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- EMDB-18689: Maps of Collagen VI half- and full-beads -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-18689
TitleMaps of Collagen VI half- and full-beads
Map datafull-bead map, with one of the half-beads not in focus
Sample
  • Organelle or cellular component: Collagen VI bead
    • Protein or peptide: CO6A1_HUMAN; Collagen alpha-1(VI) chain
    • Protein or peptide: CO6A2_HUMAN; Collagen alpha-2(VI) chain
    • Protein or peptide: CO6A3_HUMAN; Collagen alpha-3(VI) chain
KeywordsCollagen / Extracellular matrix / STRUCTURAL PROTEIN
Function / homology
Function and homology information


regulation of collagen fibril organization / response to polyamine macromolecule / response to bleomycin / muscle cell apoptotic process / collagen type VI trimer / caveola assembly / skeletal muscle tissue growth / multicellular organismal locomotion / muscle system process / apoptotic nuclear changes ...regulation of collagen fibril organization / response to polyamine macromolecule / response to bleomycin / muscle cell apoptotic process / collagen type VI trimer / caveola assembly / skeletal muscle tissue growth / multicellular organismal locomotion / muscle system process / apoptotic nuclear changes / mitochondrial transmembrane transport / reduction of food intake in response to dietary excess / limb joint morphogenesis / response to decreased oxygen levels / fat cell proliferation / Collagen chain trimerization / extracellular matrix assembly / platelet-derived growth factor binding / tissue remodeling / basement membrane organization / skeletal muscle fiber differentiation / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / collagen metabolic process / lung epithelial cell differentiation / respiratory system process / skeletal muscle tissue regeneration / sensory perception of mechanical stimulus / 2-oxoglutarate metabolic process / mitochondrial depolarization / myelination in peripheral nervous system / energy reserve metabolic process / Signaling by PDGF / collagen trimer / NCAM1 interactions / collagen fibril organization / cartilage development / response to muscle activity / muscle organ development / Assembly of collagen fibrils and other multimeric structures / regulation of cell size / response to pain / myofibril / intracellular vesicle / lung alveolus development / lung morphogenesis / bone mineralization / transmission of nerve impulse / endodermal cell differentiation / uterus development / Collagen degradation / homeostasis of number of cells / basement membrane / hair follicle development / ECM proteoglycans / single fertilization / canonical Wnt signaling pathway / Integrin cell surface interactions / adipose tissue development / skeletal muscle fiber development / response to glucose / response to mechanical stimulus / response to UV / tricarboxylic acid cycle / collagen binding / reactive oxygen species metabolic process / mitochondrion organization / phosphatidylinositol 3-kinase/protein kinase B signal transduction / insulin-like growth factor receptor signaling pathway / extracellular matrix / sarcoplasmic reticulum / response to reactive oxygen species / glycolytic process / protein tetramerization / cellular response to amino acid stimulus / serine-type endopeptidase inhibitor activity / bone development / cell morphogenesis / response to toxic substance / sarcolemma / autophagy / response to wounding / circadian rhythm / osteoblast differentiation / extracellular vesicle / insulin receptor signaling pathway / heart development / gene expression / neuron apoptotic process / collagen-containing extracellular matrix / response to lipopolysaccharide / cell adhesion / response to xenobiotic stimulus / inflammatory response / endoplasmic reticulum lumen / lysosomal membrane / protein-containing complex / mitochondrion / extracellular space / extracellular exosome
Similarity search - Function
Collagen alpha-3(VI) chain, vWA domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / von Willebrand factor type A domain / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. ...Collagen alpha-3(VI) chain, vWA domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / von Willebrand factor type A domain / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Collagen alpha-1(VI) chain / Collagen alpha-2(VI) chain / Collagen alpha-3(VI) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsSchulte T / Speranzini V / Chaves-Sanjuan A / Ricagno S
Funding support Italy, 1 items
OrganizationGrant numberCountry
Italian Ministry of EducationPRIN 2020 (20207XLJB2) Italy
CitationJournal: Nature Communications / Year: 2024
Title: Helical superstructures between amyloid and collagen in cardiac fibrils from a patient with AL amyloidosis
Authors: Schulte T / Chaves-Sanjuan A / Speranzini V / Ricagno S
History
DepositionOct 19, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18689.png

Downloads & links

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Map

FileDownload / File: emd_18689.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull-bead map, with one of the half-beads not in focus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.61 Å/pix.
x 384 pix.
= 1001.088 Å		2.61 Å/pix.
x 384 pix.
= 1001.088 Å		2.61 Å/pix.
x 384 pix.
= 1001.088 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.607 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-3.5774019 - 7.747102
Average (Standard dev.)-0.0013334955 (±0.1818145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 1001.088 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18689_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_18689_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: composite map obtained by fitting the focused half-bead...

