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- EMDB-16575: CAND1 b-hairpin++-SCF-SKP2 CAND1 rolling SCF engaged -

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Basic information

Entry
Database: EMDB / ID: EMD-16575
TitleCAND1 b-hairpin++-SCF-SKP2 CAND1 rolling SCF engaged
Map datadeepEMhancer
Sample
  • Complex: CAND1 b-hairpin++-SCF-SKP2 CAND1 rolling SCF engaged
    • Protein or peptide: Cullin-1
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed
    • Protein or peptide: Cullin-associated NEDD8-dissociated protein 1
    • Protein or peptide: S-phase kinase-associated protein 2
    • Protein or peptide: S-phase kinase-associated protein 1
Keywordscullin-RING E3 ubiquitin ligase / SCF / CAND1 / Assembly factor / LIGASE
Function / homology
Function and homology information


SCF complex assembly / positive regulation of protein polyubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects / negative regulation of catalytic activity / PcG protein complex / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex ...SCF complex assembly / positive regulation of protein polyubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects / negative regulation of catalytic activity / PcG protein complex / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / cellular response to chemical stress / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / protein neddylation / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of response to oxidative stress / ubiquitin-ubiquitin ligase activity / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / Cul4B-RING E3 ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / protein monoubiquitination / cullin family protein binding / protein K63-linked ubiquitination / positive regulation of RNA polymerase II transcription preinitiation complex assembly / ubiquitin-like ligase-substrate adaptor activity / positive regulation of double-strand break repair via homologous recombination / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / ubiquitin ligase complex / TBP-class protein binding / positive regulation of TORC1 signaling / post-translational protein modification / regulation of cellular response to insulin stimulus / intrinsic apoptotic signaling pathway / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / T cell activation / molecular function activator activity / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / Degradation of DVL / animal organ morphogenesis / Dectin-1 mediated noncanonical NF-kB signaling / cellular response to amino acid stimulus / Recognition of DNA damage by PCNA-containing replication complex / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Iron uptake and transport / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / DNA Damage Recognition in GG-NER / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / RING-type E3 ubiquitin transferase / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / beta-catenin binding / FCERI mediated NF-kB activation / Dual incision in TC-NER / Interleukin-1 signaling / Gap-filling DNA repair synthesis and ligation in TC-NER / Orc1 removal from chromatin / protein polyubiquitination / Regulation of RAS by GAPs / positive regulation of protein catabolic process / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / cellular response to UV / Regulation of PLK1 Activity at G2/M Transition
Similarity search - Function
TATA-binding protein interacting (TIP20) / Cullin-associated NEDD8-dissociated protein 1/2 / TATA-binding protein interacting (TIP20) / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / A Receptor for Ubiquitination Targets / F-box domain profile. / HEAT-like repeat / F-box-like domain superfamily / SKP1 component, dimerisation ...TATA-binding protein interacting (TIP20) / Cullin-associated NEDD8-dissociated protein 1/2 / TATA-binding protein interacting (TIP20) / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / A Receptor for Ubiquitination Targets / F-box domain profile. / HEAT-like repeat / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box-like / F-box domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Zinc finger RING-type profile. / Leucine-rich repeat domain superfamily / Zinc finger, RING-type / Armadillo-like helical / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / S-phase kinase-associated protein 1 / S-phase kinase-associated protein 2 / Cullin-1 / Cullin-associated NEDD8-dissociated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBaek K / Schulman BA
Funding support Germany, European Union, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)789016European Union
CitationJournal: Cell / Year: 2023
Title: Systemwide disassembly and assembly of SCF ubiquitin ligase complexes.
Authors: Kheewoong Baek / Daniel C Scott / Lukas T Henneberg / Moeko T King / Matthias Mann / Brenda A Schulman /
Abstract: Cells respond to environmental cues by remodeling their inventories of multiprotein complexes. Cellular repertoires of SCF (SKP1-CUL1-F box protein) ubiquitin ligase complexes, which mediate much ...Cells respond to environmental cues by remodeling their inventories of multiprotein complexes. Cellular repertoires of SCF (SKP1-CUL1-F box protein) ubiquitin ligase complexes, which mediate much protein degradation, require CAND1 to distribute the limiting CUL1 subunit across the family of ∼70 different F box proteins. Yet, how a single factor coordinately assembles numerous distinct multiprotein complexes remains unknown. We obtained cryo-EM structures of CAND1-bound SCF complexes in multiple states and correlated mutational effects on structures, biochemistry, and cellular assays. The data suggest that CAND1 clasps idling catalytic domains of an inactive SCF, rolls around, and allosterically rocks and destabilizes the SCF. New SCF production proceeds in reverse, through SKP1-F box allosterically destabilizing CAND1. The CAND1-SCF conformational ensemble recycles CUL1 from inactive complexes, fueling mixing and matching of SCF parts for E3 activation in response to substrate availability. Our data reveal biogenesis of a predominant family of E3 ligases, and the molecular basis for systemwide multiprotein complex assembly.
History
DepositionJan 31, 2023-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16575.png

