of canonical Wnt signaling pathway / glutamate receptor signaling pathway / postsynaptic cytosol / action potential / Synthesis of IP3 and IP4 in the cytosol / phosphatidylinositol-mediated signaling / photoreceptor outer segment / lipid catabolic process / release of sequestered calcium ion into cytosol / GTPase activator activity / molecular function activator activity / G protein-coupled receptor binding / negative regulation of protein kinase activity / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / cellular response to prostaglandin E stimulus / blood coagulation / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / G alpha (s) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G alpha (q) signalling events / nuclear membrane / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / molecular adaptor activity / calmodulin binding / protein stabilization / cadherin binding / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / calcium ion binding / synapse / protein-containing complex binding / GTP binding / Golgi apparatus / signal transduction / protein-containing complex / extracellular exosome / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Phospholipase C-beta, C-terminal domain / PLC-beta C terminal / PLC-beta, PH domain / Phospholipase C-beta, C-terminal domain superfamily / : / PH domain / Phosphoinositide phospholipase C beta1-4-like EF-hand domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / G-protein alpha subunit, group Q / Phosphoinositide phospholipase C family ...Phospholipase C-beta, C-terminal domain / PLC-beta C terminal / PLC-beta, PH domain / Phospholipase C-beta, C-terminal domain superfamily / : / PH domain / Phosphoinositide phospholipase C beta1-4-like EF-hand domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / G-protein alpha subunit, group Q / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / Phosphatidylinositol-specific phospholipase X-box domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / EF-hand domain pair / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein subunit gamma / Guanine nucleotide-binding protein G(q) subunit alpha / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsFalzone ME / MacKinnon R
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM142137 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: The mechanism of regulation of -catalyzed hydrolysis.
Authors: Maria E Falzone / Roderick MacKinnon /
Abstract: () enzymes cleave phosphatidylinositol 4,5-bisphosphate ( producing and (diacylglycerol). modulates the function of many ion channels, while and regulate intracellular Ca levels and protein ... () enzymes cleave phosphatidylinositol 4,5-bisphosphate ( producing and (diacylglycerol). modulates the function of many ion channels, while and regulate intracellular Ca levels and protein phosphorylation by protein kinase C, respectively. enzymes are under the control of G protein coupled receptor signaling through direct interactions with G proteins and and have been shown to be coincidence detectors for dual stimulation of and -coupled receptors. are aqueous-soluble cytoplasmic enzymes but partition onto the membrane surface to access their lipid substrate, complicating their functional and structural characterization. Using newly developed methods, we recently showed that activates by recruiting it to the membrane. Using these same methods, here we show that increases the catalytic rate constant, , of . Since stimulation of by depends on an autoinhibitory element (the X-Y linker), we propose that produces partial relief of the X-Y linker autoinhibition through an allosteric mechanism. We also determined membrane-bound structures of the and complexes, which show that these G proteins can bind simultaneously and independently of each other to regulate activity. The structures rationalize a finding in the enzyme assay, that costimulation by both G proteins follows a product rule of each independent stimulus. We conclude that baseline activity of is strongly suppressed, but the effect of G proteins, especially acting together, provides a robust stimulus upon G protein stimulation.
History
DepositionOct 24, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42476.png

Downloads & links

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Map

FileDownload / File: emd_42476.map.gz / Format: CCP4 / Size: 155.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 344 pix.
= 288.616 Å		0.84 Å/pix.
x 344 pix.
= 288.616 Å		0.84 Å/pix.
x 344 pix.
= 288.616 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0917
Minimum - Maximum-1.00423 - 1.3877876
Average (Standard dev.)0.00090857653 (±0.026403503)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions344344344
Spacing344344344
CellA=B=C: 288.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_42476_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42476_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_42476_half_map_2.map
Projections & Slices
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Sample components

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Entire : PLCb3-Gbg-Gaq complex

EntireName: PLCb3-Gbg-Gaq complex
Components
  • Complex: PLCb3-Gbg-Gaq complex
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein subunit gamma
    • Protein or peptide: Guanine nucleotide-binding protein G(q) subunit alpha
    • Protein or peptide: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TETRAFLUOROALUMINATE ION
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: PLCb3-Gbg-Gaq complex

SupramoleculeName: PLCb3-Gbg-Gaq complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.41693 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String:
MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #2: Guanine nucleotide-binding protein subunit gamma

MacromoleculeName: Guanine nucleotide-binding protein subunit gamma / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.01531 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
GPMASNNTAS IAQARKLVEQ LKMEANIDRI KVSKAAADLM AYCEAHAKED PLLTPVPASE NPFREKKFFC AIL

UniProtKB: Guanine nucleotide-binding protein subunit gamma

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Macromolecule #3: Guanine nucleotide-binding protein G(q) subunit alpha