Fileemd_18689_additional_2.map
Annotationcomposite map obtained by fitting the focused half-bead map into the unfocused half-bead of the full map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map A associated with main map

Fileemd_18689_half_map_1.map
Annotationhalf-map A associated with main map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map B associated with main map

Fileemd_18689_half_map_2.map
Annotationhalf-map B associated with main map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Collagen VI bead

EntireName: Collagen VI bead
Components
  • Organelle or cellular component: Collagen VI bead
    • Protein or peptide: CO6A1_HUMAN; Collagen alpha-1(VI) chain
    • Protein or peptide: CO6A2_HUMAN; Collagen alpha-2(VI) chain
    • Protein or peptide: CO6A3_HUMAN; Collagen alpha-3(VI) chain

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Supramolecule #1: Collagen VI bead

SupramoleculeName: Collagen VI bead / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Collagen VI co-extracted with light chain amyloid AL59
Source (natural)Organism: Homo sapiens (human) / Organ: HEART

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Macromolecule #1: CO6A1_HUMAN; Collagen alpha-1(VI) chain

MacromoleculeName: CO6A1_HUMAN; Collagen alpha-1(VI) chain / type: protein_or_peptide / ID: 1 / Details: CO6A1_HUMAN; Collagen alpha-1(VI) chain; P12109 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: HEART
SequenceString: MRAARALLPL LLQACWTAAQ DEPETPRAVA FQDCPVDLFF VLDTSESVAL RLKPYGALVD KVKSFTKRFI DNLRDRYYRC DRNLVWNAGA LHYSDEVEII QGLTRMPGGR DALKSSVDAV KYFGKGTYTD CAIKKGLEQL LVGGSHLKEN KYLIVVTDGH PLEGYKEPCG ...String:
MRAARALLPL LLQACWTAAQ DEPETPRAVA FQDCPVDLFF VLDTSESVAL RLKPYGALVD KVKSFTKRFI DNLRDRYYRC DRNLVWNAGA LHYSDEVEII QGLTRMPGGR DALKSSVDAV KYFGKGTYTD CAIKKGLEQL LVGGSHLKEN KYLIVVTDGH PLEGYKEPCG GLEDAVNEAK HLGVKVFSVA ITPDHLEPRL SIIATDHTYR RNFTAADWGQ SRDAEEAISQ TIDTIVDMIK NNVEQVCCSF ECQPARGPPG LRGDPGFEGE RGKPGLPGEK GEAGDPGRPG DLGPVGYQGM KGEKGSRGE KGSRGPKGYK GEKGKRGIDG VDGVKGEMGY PGLPGCKGSP GFDGIQGPPG PKGDPGAFGL KGEKGEPGAD GEAGRPGSSG PSGDEGQPGE PGPPGEKGEA GDEGNPGPDG APGERGGPGE RGPRGTPGTR GPRGDPGEAG PQGDQGREGP VGVPGDPGEA GPIGPKGYRG DEGPPGSEGA RGAPGPAGPP GDPGLMGERG EDGPAGNGTE GFPGFPGYPG NRGAPGINGT KGYPGLKGDE GEAGDPGDDN NDIAPRGVKG AKGYRGPEGP QGPPGHQGPP GPDECEILDI IMKMCSCCEC KCGPIDLLFV LDSSESIGLQ NFEIAKDFVV KVIDRLSRDE LVKFEPGQSY AGVVQYSHSQ MQEHVSLRSP SIRNVQELKE AIKSLQWMAG GTFTGEALQY TRDQLLPPSP NNRIALVITD GRSDTQRDTT PLNVLCSPGI QVVSVGIKDV FDFIPGSDQL NVISCQGLAP SQGRPGLSLV KENYAELLED AFLKNVTAQI CIDKKCPDYT CPITFSSPAD ITILLDGSAS VGSHNFDTTK RFAKRLAERF LTAGRTDPAH DVRVAVVQYS GTGQQRPERA SLQFLQNYTA LASAVDAMDF INDATDVNDA LGYVTRFYRE ASSGAAKKRL LLFSDGNSQG ATPAAIEKAV Q EAQRAGIE IFVVVVGRQV NEPHIRVLVT GKTAEYDVAY GESHLFRVPS YQALLRGVFH QTVSRKVALG

