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- EMDB-54352: Map E Composite map of ZSWIM8-CUL3 complex bound to AGO2-miR-7-CYRANO -

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Basic information

Entry
Database: EMDB / ID: EMD-54352
TitleMap E Composite map of ZSWIM8-CUL3 complex bound to AGO2-miR-7-CYRANO
Map dataComposite map.
Sample
  • Complex: CYRANO-AGO2-miR-7 in complex with ZSWIM8-ELONGIN B/C, CUL3
    • Protein or peptide: Protein argonaute-2
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • RNA: miR-7
    • Protein or peptide: Cullin-3
    • RNA: CYRANO trigger RNA
    • Protein or peptide: Zinc finger SWIM domain-containing protein 8
  • Ligand: ZINC ION
KeywordsmiRNA / E3 Ligase / LIGASE
Function / homology
Function and homology information


positive regulation of miRNA catabolic process / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / POZ domain binding / : / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / Post-transcriptional silencing by small RNAs ...positive regulation of miRNA catabolic process / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / POZ domain binding / : / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Regulation of PTEN mRNA translation / miRNA-mediated gene silencing by mRNA destabilization / negative regulation of amyloid precursor protein biosynthetic process / RNA stabilization / Small interfering RNA (siRNA) biogenesis / positive regulation of trophoblast cell migration / Regulation of CDH1 mRNA translation by microRNAs / polar microtubule / regulation protein catabolic process at postsynapse / anaphase-promoting complex-dependent catabolic process / Transcriptional Regulation by MECP2 / nuclear protein quality control by the ubiquitin-proteasome system / COPII vesicle coat assembly / RISC-loading complex / miRNA metabolic process / mRNA cap binding / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / RHOBTB3 ATPase cycle / miRNA processing / RNA 7-methylguanosine cap binding / pre-miRNA processing / embryonic cleavage / regulation of synapse maturation / siRNA processing / siRNA binding / mRNA 3'-UTR AU-rich region binding / M-decay: degradation of maternal mRNAs by maternally stored factors / Regulation of MITF-M-dependent genes involved in apoptosis / target-directed miRNA degradation / positive regulation of mitotic metaphase/anaphase transition / elongin complex / RISC complex / TGFBR3 expression / regulatory ncRNA-mediated gene silencing / Notch binding / fibroblast apoptotic process / Regulation of RUNX1 Expression and Activity / cell projection organization / negative regulation of Rho protein signal transduction / P-body assembly / miRNA binding / RHOBTB1 GTPase cycle / MicroRNA (miRNA) biogenesis / VCB complex / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Cul5-RING ubiquitin ligase complex / stem cell division / mitotic metaphase chromosome alignment / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / stress fiber assembly / Cul3-RING ubiquitin ligase complex / negative regulation of type I interferon production / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of cytokinesis / ubiquitin ligase complex scaffold activity / RNA polymerase II complex binding / protein quality control for misfolded or incompletely synthesized proteins / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Regulation of MECP2 expression and activity / endoplasmic reticulum to Golgi vesicle-mediated transport / protein monoubiquitination / RHOBTB2 GTPase cycle / sperm flagellum / Tat-mediated elongation of the HIV-1 transcript / core promoter sequence-specific DNA binding / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / protein autoubiquitination / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / ubiquitin-like ligase-substrate adaptor activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / Nuclear events stimulated by ALK signaling in cancer / RNA endonuclease activity / protein K48-linked ubiquitination / translation initiation factor activity / gastrulation / RNA Polymerase II Pre-transcription Events / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / negative regulation of translational initiation
Similarity search - Function
: / : / ZSWIM4-8, C-terminal / ZSWIM8, TPR repeats / Zinc finger, SWIM-type / Zinc finger SWIM-type profile. / Protein argonaute-2 / Protein argonaute, Mid domain / Mid domain of argonaute / Argonaute linker 2 domain ...: / : / ZSWIM4-8, C-terminal / ZSWIM8, TPR repeats / Zinc finger, SWIM-type / Zinc finger SWIM-type profile. / Protein argonaute-2 / Protein argonaute, Mid domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / Argonaute-like, PIWI domain / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / Cullin, N-terminal / Cullin protein neddylation domain / Cullin, conserved site / Cullin alpha solenoid domain / Cullin family signature. / PAZ domain profile. / Elongin-C / Elongin B / PAZ domain / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / 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 / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Zinc finger SWIM domain-containing protein 8 / Cullin-3 / Elongin-C / Elongin-B / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsFarnung J / Slobodyanyuk E / Bartel DP / Schulman BA
Funding supportEuropean Union, Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)101098161European Union
German Research Foundation (DFG) Germany
CitationJournal: Nature / Year: 2026
Title: The E3 ubiquitin ligase mechanism specifying targeted microRNA degradation.
Authors: Jakob Farnung / Elena Slobodyanyuk / Peter Y Wang / Lianne W Blodgett / Daniel H Lin / Susanne von Gronau / Brenda A Schulman / David P Bartel /
Abstract: MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to form complexes that down-regulate target RNAs, including messenger RNAs from most human genes. Within each complex, the miRNA pairs to ...MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to form complexes that down-regulate target RNAs, including messenger RNAs from most human genes. Within each complex, the miRNA pairs to target RNAs, and AGO provides effector function while also protecting the miRNA from cellular nucleases. Although much is known about miRNA-directed gene regulation, less is known about how miRNAs themselves are regulated. One pathway that regulates miRNAs involves unusual targets called 'trigger' RNAs, which reverse the canonical regulatory logic and instead down-regulate miRNAs. This target-directed miRNA degradation (TDMD) is thought to require a cullin-RING E3 ligase because it depends on the cullin protein CUL3 and other ubiquitylation components, including the BC-box protein ZSWIM8 (refs. ). ZSWIM8 is required for murine perinatal viability and for destabilization of most short-lived miRNAs, which suggests biological importance of TDMD. Here, biochemical and cellular assays establish AGO binding and polyubiquitylation by the ZSWIM8-CUL3 E3 ligase as the key regulatory steps of TDMD, and thereby define a unique cullin-RING E3 ligase class. Cryogenic electron microscopy analyses show ZSWIM8 recognizing distinct AGO and RNA conformations shaped by pairing of the miRNA to the trigger. Specificity of AGO ubiquitylation is established through generalizable RNA-RNA, RNA-protein and protein-protein interactions. The substrate features recognized by the E3 ligase do not conform to a conventional degron but instead establish a two-RNA-factor authentication mechanism for specifying a protein ubiquitylation substrate.
History
DepositionJul 10, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54352.png

