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- EMDB-10314: Tc holotoxin prepore TcdA1-TcdB2-TccC3-Cdc42 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-10314
TitleTc holotoxin prepore TcdA1-TcdB2-TccC3-Cdc42
Map dataEM density map of ABC holotoxin formed by TcdA1 and TcdB2-TccC3-Cdc42
Sample
  • Complex: Complex of TcdA1 pentamer and TcdB2-TccC3-Cdc42
    • Protein or peptide: TcdA1
    • Protein or peptide: chimeric protein TcdB2-TccC3-cdc42
Function / homology
Function and homology information


GBD domain binding / positive regulation of pinocytosis / COG complex / endothelin receptor signaling pathway involved in heart process / storage vacuole / cardiac neural crest cell migration involved in outflow tract morphogenesis / dendritic cell migration / neuron fate determination / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis ...GBD domain binding / positive regulation of pinocytosis / COG complex / endothelin receptor signaling pathway involved in heart process / storage vacuole / cardiac neural crest cell migration involved in outflow tract morphogenesis / dendritic cell migration / neuron fate determination / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / regulation of attachment of spindle microtubules to kinetochore / organelle transport along microtubule / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / cardiac conduction system development / host-mediated perturbation of viral process / leading edge membrane / regulation of filopodium assembly / neuropilin signaling pathway / establishment of Golgi localization / filopodium assembly / cell junction assembly / dendritic spine morphogenesis / adherens junction organization / establishment of epithelial cell apical/basal polarity / GTP-dependent protein binding / thioesterase binding / regulation of lamellipodium assembly / embryonic heart tube development / regulation of stress fiber assembly / RHO GTPases activate KTN1 / DCC mediated attractive signaling / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / Wnt signaling pathway, planar cell polarity pathway / phagocytosis, engulfment / RHOV GTPase cycle / Myogenesis / nuclear migration / regulation of mitotic nuclear division / small GTPase-mediated signal transduction / spindle midzone / positive regulation of cytokinesis / RHOJ GTPase cycle / heart contraction / RHOQ GTPase cycle / Golgi organization / establishment of cell polarity / RHOU GTPase cycle / establishment or maintenance of cell polarity / RHO GTPases activate PAKs / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / negative regulation of protein-containing complex assembly / RHO GTPases activate IQGAPs / GPVI-mediated activation cascade / positive regulation of lamellipodium assembly / phagocytic vesicle / positive regulation of stress fiber assembly / RAC1 GTPase cycle / EPHB-mediated forward signaling / positive regulation of substrate adhesion-dependent cell spreading / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / integrin-mediated signaling pathway / actin filament organization / small monomeric GTPase / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / filopodium / EGFR downregulation / RHO GTPases Activate Formins / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / MAPK6/MAPK4 signaling / cellular response to type II interferon / endocytosis / apical part of cell / cell-cell junction / cytoplasmic ribonucleoprotein granule / mitotic spindle / G beta:gamma signalling through CDC42 / intracellular protein localization / ubiquitin protein ligase activity / Factors involved in megakaryocyte development and platelet production / positive regulation of cell growth / actin cytoskeleton organization / G protein activity / midbody / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / neuron projection / postsynapse / positive regulation of cell migration / Golgi membrane
Similarity search - Function
Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / Toxin complex C-like repeat / Tripartite Tc toxins repeat / Cdc42 / : ...Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / Toxin complex C-like repeat / Tripartite Tc toxins repeat / Cdc42 / : / Rhs repeat-associated core / Small GTPase Rho / Small GTPase Rho domain profile. / Integrin alpha, N-terminal / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cell division control protein 42 homolog / TccC3 / TcdB2
Similarity search - Component
Biological speciesPhotorhabdus luminescens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsRoderer D / Raunser S / Schubert E / Sitsel O
Funding support Germany, 1 items
OrganizationGrant numberCountry
European Research Council615984 Germany
CitationJournal: Nat Commun / Year: 2019
Title: Towards the application of Tc toxins as a universal protein translocation system.
Authors: Daniel Roderer / Evelyn Schubert / Oleg Sitsel / Stefan Raunser /
Abstract: Tc toxins are bacterial protein complexes that inject cytotoxic enzymes into target cells using a syringe-like mechanism. Tc toxins are composed of a membrane translocator and a cocoon that ...Tc toxins are bacterial protein complexes that inject cytotoxic enzymes into target cells using a syringe-like mechanism. Tc toxins are composed of a membrane translocator and a cocoon that encapsulates a toxic enzyme. The toxic enzyme varies between Tc toxins from different species and is not conserved. Here, we investigate whether the toxic enzyme can be replaced by other small proteins of different origin and properties, namely Cdc42, herpes simplex virus ICP47, Arabidopsis thaliana iLOV, Escherichia coli DHFR, Ras-binding domain of CRAF kinase, and TEV protease. Using a combination of electron microscopy, X-ray crystallography and in vitro translocation assays, we demonstrate that it is possible to turn Tc toxins into customizable molecular syringes for delivering proteins of interest across membranes. We also infer the guidelines that protein cargos must obey in terms of size, charge, and fold in order to apply Tc toxins as a universal protein translocation system.
History
DepositionSep 14, 2019-
Header (metadata) releaseDec 11, 2019-
Map releaseDec 11, 2019-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.041
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.041
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10314.png

Downloads & links

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Map

FileDownload / File: emd_10314.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM density map of ABC holotoxin formed by TcdA1 and TcdB2-TccC3-Cdc42
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 480 pix.
= 547.2 Å		1.14 Å/pix.
x 480 pix.
= 547.2 Å		1.14 Å/pix.
x 480 pix.
= 547.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.041 / Movie #1: 0.041
Minimum - Maximum-0.07510522 - 0.16168544
Average (Standard dev.)0.00057571457 (±0.0055799535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 547.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.141.141.14
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z547.200547.200547.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0750.1620.001

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Supplemental data

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Sample components

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Entire : Complex of TcdA1 pentamer and TcdB2-TccC3-Cdc42

EntireName: Complex of TcdA1 pentamer and TcdB2-TccC3-Cdc42
Components
  • Complex: Complex of TcdA1 pentamer and TcdB2-TccC3-Cdc42
    • Protein or peptide: TcdA1
    • Protein or peptide: chimeric protein TcdB2-TccC3-cdc42

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Supramolecule #1: Complex of TcdA1 pentamer and TcdB2-TccC3-Cdc42

SupramoleculeName: Complex of TcdA1 pentamer and TcdB2-TccC3-Cdc42 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1.7 MDa

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Macromolecule #1: TcdA1

MacromoleculeName: TcdA1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNESVKEIPD VLKSQCGFNC LTDISHSSFN EFRQQVSEHL SWSETHDLYH DAQQAQKDNR LYEARILKRA NPQLQNAVHL AILAPNAELI GYNNQFSGRA SQYVAPGTVS SMFSPAAYLT ELYREARNLH ASDSVYYLDT RRPDLKSMAL SQQNMDIELS TLSLSNELLL ...String:
MNESVKEIPD VLKSQCGFNC LTDISHSSFN EFRQQVSEHL SWSETHDLYH DAQQAQKDNR LYEARILKRA NPQLQNAVHL AILAPNAELI GYNNQFSGRA SQYVAPGTVS SMFSPAAYLT ELYREARNLH ASDSVYYLDT RRPDLKSMAL SQQNMDIELS TLSLSNELLL ESIKTESKLE NYTKVMEMLS TFRPSGATPY HDAYENVREV IQLQDPGLEQ LNASPAIAGL MHQASLLGIN ASISPELFNI LTEEITEGNA EELYKKNFGN IEPASLAMPE YLKRYYNLSD EELSQFIGKA SNFGQQEYSN NQLITPVVNS SDGTVKVYRI TREYTTNAYQ MDVELFPFGG ENYRLDYKFK NFYNASYLSI KLNDKRELVR TEGAPQVNIE YSANITLNTA