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- EMDB-27839: Cryo-EM density of BIRC6/casp-3 (clusters) -

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Basic information

Entry
Database: EMDB / ID: EMD-27839
TitleCryo-EM density of BIRC6/casp-3 (clusters)
Map datamain map / consensus
Sample
  • Complex: BIRC6/casp-3
    • Protein or peptide: Baculoviral IAP repeat-containing protein 6
    • Protein or peptide: Caspase-3
KeywordsUbiquitin / E3 ligase / Apoptosis / Autophagy / IAP / LIGASE
Function / homology
Function and homology information


caspase-3 / phospholipase A2 activator activity / Stimulation of the cell death response by PAK-2p34 / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / glial cell apoptotic process / NADE modulates death signalling / positive regulation of pyroptotic inflammatory response / luteolysis / synapse pruning ...caspase-3 / phospholipase A2 activator activity / Stimulation of the cell death response by PAK-2p34 / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / glial cell apoptotic process / NADE modulates death signalling / positive regulation of pyroptotic inflammatory response / luteolysis / synapse pruning / response to cobalt ion / platelet formation / cellular response to staurosporine / CASP5-mediated substrate cleavage / axonal fasciculation / cyclin-dependent protein serine/threonine kinase inhibitor activity / CASP4-mediated substrate cleavage / response to anesthetic / ALK mutants bind TKIs / death-inducing signaling complex / Apoptotic cleavage of cell adhesion proteins / Apoptosis induced DNA fragmentation / Caspase activation via Dependence Receptors in the absence of ligand / SMAC, XIAP-regulated apoptotic response / (E3-independent) E2 ubiquitin-conjugating enzyme / Flemming body / Activation of caspases through apoptosome-mediated cleavage / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / death receptor binding / striated muscle cell differentiation / neurotrophin TRK receptor signaling pathway / regulation of synaptic vesicle cycle / negative regulation of cytokine production / execution phase of apoptosis / Other interleukin signaling / positive regulation of amyloid-beta formation / response to X-ray / Apoptotic cleavage of cellular proteins / keratinocyte differentiation / microtubule organizing center / ubiquitin conjugating enzyme activity / response to amino acid / response to glucose / response to tumor necrosis factor / Pyroptosis / pyroptotic inflammatory response / Caspase-mediated cleavage of cytoskeletal proteins / response to insulin-like growth factor stimulus / placenta development / cysteine-type endopeptidase inhibitor activity / swimming behavior / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / regulation of macroautophagy / protein catabolic process / response to glucocorticoid / apoptotic signaling pathway / erythrocyte differentiation / negative regulation of extrinsic apoptotic signaling pathway / hippocampus development / regulation of cytokinesis / response to hydrogen peroxide / protein processing / response to nicotine / protein maturation / trans-Golgi network / regulation of protein stability / mitotic spindle / enzyme activator activity / spindle pole / positive regulation of neuron apoptotic process / ubiquitin-protein transferase activity / Signaling by ALK fusions and activated point mutants / response to estradiol / neuron differentiation / peptidase activity / regulation of cell population proliferation / response to lipopolysaccharide / protease binding / midbody / aspartic-type endopeptidase activity / response to hypoxia / response to ethanol / learning or memory / protein phosphorylation / endosome / postsynaptic density / response to xenobiotic stimulus / protein ubiquitination / cell division / cysteine-type endopeptidase activity / apoptotic process / neuronal cell body / centrosome / negative regulation of apoptotic process / protein-containing complex binding / glutamatergic synapse / Golgi apparatus
Similarity search - Function
Baculoviral IAP repeat-containing protein 6 / Baculoviral IAP repeat-containing protein 6 / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 ...Baculoviral IAP repeat-containing protein 6 / Baculoviral IAP repeat-containing protein 6 / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
Caspase-3 / Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsHunkeler M / Fischer ES
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA066996 United States
The Mark Foundation19-001-ELA United States
CitationJournal: Science / Year: 2023
Title: Structures of BIRC6-client complexes provide a mechanism of SMAC-mediated release of caspases.
Authors: Moritz Hunkeler / Cyrus Y Jin / Eric S Fischer /
Abstract: Tight regulation of apoptosis is essential for metazoan development and prevents diseases such as cancer and neurodegeneration. Caspase activation is central to apoptosis, and inhibitor of apoptosis ...Tight regulation of apoptosis is essential for metazoan development and prevents diseases such as cancer and neurodegeneration. Caspase activation is central to apoptosis, and inhibitor of apoptosis proteins (IAPs) are the principal actors that restrain caspase activity and are therefore attractive therapeutic targets. IAPs, in turn, are regulated by mitochondria-derived proapoptotic factors such as SMAC and HTRA2. Through a series of cryo-electron microscopy structures of full-length human baculoviral IAP repeat-containing protein 6 (BIRC6) bound to SMAC, caspases, and HTRA2, we provide a molecular understanding for BIRC6-mediated caspase inhibition and its release by SMAC. The architecture of BIRC6, together with near-irreversible binding of SMAC, elucidates how the IAP inhibitor SMAC can effectively control a processive ubiquitin ligase to respond to apoptotic stimuli.
History
DepositionAug 15, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27839.png