Downloads & links

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Map

FileDownload / File: emd_16575.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdeepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272.384 Å		0.85 Å/pix.
x 320 pix.
= 272.384 Å		0.85 Å/pix.
x 320 pix.
= 272.384 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.0017595818 - 1.766334
Average (Standard dev.)0.0016431897 (±0.027416345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.384 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16575_msk_1.map
Projections & Slices
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Additional map: 3d refinement

Fileemd_16575_additional_1.map
Annotation3d refinement
Projections & Slices
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Additional map: relion postprocess

Fileemd_16575_additional_2.map
Annotationrelion postprocess
Projections & Slices
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Half map: halfmap1

Fileemd_16575_half_map_1.map
Annotationhalfmap1
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Half map: halfmap2

Fileemd_16575_half_map_2.map
Annotationhalfmap2
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Sample components

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Entire : CAND1 b-hairpin++-SCF-SKP2 CAND1 rolling SCF engaged

EntireName: CAND1 b-hairpin++-SCF-SKP2 CAND1 rolling SCF engaged
Components
  • Complex: CAND1 b-hairpin++-SCF-SKP2 CAND1 rolling SCF engaged
    • Protein or peptide: Cullin-1
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed
    • Protein or peptide: Cullin-associated NEDD8-dissociated protein 1
    • Protein or peptide: S-phase kinase-associated protein 2
    • Protein or peptide: S-phase kinase-associated protein 1

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Supramolecule #1: CAND1 b-hairpin++-SCF-SKP2 CAND1 rolling SCF engaged

SupramoleculeName: CAND1 b-hairpin++-SCF-SKP2 CAND1 rolling SCF engaged / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cullin-1