DISQPFEIGL TRVLPSGSWA YAAAKFTVEE YNQYSFLLKL NKAIRLSRAT ELSPTILEGI VRSVNLQLDI NTDVLGKVFL TKYYMQRYAI HAETALILCN APISQRSYDN QPSQFDRLFN TPLLNGQYFS TGDEEIDLNS GSTGDWRKTI LKRAFNIDDV SLFRLLKITD HDNKDGKIKN NLKNLSNLYI GKLLADIHQL TIDELDLLLI AVGEGKTNLS AISDKQLATL IRKLNTITSW LHTQKWSVFQ LFIMTSTSYN KTLTPEIKNL LDTVYHGLQG FDKDKADLLH VMAPYIAATL QLSSENVAHS VLLWADKLQP GDGAMTAEKF WDWLNTKYTP GSSEAVETQE HIVQYCQALA QLEMVYHSTG INENAFRLFV TKPEMFGAAT GAAPAHDALS LIMLTRFADW VNALGEKASS VLAAFEANSL TAEQLADAMN LDANLLLQAS IQAQNHQHLP PVTPENAFSC WTSINTILQW VNVAQQLNVA PQGVSALVGL DYIQSMKETP TYAQWENAAG VLTAGLNSQQ ANTLHAFLDE SRSAALSTYY IRQVAKAAAA IKSRDDLYQY LLIDNQVSAA IKTTRIAEAI ASIQLYVNRA LENVEENANS GVISRQFFID WDKYNKRYST WAGVSQLVYY PENYIDPTMR IGQTKMMDAL LQSVSQSQLN ADTVEDAFMS YLTSFEQVAN LKVISAYHDN INNDQGLTYF IGLSETDAGE YYWRSVDHSK FNDGKFAANA WSEWHKIDCP INPYKSTIRP VIYKSRLYLL WLEQKEITKQ TGNSKDGYQT ETDYRYELKL AHIRYDGTWN TPITFDVNKK ISELKLEKNR APGLYCAGYQ GEDTLLVMFY NQQDTLDSYK NASMQGLYIF ADMASKDMTP EQSNVYRDNS YQQFDTNNVR RVNNRYAEDY EIPSSVSSRK DYGWGDYYLS MVYNGDIPTI NYKAASSDLK IYISPKLRII HNGYEGQKRN QCNLMNKYGK LGDKFIVYTS LGVNPNNSSN KLMFYPVYQY SGNTSGLNQG RLLFHRDTTY PSKVEAWIPG AKRSLTNQNA AIGDDYATDS LNKPDDLKQY IFMTDSKGTA TDVSGPVEIN TAISPAKVQI IVKAGGKEQT FTADKDVSIQ PSPSFDEMNY QFNALEIDGS GLNFINNSAS IDVTFTAFAE DGRKLGYESF SIPVTLKVST DNALTLHHNE NGAQYMQWQS YRTRLNTLFA RQLVARATTG IDTILSMETQ NIQEPQLGKG FYATFVIPPY NLSTHGDERW FKLYIKHVVD NNSHIIYSGQ LTDTNINITL FIPLDDVPLN QDYHAKVYMT FKKSPSDGTW WGPHFVRDDK GIVTINPKSI LTHFESVNVL NNISSEPMDF SGANSLYFWE LFYYTPMLVA QRLLHEQNFD EANRWLKYVW SPSGYIVHGQ IQNYQWNVRP LLEDTSWNSD PLDSVDPDAV AQHDPMHYKV STFMRTLDLL IARGDHAYRQ LERDTLNEAK MWYMQALHLL GDKPYLPLST TWSDPRLDRA ADITTQNAHD SAIVALRQNI PTPAPLSLRS ANTLTDLFLP QINEVMMNYW QTLAQRVYNL RHNLSIDGQP LYLPIYATPA DPKALLSAAV ATSQGGGKLP ESFMSLWRFP HMLENARGMV SQLTQFGSTL QNIIERQDAE ALNALLQNQA AELILTNLSI QDKTIEELDA EKTVLEKSKA GAQSRFDSYG KLYDENINAG ENQAMTLRAS AAGLTTAVQA SRLAGAAADL VPNIFGFAGG GSRWGAIAEA TGYVMEFSAN VMNTEADKIS QSETYRRRRQ EWEIQRNNAE AELKQIDAQL KSLAVRREAA VLQKTSLKTQ QEQTQSQLAF LQRKFSNQAL YNWLRGRLAA IYFQFYDLAV ARCLMAEQAY RWELNDDSAR FIKPGAWQGT YAGLLAGETL MLSLAQMEDA HLKRDKRALE VERTVSLAEV YAGLPKDNGP FSLAQEIDKL VSQGSGSAGS GNNNLAFGAG TDTKTSLQAS VSFADLKIRE DYPASLGKIR RIKQISVTLP ALLGPYQDVQ AILSYGDKAG LANGCEALAV SHGMNDSGQF QLDFNDGKFL PFEGIAIDQG TLTLSFPNAS MPEKGKQATM LKTLNDIILH IRYTIK