Downloads & links

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Map

FileDownload / File: emd_27839.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map / consensus
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 352 pix.
= 424.829 Å		1.21 Å/pix.
x 352 pix.
= 424.829 Å		1.21 Å/pix.
x 352 pix.
= 424.829 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2069 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.31
Minimum - Maximum-1.367971 - 2.6989758
Average (Standard dev.)-0.0009771738 (±0.05966204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 424.8288 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27839_msk_1.map
Projections & Slices
AxesZYX

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Mask #2

Fileemd_27839_msk_2.map
Projections & Slices
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Additional map: cluster 1

Fileemd_27839_additional_1.map
Annotationcluster 1
Projections & Slices
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Additional map: cluster 3

Fileemd_27839_additional_2.map
Annotationcluster 3
Projections & Slices
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Additional map: cluster 2

Fileemd_27839_additional_3.map
Annotationcluster 2
Projections & Slices
AxesZYX

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Additional map: cluster 4

Fileemd_27839_additional_4.map
Annotationcluster 4
Projections & Slices
AxesZYX

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Additional map: cluster 5

Fileemd_27839_additional_5.map
Annotationcluster 5
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cluster 6

Fileemd_27839_additional_6.map
Annotationcluster 6
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 2

Fileemd_27839_half_map_1.map
Annotationhalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 1

Fileemd_27839_half_map_2.map
Annotationhalf-map 1
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : BIRC6/casp-3

EntireName: BIRC6/casp-3
Components
  • Complex: BIRC6/casp-3
    • Protein or peptide: Baculoviral IAP repeat-containing protein 6
    • Protein or peptide: Caspase-3

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Supramolecule #1: BIRC6/casp-3

SupramoleculeName: BIRC6/casp-3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.132 MDa

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Macromolecule #1: Baculoviral IAP repeat-containing protein 6

