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- EMDB-30708: Cryo-EM structure of human TSC complex -

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Basic information

Entry
Database: EMDB / ID: EMD-30708
TitleCryo-EM structure of human TSC complex
Map data
Sample
  • Complex: Cryo-EM structure of human TSC complex
    • Protein or peptide: Hamartin
    • Protein or peptide: Isoform 7 of Tuberin
    • Protein or peptide: TBC1 domain family member 7
    • Protein or peptide: unknown protein
KeywordsTSC complex / Regulator of cell growth / GTPase-activating protein / Elongated arch-shaped fold / GENE REGULATION
Function / homology
Function and homology information


memory T cell differentiation / TSC1-TSC2 complex binding / TSC1-TSC2 complex / Inhibition of TSC complex formation by PKB / regulation of insulin receptor signaling pathway / cellular response to decreased oxygen levels / negative regulation of cilium assembly / regulation of cell-matrix adhesion / negative regulation of ATP-dependent activity / response to growth factor ...memory T cell differentiation / TSC1-TSC2 complex binding / TSC1-TSC2 complex / Inhibition of TSC complex formation by PKB / regulation of insulin receptor signaling pathway / cellular response to decreased oxygen levels / negative regulation of cilium assembly / regulation of cell-matrix adhesion / negative regulation of ATP-dependent activity / response to growth factor / cardiac muscle cell differentiation / activation of GTPase activity / Energy dependent regulation of mTOR by LKB1-AMPK / ATPase inhibitor activity / cell projection organization / regulation of stress fiber assembly / negative regulation of cell size / negative regulation of TOR signaling / anoikis / regulation of small GTPase mediated signal transduction / TBC/RABGAPs / AKT phosphorylates targets in the cytosol / protein folding chaperone complex / negative regulation of macroautophagy / Macroautophagy / positive chemotaxis / negative regulation of mitophagy / D-glucose import / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of Wnt signaling pathway / regulation of endocytosis / associative learning / positive regulation of macroautophagy / positive regulation of GTPase activity / positive regulation of focal adhesion assembly / phosphatase binding / vesicle-mediated transport / negative regulation of TORC1 signaling / lipid droplet / myelination / Hsp70 protein binding / protein folding chaperone / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of insulin receptor signaling pathway / GTPase activator activity / cellular response to starvation / cell-matrix adhesion / positive regulation of protein ubiquitination / adult locomotory behavior / TP53 Regulates Metabolic Genes / neural tube closure / hippocampus development / kidney development / Hsp90 protein binding / response to insulin / synapse organization / cerebral cortex development / potassium ion transport / small GTPase binding / endocytosis / protein import into nucleus / intracellular protein localization / lamellipodium / protein-folding chaperone binding / heart development / cytoplasmic vesicle / cell cortex / adaptive immune response / cell population proliferation / lysosome / regulation of cell cycle / postsynaptic density / protein stabilization / ciliary basal body / negative regulation of cell population proliferation / lysosomal membrane / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / protein-containing complex / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Tuberin / Tuberin-type domain / Tuberin, N-terminal / Tuberin / Domain of unknown function (DUF3384) / TBC1 domain family member 7 / TBC1 domain family member 7, domain 2 / Hamartin / Hamartin protein / Tuberin/Ral GTPase-activating protein subunit alpha ...Tuberin / Tuberin-type domain / Tuberin, N-terminal / Tuberin / Domain of unknown function (DUF3384) / TBC1 domain family member 7 / TBC1 domain family member 7, domain 2 / Hamartin / Hamartin protein / Tuberin/Ral GTPase-activating protein subunit alpha / Rap/Ran-GAP domain / Rap/Ran-GAP superfamily / Rap/ran-GAP / Rap GTPase activating proteins domain profile. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Tuberin / Hamartin / TBC1 domain family member 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsYang H / Yu Z / Chen X / Li J / Li N / Cheng J / Gao N / Yuan H / Ye D / Guan K / Xu Y
CitationJournal: Nat Commun / Year: 2021
Title: Structural insights into TSC complex assembly and GAP activity on Rheb.
Authors: Huirong Yang / Zishuo Yu / Xizi Chen / Jiabei Li / Ningning Li / Jiaxuan Cheng / Ning Gao / Hai-Xin Yuan / Dan Ye / Kun-Liang Guan / Yanhui Xu /
Abstract: Tuberous sclerosis complex (TSC) integrates upstream stimuli and regulates cell growth by controlling the activity of mTORC1. TSC complex functions as a GTPase-activating protein (GAP) towards small ...Tuberous sclerosis complex (TSC) integrates upstream stimuli and regulates cell growth by controlling the activity of mTORC1. TSC complex functions as a GTPase-activating protein (GAP) towards small GTPase Rheb and inhibits Rheb-mediated activation of mTORC1. Mutations in TSC genes cause tuberous sclerosis. In this study, the near-atomic resolution structure of human TSC complex reveals an arch-shaped architecture, with a 2:2:1 stoichiometry of TSC1, TSC2, and TBC1D7. This asymmetric complex consists of two interweaved TSC1 coiled-coil and one TBC1D7 that spans over the tail-to-tail TSC2 dimer. The two TSC2 GAP domains are symmetrically cradled within the core module formed by TSC2 dimerization domain and central coiled-coil of TSC1. Structural and biochemical analyses reveal TSC2 GAP-Rheb complimentary interactions and suggest a catalytic mechanism, by which an asparagine thumb (N1643) stabilizes γ-phosphate of GTP and accelerate GTP hydrolysis of Rheb. Our study reveals mechanisms of TSC complex assembly and GAP activity.
History
DepositionNov 25, 2020-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dl2
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30708.png