UniProtKB: Collagen alpha-1(VI) chain

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Macromolecule #2: CO6A2_HUMAN; Collagen alpha-2(VI) chain

MacromoleculeName: CO6A2_HUMAN; Collagen alpha-2(VI) chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: HEART
SequenceString: MLQGTCSVLL LWGILGAIQA QQQEVISPDT TERNNNCPEK TDCPIHVYFV LDTSESVTMQ SPTDILLFHM KQFVPQFISQ LQNEFYLDQV ALSWRYGGLH FSDQVEVFSP PGSDRASFIK NLQGISSFRR GTFTDCALAN MTEQIRQDRS KGTVHFAVVI TDGHVTGSPC ...String:
MLQGTCSVLL LWGILGAIQA QQQEVISPDT TERNNNCPEK TDCPIHVYFV LDTSESVTMQ SPTDILLFHM KQFVPQFISQ LQNEFYLDQV ALSWRYGGLH FSDQVEVFSP PGSDRASFIK NLQGISSFRR GTFTDCALAN MTEQIRQDRS KGTVHFAVVI TDGHVTGSPC GGIKLQAERA REEGIRLFAV APNQNLKEQG LRDIASTPHE LYRNDYATML PDSTEIDQDT INRIIKVMKH EAYGECYKVS CLEIPGPSGP KGYRGQKGAK GNMGEPGEPG QKGRQGDPGI EGPIGFPGPK GVPGFKGEKG EFGADGRKGA PGLAGKNGTD GQKGKLGRIG PPGCKGDPGN RGPDGYPGEA GSPGERGDQG GKGDPGRPGR RGPPGEIGAK GSKGYQGNSG APGSPGVKGA KGGPGPRGPK GEPGRRGDPG TKGSPGSDGP KGEKGDPGPE GPRGLAGEVG NKGAKGDRGL PGPRGPQGAL GEPGKQGSRG DPGDAGPRGD SGQPGPKGDP GRPGFSYPGP RGAPGEKGEP GPRGPEGGRG DFGLKGEPGR KGEKGEPADP GPPGEPGPRG PRGVPGPEGE PGPPGDPGLT ECDVMTYVRE TCGCCDCEKR CGALDVVFVI DSSESIGYTN FTLEKNFVIN VVNRLGAIAK DPKSETGTRV GVVQYSHEGT FEAIQLDDER IDSLSSFKEA VKNLEWIAGG TWTPSALKFA YDRLIKESRR QKTRVFAVVI TDGRHDPRDD DLNLRALCDR DVTVTAIGIG DMFHEKHESE NLYSIACDKP QQVRNMTLFS DLVAEKFIDD MEDVLCPDPQ IVCPDLPCQT ELSVAQCTQR PVDIVFLLDG SERLGEQNFH KARRFVEQVA RRLTLARRDD DPLNARVALL QFGGPGEQQV AFPLSHNLTA IHEALETTQY LNSFSHVGAG VVHAINAIVR SPRGGARRHA ELSFVFLTDG VTGNDSLHES AHSMRKQNVV PTVLALGSDV DMDVLTTLSL GDRAAVFHEK DYDSLAQPGF FDRFIRWIC

UniProtKB: Collagen alpha-2(VI) chain

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Macromolecule #3: CO6A3_HUMAN; Collagen alpha-3(VI) chain