MacromoleculeName: Baculoviral IAP repeat-containing protein 6 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: Ligases
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGDWSHPQFE KSGGGSGGLE VLFQGPSRTM VTGGGAAPPG TVTEPLPSVI VLSAGRKMAA AAAAASGPGC SSAAGAGAAG VSEWLVLRDG CMHCDADGLH SLSYHPALNA ILAVTSRGTI KVIDGTSGAT LQASALSAKP GGQVKCQYIS AVDKVIFVDD YAVGCRKDLN ...String:
MGDWSHPQFE KSGGGSGGLE VLFQGPSRTM VTGGGAAPPG TVTEPLPSVI VLSAGRKMAA AAAAASGPGC SSAAGAGAAG VSEWLVLRDG CMHCDADGLH SLSYHPALNA ILAVTSRGTI KVIDGTSGAT LQASALSAKP GGQVKCQYIS AVDKVIFVDD YAVGCRKDLN GILLLDTALQ TPVSKQDDVV QLELPVTEAQ QLLSACLEKV DISSTEGYDL FITQLKDGLK NTSHETAANH KVAKWATVTF HLPHHVLKSI ASAIVNELKK INQNVAALPV ASSVMDRLSY LLPSARPELG VGPGRSVDRS LMYSEANRRE TFTSWPHVGY RWAQPDPMAQ AGFYHQPASS GDDRAMCFTC SVCLVCWEPT DEPWSEHERH SPNCPFVKGE HTQNVPLSVT LATSPAQFPC TDGTDRISCF GSGSCPHFLA AATKRGKICI WDVSKLMKVH LKFEINAYDP AIVQQLILSG DPSSGVDSRR PTLAWLEDSS SCSDIPKLEG DSDDLLEDSD SEEHSRSDSV TGHTSQKEAM EVSLDITALS ILQQPEKLQW EIVANVLEDT VKDLEELGAN PCLTNSKSEK TKEKHQEQHN IPFPCLLAGG LLTYKSPATS PISSNSHRSL DGLSRTQGES ISEQGSTDNE SCTNSELNSP LVRRTLPVLL LYSIKESDEK AGKIFSQMNN IMSKSLHDDG FTVPQIIEME LDSQEQLLLQ DPPVTYIQQF ADAAANLTSP DSEKWNSVFP KPGTLVQCLR LPKFAEEENL CIDSITPCAD GIHLLVGLRT CPVESLSAIN QVEALNNLNK LNSALCNRRK GELESNLAVV NGANISVIQH ESPADVQTPL IIQPEQRNVS GGYLVLYKMN YATRIVTLEE EPIKIQHIKD PQDTITSLIL LPPDILDNRE DDCEEPIEDM QLTSKNGFER EKTSDISTLG HLVITTQGGY VKILDLSNFE ILAKVEPPKK EGTEEQDTFV SVIYCSGTDR LCACTKGGEL HFLQIGGTCD DIDEADILVD GSLSKGIEPS SEGSKPLSNP SSPGISGVDL LVDQPFTLEI LTSLVELTRF ETLTPRFSAT VPPCWVEVQQ EQQQRRHPQH LHQQHHGDAA QHTRTWKLQT DSNSWDEHVF ELVLPKACMV GHVDFKFVLN SNITNIPQIQ VTLLKNKAPG LGKVNALNIE VEQNGKPSLV DLNEEMQHMD VEESQCLRLC PFLEDHKEDI LCGPVWLASG LDLSGHAGML TLTSPKLVKG MAGGKYRSFL IHVKAVNERG TEEICNGGMR PVVRLPSLKH QSNKGYSLAS LLAKVAAGKE KSSNVKNENT SGTRKSENLR GCDLLQEVSV TIRRFKKTSI SKERVQRCAM LQFSEFHEKL VNTLCRKTDD GQITEHAQSL VLDTLCWLAG VHSNGPGSSK EGNENLLSKT RKFLSDIVRV CFFEAGRSIA HKCARFLALC ISNGKCDPCQ PAFGPVLLKA LLDNMSFLPA ATTGGSVYWY FVLLNYVKDE DLAGCSTACA SLLTAVSRQL QDRLTPMEAL LQTRYGLYSS PFDPVLFDLE MSGSSCKNVY NSSIGVQSDE IDLSDVLSGN GKVSSCTAAE GSFTSLTGLL EVEPLHFTCV STSDGTRIER DDAMSSFGVT PAVGGLSSGT VGEASTALSS AAQVALQSLS HAMASAEQQL QVLQEKQQQL LKLQQQKAKL EAKLHQTTAA AAAAASAVGP VHNSVPSNPV AAPGFFIHPS DVIPPTPKTT PLFMTPPLTP PNEAVSVVIN AELAQLFPGS VIDPPAVNLA AHNKNSNKSR MNPLGSGLAL AISHASHFLQ PPPHQSIIIE RMHSGARRFV TLDFGRPILL TDVLIPTCGD LASLSIDIWT LGEEVDGRRL VVATDISTHS LILHDLIPPP VCRFMKITVI GRYGSTNARA KIPLGFYYGH TYILPWESEL KLMHDPLKGE GESANQPEID QHLAMMVALQ EDIQCRYNLA CHRLETLLQS IDLPPLNSAN NAQYFLRKPD KAVEEDSRVF SAYQDCIQLQ LQLNLAHNAV QRLKVALGAS RKMLSETSNP EDLIQTSSTE QLRTIIRYLL DTLLSLLHAS NGHSVPAVLQ STFHAQACEE LFKHLCISGT PKIRLHTGLL LVQLCGGERW WGQFLSNVLQ ELYNSEQLLI FPQDRVFMLL SCIGQRSLSN SGVLESLLNL LDNLLSPLQP QLPMHRRTEG VLDIPMISWV VMLVSRLLDY VATVEDEAAA AKKPLNGNQW SFINNNLHTQ SLNRSSKGSS SLDRLYSRKI RKQLVHHKQQ LNLLKAKQKA LVEQMEKEKI QSNKGSSYKL LVEQAKLKQA TSKHFKDLIR LRRTAEWSRS NLDTEVTTAK ESPEIEPLPF TLAHERCISV VQKLVLFLLS MDFTCHADLL LFVCKVLARI ANATRPTIHL CEIVNEPQLE RLLLLLVGTD FNRGDISWGG AWAQYSLTCM LQDILAGELL APVAAEAMEE GTVGDDVGAT AGDSDDSLQQ SSVQLLETID EPLTHDITGA PPLSSLEKDK EIDLELLQDL MEVDIDPLDI DLEKDPLAAK VFKPISSTWY DYWGADYGTY NYNPYIGGLG IPVAKPPANT EKNGSQTVSV SVSQALDARL EVGLEQQAEL MLKMMSTLEA DSILQALTNT SPTLSQSPTG TDDSLLGGLQ AANQTSQLII QLSSVPMLNV CFNKLFSMLQ VHHVQLESLL QLWLTLSLNS SSTGNKENGA DIFLYNANRI PVISLNQASI TSFLTVLAWY PNTLLRTWCL VLHSLTLMTN MQLNSGSSSA IGTQESTAHL LVSDPNLIHV LVKFLSGTSP HGTNQHSPQV GPTATQAMQE FLTRLQVHLS STCPQIFSEF LLKLIHILST ERGAFQTGQG PLDAQVKLLE FTLEQNFEVV SVSTISAVIE SVTFLVHHYI TCSDKVMSRS GSDSSVGARA CFGGLFANLI RPGDAKAVCG EMTRDQLMFD LLKLVNILVQ LPLSGNREYS ARVSVTTNTT DSVSDEEKVS GGKDGNGSST SVQGSPAYVA DLVLANQQIM SQILSALGLC NSSAMAMIIG ASGLHLTKHE NFHGGLDAIS VGDGLFTILT TLSKKASTVH MMLQPILTYM ACGYMGRQGS LATCQLSEPL LWFILRVLDT SDALKAFHDM GGVQLICNNM VTSTRAIVNT ARSMVSTIMK FLDSGPNKAV DSTLKTRILA SEPDNAEGIH NFAPLGTITS SSPTAQPAEV LLQATPPHRR ARSAAWSYIF LPEEAWCDLT IHLPAAVLLK EIHIQPHLAS LATCPSSVSV EVSADGVNML PLSTPVVTSG LTYIKIQLVK AEVASAVCLR LHRPRDASTL GLSQIKLLGL TAFGTTSSAT VNNPFLPSED QVSKTSIGWL RLLHHCLTHI SDLEGMMASA AAPTANLLQT CAALLMSPYC GMHSPNIEVV LVKIGLQSTR IGLKLIDILL RNCAASGSDP TDLNSPLLFG RLNGLSSDST IDILYQLGTT QDPGTKDRIQ ALLKWVSDSA RVAAMKRSGR MNYMCPNSST VEYGLLMPSP SHLHCVAAIL WHSYELLVEY DLPALLDQEL FELLFNWSMS LPCNMVLKKA VDSLLCSMCH VHPNYFSLLM GWMGITPPPV QCHHRLSMTD DSKKQDLSSS LTDDSKNAQA PLALTESHLA TLASSSQSPE AIKQLLDSGL PSLLVRSLAS FCFSHISSSE SIAQSIDISQ DKLRRHHVPQ QCNKMPITAD LVAPILRFLT EVGNSHIMKD WLGGSEVNPL WTALLFLLCH SGSTSGSHNL GAQQTSARSA SLSSAATTGL TTQQRTAIEN ATVAFFLQCI SCHPNNQKLM AQVLCELFQT SPQRGNLPTS GNISGFIRRL FLQLMLEDEK VTMFLQSPCP LYKGRINATS HVIQHPMYGA GHKFRTLHLP VSTTLSDVLD RVSDTPSITA KLISEQKDDK EKKNHEEKEK VKAENGFQDN YSVVVASGLK SQSKRAVSAT PPRPPSRRGR TIPDKIGSTS GAEAANKIIT VPVFHLFHKL LAGQPLPAEM TLAQLLTLLY DRKLPQGYRS IDLTVKLGSR VITDPSLSKT DSYKRLHPEK DHGDLLASCP EDEALTPGDE CMDGILDESL LETCPIQSPL QVFAGMGGLA LIAERLPMLY PEVIQQVSAP VVTSTTQEKP KDSDQFEWVT IEQSGELVYE APETVAAEPP PIKSAVQTMS PIPAHSLAAF GLFLRLPGYA EVLLKERKHA QCLLRLVLGV TDDGEGSHIL QSPSANVLPT LPFHVLRSLF STTPLTTDDG VLLRRMALEI GALHLILVCL SALSHHSPRV PNSSVNQTEP QVSSSHNPTS TEEQQLYWAK GTGFGTGSTA SGWDVEQALT KQRLEEEHVT CLLQVLASYI NPVSSAVNGE AQSSHETRGQ NSNALPSVLL ELLSQSCLIP AMSSYLRNDS VLDMARHVPL YRALLELLRA IASCAAMVPL LLPLSTENGE EEEEQSECQT SVGTLLAKMK TCVDTYTNRL RSKRENVKTG VKPDASDQEP EGLTLLVPDI QKTAEIVYAA TTSLRQANQE KKLGEYSKKA AMKPKPLSVL KSLEEKYVAV MKKLQFDTFE MVSEDEDGKL GFKVNYHYMS QVKNANDANS AARARRLAQE AVTLSTSLPL SSSSSVFVRC DEERLDIMKV LITGPADTPY ANGCFEFDVY FPQDYPSSPP LVNLETTGGH SVRFNPNLYN DGKVCLSILN TWHGRPEEKW NPQTSSFLQV LVSVQSLILV AEPYFNEPGY ERSRGTPSGT QSSREYDGNI RQATVKWAML EQIRNPSPCF KEVIHKHFYL KRVEIMAQCE EWIADIQQYS SDKRVGRTMS HHAAALKRHT AQLREELLKL PCPEGLDPDT DDAPEVCRAT TGAEETLMHD QVKPSSSKEL PSDFQL