Downloads & links

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Map

FileDownload / File: emd_54352.map.gz / Format: CCP4 / Size: 891.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.85 Å/pix.
x 616 pix.
= 524.339 Å		0.85 Å/pix.
x 616 pix.
= 524.339 Å		0.85 Å/pix.
x 616 pix.
= 524.339 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0
Minimum - Maximum-6.3122716 - 188.06674000000001
Average (Standard dev.)0.013301439 (±1.1448759)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions616616616
Spacing616616616
CellA=B=C: 524.3392 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : CYRANO-AGO2-miR-7 in complex with ZSWIM8-ELONGIN B/C, CUL3

EntireName: CYRANO-AGO2-miR-7 in complex with ZSWIM8-ELONGIN B/C, CUL3
Components
  • Complex: CYRANO-AGO2-miR-7 in complex with ZSWIM8-ELONGIN B/C, CUL3
    • Protein or peptide: Protein argonaute-2
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • RNA: miR-7
    • Protein or peptide: Cullin-3
    • RNA: CYRANO trigger RNA
    • Protein or peptide: Zinc finger SWIM domain-containing protein 8
  • Ligand: ZINC ION

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Supramolecule #1: CYRANO-AGO2-miR-7 in complex with ZSWIM8-ELONGIN B/C, CUL3