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Macromolecule #2: chimeric protein TcdB2-TccC3-cdc42

MacromoleculeName: chimeric protein TcdB2-TccC3-cdc42 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQNSQDFSIT ELSLPKGGGA ITGMGEALTP TGPDGMAALS LPLPISAGRG YAPAFTLNYN SGAGNSPFGL GWDCNVMTIR RRTHFGVPHY DETDTFLGPE GEVLVVADQP RDESTLQGIN LGATFTVTGY RSRLESHFSR LEYWQPKTTG KTDFWLIYSP DGQVHLLGKS ...String:
MQNSQDFSIT ELSLPKGGGA ITGMGEALTP TGPDGMAALS LPLPISAGRG YAPAFTLNYN SGAGNSPFGL GWDCNVMTIR RRTHFGVPHY DETDTFLGPE GEVLVVADQP RDESTLQGIN LGATFTVTGY RSRLESHFSR LEYWQPKTTG KTDFWLIYSP DGQVHLLGKS PQARISNPSQ TTQTAQWLLE ASVSSRGEQI YYQYRAEDDT GCEADEITHH LQATAQRYLH IVYYGNRTAS ETLPGLDGSA PSQADWLFYL VFDYGERSNN LKTPPAFSTT GSWLCRQDRF SRYEYGFEIR TRRLCRQVLM YHHLQALDSK ITEHNGPTLV SRLILNYDES AIASTLVFVR RVGHEQDGNV VTLPPLELAY QDFSPRHHAH WQPMDVLANF NAIQRWQLVD LKGEGLPGLL YQDKGAWWYR SAQRLGEIGS DAVTWEKMQP LSVIPSLQSN ASLVDINGDG QLDWVITGPG LRGYHSQRPD GSWTRFTPLN ALPVEYTHPR AQLADLMGAG LSDLVLIGPK SVRLYANTRD GFAKGKDVVQ SGDITLPVPG TDPRKLVAFS DVLGSGQAHL VEVSATKVTC WPNLGRGRFG QPITLPGFSQ PATEFNPAQV YLADLDGSGP TDLIYVHTNR LDIFLNKSGN GFAEPVTLRF PEGLRFDHTC QLQMADVQGL GVASLILSVP HMSPHHWRCD LTNMKPWLLN EMNNNMGVHH TLRYRSSSQF WLDEKAAALT TGQTPVCYLP FPIHTLWQTE TEDEISGNKL VTTLRYARGA WDGREREFRG FGYVEQTDSH QLAQGNAPER TPPALTKNWY ATGLPVIDNA LSTEYWRDDQ AFAGFSPRFT TWQDNKDVPL TPEDDNSRYW FNRALKGQLL RSELYGLDDS TNKHVPYTVT EFRSQVRRLQ HTDSRYPVLW SSVVESRNYH YERIASDPQC SQNITLSSDR FGQPLKQLSV QYPRRQQPAI NLYPDTLPDK LLANSYDDQQ RQLRLTYQQS SWHHLTNNTV RVLGLPDSTR SDIFTYVAEN VPAGGLNLEL LSDKNSLIAD DKPREYLGQQ KTAYTDGQNT TPLQTPTRQA LIAFTETTVF NQSTLSAFNG SIPSDKLSTT LEQAGYQQTN