UniProtKB: Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6

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Macromolecule #2: Caspase-3

MacromoleculeName: Caspase-3 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO / EC number: caspase-3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MENTENSVDS KSIKNLEPKI IHGSESMDSG ISLDNSYKMD YPEMGLCIII NNKNFHKSTG MTSRSGTDVD AANLRETFRN LKYEVRNKND LTREEIVELM RDVSKEDHSK RSSFVCVLLS HGEEGIIFGT NGPVDLKKIT NFFRGDRCRS LTGKPKLFII QACRGTELDC ...String:
MENTENSVDS KSIKNLEPKI IHGSESMDSG ISLDNSYKMD YPEMGLCIII NNKNFHKSTG MTSRSGTDVD AANLRETFRN LKYEVRNKND LTREEIVELM RDVSKEDHSK RSSFVCVLLS HGEEGIIFGT NGPVDLKKIT NFFRGDRCRS LTGKPKLFII QACRGTELDC GIETDSGVDD DMACHKIPVE ADFLYAYSTA PGYYSWRNSK DGSWFIQSLC AMLKQYADKL EFMHILTRVN RKVATEFESF SFDATFHAKK QIPCIVSMLT KELYFYHLEH HHHHH

UniProtKB: Caspase-3

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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

Concentration2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
30.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium chloride
3.0 mMC9H15O6PTCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283.15 K / Instrument: LEICA EM GP
Detailsadded CHAPSO to 0.4 mM

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
DetailsData collection in counting mode, using multi-shot scheme (9 holes per stage position, 2 movies per hole)
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 10422 / Average exposure time: 2.5 sec. / Average electron dose: 51.401 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: 0.8 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 2533321
Startup modelType of model: OTHER / Details: ab initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 671917
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 8 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER

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