SupramoleculeName: CYRANO-AGO2-miR-7 in complex with ZSWIM8-ELONGIN B/C, CUL3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: Complex formed of CYRANO-AGO2-miR-7 in complex with ZSWIM8-ELONGIN B/C, CUL3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein argonaute-2

MacromoleculeName: Protein argonaute-2 / type: protein_or_peptide / ID: 1
Details: N-terminal hexahistidine purification tag was not removed.
Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.554383 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MGSSHHHHHH GSYSGAGPAL APPAPPPPIQ GYAFKPPPRP DFGTSGRTIK LQANFFEMDI PKIDIYHYEL DIKPEKCPRR VNREIVEHM VQHFKTQIFG DRKPVFDGRK NLYTAMPLPI GRDKVELEVT LPGEGKDRIF KVSIKWVSCV SLQALHDALS G RLPSVPFE ...String:
MGSSHHHHHH GSYSGAGPAL APPAPPPPIQ GYAFKPPPRP DFGTSGRTIK LQANFFEMDI PKIDIYHYEL DIKPEKCPRR VNREIVEHM VQHFKTQIFG DRKPVFDGRK NLYTAMPLPI GRDKVELEVT LPGEGKDRIF KVSIKWVSCV SLQALHDALS G RLPSVPFE TIQALDVVMR HLPSMRYTPV GRSFFTASEG CSNPLGGGRE VWFGFHQSVR PSLWKMMLNI DVSATAFYKA QP VIEFVCE VLDFKSIEEQ QKPLTDSQRV KFTKEIKGLK VEITHCGQMK RKYRVCNVTR RPASHQTFPL QQESGQTVEC TVA QYFKDR HKLVLRYPHL PCLQVGQEQK HTYLPLEVCN IVAGQRCIKK LTDNQTSTMI RATARSAPDR QEEISKLMRS ASFN TDPYV REFGIMVKDE MTDVTGRVLQ PPSILYGGRN KAIATPVQGV WDMRNKQFHT GIEIKVWAIA CFAPQRQCTE VHLKS FTEQ LRKISRDAGM PIQGQPCFCK YAQGADSVEP MFRHLKNTYA GLQLVVVILP GKTPVYAEVK RVGDTVLGMA TQCVQM KNV QRTTPQTLSN LCLKINVKLG GVNNILLPQG RPPVFQQPVI FLGADVTHPP AGDGKKPSIA AVVGSMDAHP NRYCATV RV QQHRQEIIQD LAAMVRELLI QFYKSTRFKP TRIIFYRDGV SEGQFQQVLH HELLAIREAC IKLEKDYQPG ITFIVVQK R HHTRLFCTDK NERVGKSGNI PAGTTVDTKI THPTEFDFYL CSHAGIQGTS RPSHYHVLWD DNRFSSDELQ ILTYQLCHT YVRCTRSVSI PAPAYYAHLV AFRARYHLVD KEHDSAEGSH TSGQSNGRDH QALAKAVQVH QDTLRTMYFA

UniProtKB: Protein argonaute-2

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Macromolecule #2: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.147781 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString:
MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMKPQDSG SSANEQAVQ

UniProtKB: Elongin-B

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Macromolecule #3: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.485135 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString:
MDGEEKTYGG CEGPDAMYVK LISSDGHEFI VKREHALTSG TIKAMLSGPG QFAENETNEV NFREIPSHVL SKVCMYFTYK VRYTNSSTE IPEFPIAPEI ALELLMAANF LDC