YLFPRTGEDK VWVAHHGYTD YGTAAQFWRP QKQSNTQLTG KITLIWDANY CVVVQTRDAA GLTTSAKYDW RFLTPVQLTD INDNQHLITL DALGRPITLR FWGTENGKMT GYSSPEKASF SPPSDVNAAI ELKKPLPVAQ CQVYAPESWM PVLSQKTFNR LAEQDWQKLY NARIITEDGR ICTLAYRRWV QSQKAIPQLI SLLNNGPRLP PHSLTLTTDR YDHDPEQQIR QQVVFSDGFG RLLQAAARHE AGMARQRNED GSLIINVQHT ENRWAVTGRT EYDNKGQPIR TYQPYFLNDW RYVSNDSARQ EKEAYADTHV YDPIGREIKV ITAKGWFRRT LFTPWFTVNE DENDTAAEVK KVKMPGSRPM KNIDPKLYQK TPTVSVYDNR GLIIRNIDFH RTTANGDPDT RITRHQYDIH GHLNQSIDPR LYEAKQTNNT IKPNFLWQYD LTGNPLCTES IDAGRTVTLN DIEGRPLLTV TATGVIQTRQ YETSSLPGRL LSVAEQTPEE KTSRITERLI WAGNTEAEKD HNLAGQCVRH YDTAGVTRLE SLSLTGTVLS QSSQLLIDTQ EANWTGDNET VWQNMLADDI YTTLSTFDAT GALLTQTDAK GNIQRLAYDV AGQLNGSWLT LKGQTEQVII KSLTYSAAGQ KLREEHGNDV ITEYSYEPET QRLIGIKTRR PSDTKVLQDL RYEYDPVGNV ISIRNDAEAT RFWHNQKVMP ENTYTYDSLY QLISATGREM ANIGQQSHQF PSPALPSDNN TYTNYTRTYT YDRGGNLTKI QHSSPATQNN YTTNITVSNR SNRAVLSTLT EDPAQVDALF DAGGHQNTLI SGQNLNWNTR GELQQVTLVK RDKGANDDRE WYRYSGDGRR MLKINEQQAS NNAQTQRVTY LPNLELRLTQ NSTATTEDLQ VITVGEAGRA QVRVLHWESG KPEDIDNNQL RYSYDNLIGS SQLELDSEGQ IISEEEYYPY GGTALWAARN QTEASYKTIR YSGKERDATG LYYYGYRYYQ PWIGRWLSSD PAGTIDGLNL YRMVRNNPVT LLDPDGLEPM AMQTIKCVVV GDGAVGKTCL LISYTTNKFP SEYVPTVFDN YAVTVMIGGE PYTLGLFDTA GQEDYDRLRP LSYPQTDVFL VCFSVVSPSS FENVKEKWVP EITHHCPKTP FLLVGTQIDL RDDPSTIEKL AKNKQKPITP ETAEKLARDL KAVKYVECSA LTQRGLKNVF DEAILAALEP

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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

Concentration1.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 56665
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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