Downloads & links

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Map

FileDownload / File: emd_30708.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 520 pix.
= 705.12 Å		1.36 Å/pix.
x 520 pix.
= 705.12 Å		1.36 Å/pix.
x 520 pix.
= 705.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.356 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.02987119 - 0.06478125
Average (Standard dev.)-0.000027884756 (±0.0011846756)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 705.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3561.3561.356
M x/y/z520520520
origin x/y/z0.0000.0000.000
length x/y/z705.120705.120705.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-225-225-225
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS520520520
D min/max/mean-0.0300.065-0.000

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of human TSC complex

EntireName: Cryo-EM structure of human TSC complex
Components
  • Complex: Cryo-EM structure of human TSC complex
    • Protein or peptide: Hamartin
    • Protein or peptide: Isoform 7 of Tuberin
    • Protein or peptide: TBC1 domain family member 7
    • Protein or peptide: unknown protein

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Supramolecule #1: Cryo-EM structure of human TSC complex

SupramoleculeName: Cryo-EM structure of human TSC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Hamartin

MacromoleculeName: Hamartin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.945367 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAQQANVGEL LAMLDSPMLG VRDDVTAVFK ENLNSDRGPM LVNTLVDYYL ETSSQPALHI LTTLQEPHDK HLLDRINEYV GKAATRLSI LSLLGHVIRL QPSWKHKLSQ APLLPSLLKC LKMDTDVVVL TTGVLVLITM LPMIPQSGKQ HLLDFFDIFG R LSSWCLKK ...String:
MAQQANVGEL LAMLDSPMLG VRDDVTAVFK ENLNSDRGPM LVNTLVDYYL ETSSQPALHI LTTLQEPHDK HLLDRINEYV GKAATRLSI LSLLGHVIRL QPSWKHKLSQ APLLPSLLKC LKMDTDVVVL TTGVLVLITM LPMIPQSGKQ HLLDFFDIFG R LSSWCLKK PGHVAEVYLV HLHASVYALF HRLYGMYPCN FVSFLRSHYS MKENLETFEE VVKPMMEHVR IHPELVTGSK DH ELDPRRW KRLETHDVVI ECAKISLDPT EASYEDGYSV SHQISARFPH RSADVTTSPY ADTQNSYGCA TSTPYSTSRL MLL NMPGQL PQTLSSPSTR LITEPPQATL WSPSMVCGMT TPPTSPGNVP PDLSHPYSKV FGTTAGGKGT PLGTPATSPP PAPL CHSDD YVHISLPQAT VTPPRKEERM DSARPCLHRQ HHLLNDRGSE EPPGSKGSVT LSDLPGFLGD LASEEDSIEK DKEEA AISR ELSEITTAEA EPVVPRGGFD SPFYRDSLPG SQRKTHSAAS SSQGASVNPE PLHSSLDKLG PDTPKQAFTP IDLPCG SAD ESPAGDRECQ TSLETSIFTP SPCKIPPPTR VGFGSGQPPP YDHLFEVALP KTAHHFVIRK TEELLKKAKG NTEEDGV PS TSPMEVLDRL IQQGADAHSK ELNKLPLPSK SVDWTHFGGS PPSDEIRTLR DQLLLLHNQL LYERFKRQQH ALRNRRLL R KVIKAAALEE HNAAMKDQLK LQEKDIQMWK VSLQKEQARY NQLQEQRDTM VTKLHSQIRQ LQHDREEFYN QSQELQTKL EDCRNMIAEL RIELKKANNK VCHTELLLSQ VSQKLSNSES VQQQMEFLNR QLLVLGEVNE LYLEQLQNKH SDTTKEVEMM KAAYRKELE KNRSHVLQQT QRLDTSQKRI LELESHLAKK DHLLLEQKKY LEDVKLQARG QLQAAESRYE AQKRITQVFE L EILDLYGR LEKDGLLKKL EEEKAEAAEA AEERLDCCND GCSDSMVGHN EEASGHNGET KTPRPSSARG SSGSRGGGGS SS SSSELST PEKPPHQRAG PFSSRWETTM GEASASIPTT VGSLPSSKSF LGMKARELFR NKSESQCDED GMTSSLSESL KTE LGKDLG VEAKIPLNLD GPHPSPPTPD SVGQLHIMDY NETHHEHS

UniProtKB: Hamartin

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Macromolecule #2: Isoform 7 of Tuberin