MacromoleculeName: CO6A3_HUMAN; Collagen alpha-3(VI) chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: HEART
SequenceString: MRKHRHLPLV AVFCLFLSGF PTTHAQQQQA DVKNGAAADI IFLVDSSWTI GEEHFQLVRE FLYDVVKSLA VGENDFHFAL VQFNGNPHTE FLLNTYRTKQ EVLSHISNMS YIGGTNQTGK GLEYIMQSHL TKAAGSRAGD GVPQVIVVLT DGHSKDGLAL PSAELKSADV ...String:
MRKHRHLPLV AVFCLFLSGF PTTHAQQQQA DVKNGAAADI IFLVDSSWTI GEEHFQLVRE FLYDVVKSLA VGENDFHFAL VQFNGNPHTE FLLNTYRTKQ EVLSHISNMS YIGGTNQTGK GLEYIMQSHL TKAAGSRAGD GVPQVIVVLT DGHSKDGLAL PSAELKSADV NVFAIGVEDA DEGALKEIAS EPLNMHMFNL ENFTSLHDIV GNLVSCVHSS VSPERAGDTE TLKDITAQDS ADIIFLIDGS NNTGSVNFAV ILDFLVNLLE KLPIGTQQIR VGVVQFSDEP RTMFSLDTYS TKAQVLGAVK ALGFAGGELA NIGLALDFVV ENHFTRAGGS RVEEGVPQVL VLISAGPSSD EIRYGVVALK QASVFSFGLG AQAASRAELQ HIATDDNLVF TVPEFRSFGD LQEKLLPYIV GVAQRHIVLK PPTIVTQVIE VNKRDIVFLV DGSSALGLAN FNAIRDFIAK VIQRLEIGQD LIQVAVAQYA DTVRPEFYFN THPTKREVIT AVRKMKPLDG SALYTGSALD FVRNNLFTSS AGYRAAEGIP KLLVLITGGK SLDEISQPAQ ELKRSSIMAF AIGNKGADQA ELEEIAFDSS LVFIPAEFRA APLQGMLPGL LAPLRTLSGT PEVHSNKRDI IFLLDGSANV GKTNFPYVRD FVMNLVNSLD IGNDNIRVGL VQFSDTPVTE FSLNTYQTKS DILGHLRQLQ LQGGSGLNTG SALSYVYANH FTEAGGSRIR EHVPQLLLLL TAGQSEDSYL QAANALTRAG ILTFCVGASQ ANKAELEQIA FNPSLVYLMD DFSSLPALPQ QLIQPLTTYV SGGVEEVPLA QPESKRDILF LFDGSANLVG QFPVVRDFLY KIIDELNVKP EGTRIAVAQY SDDVKVESRF DEHQSKPEIL NLVKRMKIKT GKALNLGYAL DYAQRYIFVK SAGSRIEDGV LQFLVLLVAG RSSDRVDGPA SNLKQSGVVP FIFQAKNADP AELEQIVLSP AFILAAESLP KIGDLHPQIV NLLKSVHNGA PAPVSGEKDV VFLLDGSEGV RSGFPLLKEF VQRVVESLDV GQDRVRVAVV QYSDRTRPEF YLNSYMNKQD VVNAVRQLTL LGGPTPNTGA ALEFVLRNIL VSSAGSRITE GVPQLLIVLT ADRSGDDVRN PSVVVKRGGA VPIGIGIGNA DITEMQTISF IPDFAVAIPT FRQLGTVQQV ISERVTQLTR EELSRLQPVL QPLPSPGVGG KRDVVFLIDG SQSAGPEFQY VRTLIERLVD YLDVGFDTTR VAVIQFSDDP KVEFLLNAHS SKDEVQNAVQ RLRPKGGRQI NVGNALEYVS RNIFKRPLGS RIEEGVPQFL VLISSGKSDD EVDDPAVELK QFGVAPFTIA RNADQEELVK ISLSPEYVFS VSTFRELPSL EQKLLTPITT LTSEQIQKLL ASTRYPPPAV ESDAADIVFL IDSSEGVRPD GFAHIRDFVS RIVRRLNIGP SKVRVGVVQF SNDVFPEFYL KTYRSQAPVL DAIRRLRLRG GSPLNTGKAL EFVARNLFVK SAGSRIEDGV PQHLVLVLGG KSQDDVSRFA QVIRSSGIVS LGVGDRNIDR TELQTITNDP RLVFTVREFR ELPNIEERIM NSFGPSAATP APPGVDTPPP SRPEKKKADI VFLLDGSINF RRDSFQEVLR FVSEIVDTVY EDGDSIQVGL VQYNSDPTDE FFLKDFSTKR QIIDAINKVV YKGGRHANTK VGLEHLRVNH FVPEAGSRLD QRVPQIAFVI TGGKSVEDAQ DVSLALTQRG VKVFAVGVRN IDSEEVGKIA SNSATAFRVG NVQELSELSE QVLETLHDAM HETLCPGVTD AAKACNLDVI LGFDGSRDQN VFVAQKGFES KVDAILNRIS QMHRVSCSGG RSPTVRVSVV ANTPSGPVEA FDFDEYQPEM LEKFRNMRSQ HPYVLTEDTL KVYLNKFRQS SPDSVKVVIH FTDGADGDLA DLHRASENLR QEGVRALILV GLERVVNLER LMHLEFGRGF MYDRPLRLNL LDLDYELAEQ LDNIAEKACC GVPCKCSGQR GDRGPIGSIG PKGIPGEDGY RGYPGDEGGP GERGPPGVNG TQGFQGCPGQ RGVKGSRGFP GEKGEVGEIG LDGLDGEDGD KGLPGSSGEK GNPGRRGDKG PRGEKGERGD VGIRGDPGNP GQDSQERGPK GETGDLGPMG VPGRDGVPGG PGETGKNGGF GRRGPPGAKG NKGGPGQPGF EGEQGTRGAQ GPAGPAGPPG LIGEQGISGP RGSGGAAGAP GERGRTGPLG RKGEPGEPGP KGGIGNRGPR GETGDDGRDG VGSEGRRGKK GERGFPGYPG PKGNPGEPGL NGTTGPKGIR GRRGNSGPPG IVGQKGDPGY PGPAGPKGNR GDSIDQCALI QSIKDKCPCC YGPLECPVFP TELAFALDTS EGVNQDTFGR MRDVVLSIVN DLTIAESNCP RGARVAVVTY NNEVTTEIRF ADSKRKSVLL DKIKNLQVAL TSKQQSLETA MSFVARNTFK RVRNGFLMRK VAVFFSNTPT RASPQLREAV LKLSDAGITP LFLTRQEDRQ LINALQINNT AVGHALVLPA GRDLTDFLEN VLTCHVCLDI CNIDPSCGFG SWRPSFRDRR AAGSDVDIDM AFILDSAETT TLFQFNEMKK YIAYLVRQLD MSPDPKASQH FARVAVVQHA PSESVDNASM PPVKVEFSLT DYGSKEKLVD FLSRGMTQLQ GTRALGSAIE YTIENVFESA PNPRDLKIVV LMLTGEVPEQ QLEEAQRVIL QAKCKGYFFV VLGIGRKVNI KEVYTFASEP NDVFFKLVDK STELNEEPLM RFGRLLPSFV SSENAFYLSP DIRKQCDWFQ GDQPTKNLVK FGHKQVNVPN NVTSSPTSNP VTTTKPVTTT KPVTTTTKPV TTTTKPVTII NQPSVKPAAA KPAPAKPVAA KPVATKMATV RPPVAVKPAT AAKPVAAKPA AVRPPAAAAA KPVATKPEVP RPQAAKPAAT KPATTKPMVK MSREVQVFEI TENSAKLHWE RAEPPGPYFY DLTVTSAHDQ SLVLKQNLTV TDRVIGGLLA GQTYHVAVVC YLRSQVRATY HGSFSTKKSQ PPPPQPARSA SSSTINLMVS TEPLALTETD ICKLPKDEGT CRDFILKWYY DPNTKSCARF WYGGCGGNEN KFGSQKECEK VCAPVLAKPG VISVMGT