MacromoleculeName: Guanine nucleotide-binding protein G(q) subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.676387 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPMACCLSEE AKEARRINDE IERQLRRDKR DARRELKLLL LGTGESGKST FIKQMRIIHG SGYSDEDKRG FTKLVYQNIF TAMQAMIRA MDTLKIPYKY EHNKAHAQLV REVDVEKVSA FENPYVDAIK SLWNDPGIQE CYDRRREYQL SDSTKYYLND L DRVADPAY ...String:
GPMACCLSEE AKEARRINDE IERQLRRDKR DARRELKLLL LGTGESGKST FIKQMRIIHG SGYSDEDKRG FTKLVYQNIF TAMQAMIRA MDTLKIPYKY EHNKAHAQLV REVDVEKVSA FENPYVDAIK SLWNDPGIQE CYDRRREYQL SDSTKYYLND L DRVADPAY LPTQQDVLRV RVPTTGIIEY PFDLQSVIFR MVDVGGQRSE RRKWIHCFEN VTSIMFLVAL SEYDQVLVES DN ENRMEES KALFRTIITY PWFQNSSVIL FLNKKDLLEE KIMYSHLVDY FPEYDGPQRD AQAAREFILK MFVDLNPDSD KII YSHFTC ATDTENIRFV FAAVKDTILQ LNLKEYNLV

UniProtKB: Guanine nucleotide-binding protein G(q) subunit alpha

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Macromolecule #4: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3

MacromoleculeName: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: phosphoinositide phospholipase C
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 139.104719 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPAMDPEFMA LQLEPPTVVE TLRRGSKFIK WDEETSSRNL VTLRVDPNGF FLYWTGPNME VDTLDISSIR DTRTGRYARL PKDPKIREV LGFGGPDARL EEKLMTVVSG PDPVNTVFLN FMAVQDDTAK VWSEELFKLA MNILAQNASR NTFLRKAYTK L KLQVNQDG ...String:
GPAMDPEFMA LQLEPPTVVE TLRRGSKFIK WDEETSSRNL VTLRVDPNGF FLYWTGPNME VDTLDISSIR DTRTGRYARL PKDPKIREV LGFGGPDARL EEKLMTVVSG PDPVNTVFLN FMAVQDDTAK VWSEELFKLA MNILAQNASR NTFLRKAYTK L KLQVNQDG RIPVKNILKM FSADKKRVET ALESCGLKFN RSESIRPDEF SLEIFERFLN KLCLRPDIDK ILLEIGAKGK PY LTLEQLM DFINQKQRDP RLNEVLYPPL RPSQARLLIE KYEPNQQFLE RDQMSMEGFS RYLGGEENGI LPLEALDLST DMT QPLSAY FINSSHNTYL TAGQLAGTSS VEMYRQALLW GCRCVELDVW KGRPPEEEPF ITHGFTMTTE VPLRDVLEAI AETA FKTSP YPVILSFENH VDSAKQQAKM AEYCRSIFGD ALLIEPLDKY PLAPGVPLPS PQDLMGRILV KNKKRHRPSA GGPDS AGRK RPLEQSNSAL SESSAATEPS SPQLGSPSSD SCPGLSNGEE VGLEKPSLEP QKSLGDEGLN RGPYVLGPAD REDEEE DEE EEEQTDPKKP TTDEGTASSE VNATEEMSTL VNYIEPVKFK SFEAARKRNK CFEMSSFVET KAMEQLTKSP MEFVEYN KQ QLSRIYPKGT RVDSSNYMPQ LFWNVGCQLV ALNFQTLDVA MQLNAGVFEY NGRSGYLLKP EFMRRPDKSF DPFTEVIV D GIVANALRVK VISGQFLSDR KVGIYVEVDM FGLPVDTRRK YRTRTSQGNS FNPVWDEEPF DFPKVVLPTL ASLRIAAFE EGGKFVGHRI LPVSAIRSGY HYVCLRNEAN QPLCLPALLI YTEASDYIPD DHQDYAEALI NPIKHVSLMD QRARQLAALI GESEAQAGQ ETCQDTQSQQ LGSQPSSNPT PSPLDASPRR PPGPTTSPAS TSLSSPGQRD DLIASILSEV APTPLDELRG H KALVKLRS RQERDLRELR KKHQRKAVTL TRRLLDGLAQ AQAEGRCRLR PGALGGAADV EDTKEGEDEA KRYQEFQNRQ VQ SLLELRE AQVDAEAQRR LEHLRQALQR LREVVLDANT TQFKRLKEMN EREKKELQKI LDRKRHNSIS EAKMRDKHKK EAE LTEINR RHITESVNSI RRLEEAQKQR HDRLVAGQQQ VLQQLAEEEP KLLAQLAQEC QEQRARLPQE IRRSLLGEMP EGLG DGPLV ACASNGHAPG SSGHLSGADS ESQEENTQL

UniProtKB: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3

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Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #6: TETRAFLUOROALUMINATE ION

MacromoleculeName: TETRAFLUOROALUMINATE ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ALF
Molecular weightTheoretical: 102.975 Da
Chemical component information

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 359215
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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