MacromoleculeName: Isoform 7 of Tuberin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 188.182312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MECGLNNRIR MIGQICEVAK TKKFEEHAVE ALWKAVADLL QPERPLEARH AVLALLKAIV QGQGERLGVL RALFFKVIKD YPSNEDLHE RLEVFKALTD NGRHITYLEE ELADFVLQWM DVGLSSEFLL VLVNLVKFNS CYLDEYIARM VQMICLLCVR T ASSVDIEV ...String:
MECGLNNRIR MIGQICEVAK TKKFEEHAVE ALWKAVADLL QPERPLEARH AVLALLKAIV QGQGERLGVL RALFFKVIKD YPSNEDLHE RLEVFKALTD NGRHITYLEE ELADFVLQWM DVGLSSEFLL VLVNLVKFNS CYLDEYIARM VQMICLLCVR T ASSVDIEV SLQVLDAVVC YNCLPAESLP LFIVTLCRTI NVKELCEPCW KLMRNLLGTH LGHSAIYNMC HLMEDRAYME DA PLLRGAV FFVGMALWGA HRLYSLRNSP TSVLPSFYQA MACPNEVVSY EIVLSITRLI KKYRKELQVV AWDILLNIIE RLL QQLQTL DSPELRTIVH DLLTTVEELC DQNEFHGSQE RYFELVERCA DQRPESSLLN LISYRAQSIH PAKDGWIQNL QALM ERFFR SESRGAVRIK VLDVLSFVLL INRQFYEEEL INSVVISQLS HIPEDKDHQV RKLATQLLVD LAEGCHTHHF NSLLD IIEK VMARSLSPPP ELEERDVAAY SASLEDVKTA VLGLLVILQT KLYTLPASHA TRVYEMLVSH IQLHYKHSYT LPIASS IRL QAFDFLLLLR ADSLHRLGLP NKDGVVRFSP YCVCDYMEPE RGSEKKTSGP LSPPTGPPGP APAGPAVRLG SVPYSLL FR VLLQCLKQES DWKVLKLVLG RLPESLRYKV LIFTSPCSVD QLCSALCSML SGPKTLERLR GAPEGFSRTD LHLAVVPV L TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLST LARLPHLYRN FAAEQYASVF AISLPYTNPS KFNQYIVCLA HHVIAMWFIR CRLPFRKDFV PFITKGLRSN VLLSFDDTPE KDSFRARST SLNERPKSRI QTSLTSASLG SADENSVAQA DDSLKNLHLE LTETCLDMMA RYVFSNFTAV PKRSPVGEFL L AGGRTKTW LVGNKLVTVT TSVGTGTRSL LGLDSGELQS GPESSSSPGV HVRQTKEAPA KLESQAGQQV SRGARDRVRS MS GGHGLRV GALDVPASQF LGSATSPGPR TAPAAKPEKA SAGTRVPVQE KTNLAAYVPL LTQGWAEILV RRPTGNTSWL MSL ENPLSP FSSDINNMPL QELSNALMAA ERFKEHRDTA LYKSLSVPAA STAKPPPLPR SNTDSAVVME EGSPGEVPVL VEPP GLEDV EAALGMDRRT DAYSRSSSVS SQEEKSLHAE ELVGRGIPIE RVVSSEGGRP SVDLSFQPSQ PLSKSSSSPE LQTLQ DILG DPGDKADVGR LSPEVKARSQ SGTLDGESAA WSASGEDSRG QPEGPLPSSS PRSPSGLRPR GYTISDSAPS RRGKRV ERD ALKSRATASN AEKVPGINPS FVFLQLYHSP FFGDESNKPI LLPNESQSFE RSVQLLDQIP SYDTHKIAVL YVGEGQS NS ELAILSNEHG SYRYTEFLTG LGRLIELKDC QPDKVYLGGL DVCGEDGQFT YCWHDDIMQA VFHIATLMPT KDVDKHRC D KKRHLGNDFV SIVYNDSGED FKLGTIKGQF NFVHVIVTPL DYECNLVSLQ CRKDMEGLVD TSVAKIVSDR NLPFVARQM ALHANMASQV HHSRSNPTDI YPSKWIARLR HIKRLRQRIC EEAAYSNPSL PLVHPPSHSK APAQTPAEPT PGYEVGQRKR LISSVEDFT EFV

UniProtKB: Tuberin

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Macromolecule #3: TBC1 domain family member 7

MacromoleculeName: TBC1 domain family member 7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.911129 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GVEEKKSLEI LLKDDRLDTE KLCTFSQRFP LPSMYRALVW KVLLGILPPH HESHAKVMMY RKEQYLDVLH ALKVVRFVSD ATPQAEVYL RMYQLESGKL PRSPSFPLEP DDEVFLAIAK AMEEMVEDSV DCYWITRRFV NQLNTKYRDS LPQLPKAFEQ Y LNLEDGRL ...String:
GVEEKKSLEI LLKDDRLDTE KLCTFSQRFP LPSMYRALVW KVLLGILPPH HESHAKVMMY RKEQYLDVLH ALKVVRFVSD ATPQAEVYL RMYQLESGKL PRSPSFPLEP DDEVFLAIAK AMEEMVEDSV DCYWITRRFV NQLNTKYRDS LPQLPKAFEQ Y LNLEDGRL LTHLRMCSAA PKLPYDLWFK RCFAGCLPES SLQRVWDKVV SGSCKILVFV AVEILLTFKI KVMALNSAEK IT KFLENIP QDSSDAIVSK AIDLWHKHCG

UniProtKB: TBC1 domain family member 7

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Macromolecule #4: unknown protein

MacromoleculeName: unknown protein / type: protein_or_peptide / ID: 4
Details: The author does not know what chain F is derived from.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.230297 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131022
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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