UniProtKB: Collagen alpha-3(VI) chain

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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
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TALOS ARCTICA
Image recordingImage recording ID: 1 / Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 2049 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 120000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Electron microscopy #1~

Microscopy ID1
MicroscopeFEI TALOS ARCTICA
Image recordingImage recording ID: 2 / Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 2556 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 73000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Image recording ID1
Particle selectionNumber selected: 2772
Details: 1,768 particles were picked manually in the micrographs of the main dataset with a pixel size of 0.889 Ang. The particles were extracted applying particle-box and diameter-background sizes ...Details: 1,768 particles were picked manually in the micrographs of the main dataset with a pixel size of 0.889 Ang. The particles were extracted applying particle-box and diameter-background sizes of 1,126 and 844 pixels, respectively. To increase the number of particles, additional 1,004 particles were picked manually from the second dataset with a pixel size of 1.43 Ang. These particles were extracted applying particle-box and diameter-background sizes of 700 and 525, respectively. To match box- and pixel-size, the larger box was scaled to match the smaller one. After import of the particles into cryoSPARC, the particle box was scaled to 384 pixels, yielding a pixel size of 2.607 Ang.
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: After map and particle re-orientation in ChimeraX, the number of particles was doubled by symmetry expansion and the map was subsequently refined locally to a resolution of 15 Ang.
Number images used: 4416
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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