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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-cdc42Chimera
Function / homology
Function and homology information


GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity ...GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / storage vacuole / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / neuron fate determination / modulation by host of viral process / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / cardiac conduction system development / GTP-dependent protein binding / regulation of filopodium assembly / establishment of Golgi localization / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / dendritic spine morphogenesis / mitogen-activated protein kinase kinase kinase binding / embryonic heart tube development / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / nuclear migration / DCC mediated attractive signaling / adherens junction organization / sprouting angiogenesis / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / regulation of mitotic nuclear division / establishment or maintenance of cell polarity / phagocytosis, engulfment / RHOV GTPase cycle / heart contraction / Myogenesis / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / positive regulation of cytokinesis / RHO GTPases activate PAKs / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / positive regulation of DNA replication / negative regulation of protein-containing complex assembly / phagocytic vesicle / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / small monomeric GTPase / G protein activity / filopodium / secretory granule / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / EGFR downregulation / positive regulation of JNK cascade / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / protein localization / G beta:gamma signalling through CDC42 / cytoplasmic ribonucleoprotein granule / mitotic spindle / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / cellular response to type II interferon / endocytosis / positive regulation of neuron apoptotic process / ubiquitin protein ligase activity
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 / Rhs repeat-associated core ...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 family 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
Voxel sizeX=Y=Z: 1.14 Å
Density
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-cdc42Chimera

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

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
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

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