MacromoleculeName: Cullin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.800367 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSSTRSQNPH GLKQIGLDQI WDDLRAGIQQ VYTRQSMAKS RYMELYTHVY NYCTSVHQSN QARGAGVPPS KSKKGQTPGG AQFVGLELY KRLKEFLKNY LTNLLKDGED LMDESVLKFY TQQWEDYRFS SKVLNGICAY LNRHWVRREC DEGRKGIYEI Y SLALVTWR ...String:
MSSTRSQNPH GLKQIGLDQI WDDLRAGIQQ VYTRQSMAKS RYMELYTHVY NYCTSVHQSN QARGAGVPPS KSKKGQTPGG AQFVGLELY KRLKEFLKNY LTNLLKDGED LMDESVLKFY TQQWEDYRFS SKVLNGICAY LNRHWVRREC DEGRKGIYEI Y SLALVTWR DCLFRPLNKQ VTNAVLKLIE KERNGETINT RLISGVVQSY VELGLNEDDA FAKGPTLTVY KESFESQFLA DT ERFYTRE STEFLQQNPV TEYMKKAEAR LLEEQRRVQV YLHESTQDEL ARKCEQVLIE KHLEIFHTEF QNLLDADKNE DLG RMYNLV SRIQDGLGEL KKLLETHIHN QGLAAIEKCG EAALNDPKMY VQTVLDVHKK YNALVMSAFN NDAGFVAALD KACG RFINN NAVTKMAQSS SKSPELLARY CDSLLKKSSK NPEEAELEDT LNQVMVVFKY IEDKDVFQKF YAKMLAKRLV HQNSA SDDA EASMISKLKQ ACGFEYTSKL QRMFQDIGVS KDLNEQFKKH LTNSEPLDLD FSIQVLSSGS WPFQQSCTFA LPSELE RSY QRFTAFYASR HSGRKLTWLY QLSKGELVTN CFKNRYTLQA STFQMAILLQ YNTEDAYTVQ QLTDSTQIKM DILAQVL QI LLKSKLLVLE DENANVDEVE LKPDTLIKLY LGYKNKKLRV NINVPMKTEQ KQEQETTHKN IEEDRKLLIQ AAIVRIMK M RKVLKHQQLL GEVLTQLSSR FKPRVPVIKK CIDILIEKEY LERVDGEKDT YSYLA

UniProtKB: Cullin-1

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Macromolecule #2: E3 ubiquitin-protein ligase RBX1, N-terminally processed

MacromoleculeName: E3 ubiquitin-protein ligase RBX1, N-terminally processed
type: protein_or_peptide / ID: 2 / Details: RING domain not visible / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.089677 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
GSMDVDTPSG TNSGAGKKRF EVKKWNAVAL WAWDIVVDNC AICRNHIMDL CIECQANQAS ATSEECTVAW GVCNHAFHFH CISRWLKTR QVCPLDNREW EFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #3: Cullin-associated NEDD8-dissociated protein 1

MacromoleculeName: Cullin-associated NEDD8-dissociated protein 1 / type: protein_or_peptide / ID: 3 / Details: CAND1 b-hairpin++ (with M1068W P1070Q mutant) / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 137.472297 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSPEFPGRMA SASYHISNLL EKMTSSDKDF RFMATNDLMT ELQKDSIKLD DDSERKVVKM ILKLLEDKNG EVQNLAVKCL GPLVSKVKE YQVETIVDTL CTNMLSDKEQ LRDISSIGLK TVIGELPPAS SGSALAANVC KKITGRLTSA IAKQEDVSVQ L EALDIMAD ...String:
GSPEFPGRMA SASYHISNLL EKMTSSDKDF RFMATNDLMT ELQKDSIKLD DDSERKVVKM ILKLLEDKNG EVQNLAVKCL GPLVSKVKE YQVETIVDTL CTNMLSDKEQ LRDISSIGLK TVIGELPPAS SGSALAANVC KKITGRLTSA IAKQEDVSVQ L EALDIMAD MLSRQGGLLV NFHPSILTCL LPQLTSPRLA VRKRTIIALG HLVMSCGNIV FVDLIEHLLS ELSKNDSMST TR TYIQCIA AISRQAGHRI GEYLEKIIPL VVKFCNVDDD ELREYCIQAF ESFVRRCPKE VYPHVSTIIN ICLKYLTYDP NYN YDDEDE DENAMDADGG DDDDQGSDDE YSDDDDMSWK VRRAAAKCLD AVVSTRHEML PEFYKTVSPA LISRFKEREE NVKA DVFHA YLSLLKQTRP VQSWLCDPDA MEQGETPLTM LQSQVPNIVK ALHKQMKEKS VKTRQCCFNM LTELVNVLPG ALTQH IPVL VPGIIFSLND KSSSSNLKID ALSCLYVILC NHSPQVFHPH VQALVPPVVA CVGDPFYKIT SEALLVTQQL VKVIRP LDQ PSSFDATPYI KDLFTCTIKR LKAADIDQEV KERAISCMGQ IICNLGDNLG SDLPNTLQIF LERLKNEITR LTTVKAL TL IAGSPLKIDL RPVLGEGVPI LASFLRKNQR ALKLGTLSAL DILIKNYSDS LTAAMIDAVL DELPPLISES DMHVSQMA I SFLTTLAKVY PSSLSKISGS ILNELIGLVR SPLLQGGALS AMLDFFQALV VTGTNNLGYM DLLRMLTGPV YSQSTALTH KQSYYSIAKC VAALTRACPK EGPAVVGQFI QDVKNSRSTD SIRLLALLSL GEVGHHIDLS GQLELKSVIL EAFSSPSEEV KSAASYALG SISVGNLPEY LPFVLQEITS QPKRQYLLLH SLKEIISSAS VVGLKPYVEN IWALLLKHCE CAEEGTRNVV V ECLGKLTL IDPETLLPRL KGYLISGSSY ARSSVVTAVK FTISDHPQPI DPLLKNCIGD FLKTLEDPDL NVRRVALVTF NS AAHNKPS LIRDLLDTVL PHLYNETKVR KELIREVEWG QFKHTVDDGL DIRKAAFECM YTLLDSCLDR LDIFEFLNHV EDG LKDHYD IKMLTFLMLV RLSTLCPSAV LQRLDRLVEP LRATCTTKVK ANSVKQEFEK QDELKRSAMR AVAALLTIPE AEKS PLMSE FQSQISSNPE LAAIFESIQK DSSSTNLESM DTS

UniProtKB: Cullin-associated NEDD8-dissociated protein 1

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Macromolecule #4: S-phase kinase-associated protein 2

MacromoleculeName: S-phase kinase-associated protein 2 / type: protein_or_peptide / ID: 4
Details: SKP2 N-terminal region not visible in EM density. The LRR region of SKP2 was wholesale docked from previous structure with all sidechains removed.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.96191 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSMHRKHLQE IPDLSSNVAT SFTWGWDSSK TSELLSGMGV SALEKEEPDS ENIPQELLSN LGHPESPPRK RLKSKGSDKD FVIVRRPKL NRENFPGVSW DSLPDELLLG IFSCLCLPEL LKVSGVCKRW YRLASDESLW QTLDLTGKNL HPDVTGRLLS Q GVIAFRCP ...String:
GSMHRKHLQE IPDLSSNVAT SFTWGWDSSK TSELLSGMGV SALEKEEPDS ENIPQELLSN LGHPESPPRK RLKSKGSDKD FVIVRRPKL NRENFPGVSW DSLPDELLLG IFSCLCLPEL LKVSGVCKRW YRLASDESLW QTLDLTGKNL HPDVTGRLLS Q GVIAFRCP RSFMDQPLAE HFSPFRVQHM DLSNSVIEVS TLHGILSQCS KLQNLSLEGL RLSDPIVNTL AKNSNLVRLN LS GCSGFSE FALQTLLSSC SRLDELNLSW CFDFTEKHVQ VAVAHVSETI TQLNLSGYRK NLQKSDLSTL VRRCPNLVHL DLS DSVMLK NDCFQEFFQL NYLQHLSLSR CYDIIPETLL ELGEIPTLKT LQVFGIVPDG TLQLLKEALP HLQINCSHFT TIAR PTIGN KKNQEIWGIK CRLTLQKPSC L

UniProtKB: S-phase kinase-associated protein 2

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Macromolecule #5: S-phase kinase-associated protein 1

MacromoleculeName: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.679965 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MPSIKLQSSD GEIFEVDVEI AKQSVTIKTM LEDLGMDDEG DDDPVPLPNV NAAILKKVIQ WCTHHKDDPP PPEDDENKEK RTDDIPVWD QEFLKVDQGT LFELILAANY LDIKGLLDVT CKTVANMIKG KTPEEIRKTF NIKNDFTEEE EAQVRKENQW C EEK

UniProtKB: S-phase kinase-associated protein 1

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 68.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124721
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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