UniProtKB: Elongin-C

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Macromolecule #5: Cullin-3

MacromoleculeName: Cullin-3 / type: protein_or_peptide / ID: 5
Details: CUL3 NTD containing solubilizing mutations I342R, L346D, and remnant of C-terminal TEV protease cleavage site.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.410113 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNLSKGTGS RKDTKMRIRA FPMTMDEKYV NSIWDLLKNA IQEIQRKNNS GLSFEELYRN AYTMVLHKHG EKLYTGLREV VTEHLINKV REDVLNSLNN NFLQTLNQAW NDHQTAMVMI RDILMYMDRV YVQQNNVENV YNLGLIIFRD QVVRYGCIRD H LRQTLLDM ...String:
MSNLSKGTGS RKDTKMRIRA FPMTMDEKYV NSIWDLLKNA IQEIQRKNNS GLSFEELYRN AYTMVLHKHG EKLYTGLREV VTEHLINKV REDVLNSLNN NFLQTLNQAW NDHQTAMVMI RDILMYMDRV YVQQNNVENV YNLGLIIFRD QVVRYGCIRD H LRQTLLDM IARERKGEVV DRGAIRNACQ MLMILGLEGR SVYEEDFEAP FLEMSAEFFQ MESQKFLAEN SASVYIKKVE AR INEEIER VMHCLDKSTE EPIVKVVERE LISKHMKTIV EMENSGLVHM LKNGKTEDLG CMYKLFSRVP NGLKTMCECM SSY LREQGK ALVSEEGEGK NPVDYRQGLD DLKSRFDRFL LESFNNDRLF KQTIAGDFEY FLNLNSRSPE YLSLENLYFQ

UniProtKB: Cullin-3

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Macromolecule #7: Zinc finger SWIM domain-containing protein 8

MacromoleculeName: Zinc finger SWIM domain-containing protein 8 / type: protein_or_peptide / ID: 7
Details: C-terminal twin-strep purification tag was not removed.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200.458016 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MELMFAEWED GERFSFEDSD RFEEDSLCSF ISEAESLCQN WRGWRKQSAG PNSPTGGGGG GGSGGTRMRD GLVIPLVELS AKQVAFHIP FEVVEKVYPP VPEQLQLRIA FWSFPENEED IRLYSCLANG SADEFQRGDQ LFRMRAVKDP LQIGFHLSAT V VPPQMVPP ...String:
MELMFAEWED GERFSFEDSD RFEEDSLCSF ISEAESLCQN WRGWRKQSAG PNSPTGGGGG GGSGGTRMRD GLVIPLVELS AKQVAFHIP FEVVEKVYPP VPEQLQLRIA FWSFPENEED IRLYSCLANG SADEFQRGDQ LFRMRAVKDP LQIGFHLSAT V VPPQMVPP KGAYNVAVMF DRCRVTSCSC TCGAGAKWCT HVVALCLFRI HNASAVCLRA PVSESLSRLQ RDQLQKFAQY LI SELPQQI LPTAQRLLDE LLSSQSTAIN TVCGAPDPTA GPSASDQSTW YLDESTLTDN IKKTLHKFCG PSPVVFSDVN SMY LSSTEP PAAAEWACLL RPLRGREPEG VWNLLSIVRE MFKRRDSNAA PLLEILTDQC LTYEQITGWW YSVRTSASHS SASG HTGRS NGQSEVAAHA CASMCDEMVT LWRLAVLDPA LSPQRRRELC TQLRQWQLKV IENVKRGQHK KTLERLFPGF RPAVE ACYF NWEEAYPLPG VTYSGTDRKL ALCWARALPS RPGASRSGGL EESRDRPRPL PTEPAVRPKE PGTKRKGLGE GVPSSQ RGP RRLSAEGGDK ALHKMGPGGG KAKALGGAGS GSKGSAGGGS KRRLSSEDSS LEPDLAEMSL DDSSLALGAE ASTFGGF PE SPPPCPLHGG SRGPSTFLPE PPDTYEEDGG VYFSEGPEPP TASVGPPGLL PGDVCTQDDL PSTDESGNGL PKTKEAAP A VGEEDDDYQA YYLNAQDGAG GEEEKAEGGA GEEHDLFAGL KPLEQESRME VLFACAEALH AHGYSSEASR LTVELAQDL LANPPDLKVE PPPAKGKKNK VSTSRQTWVA TNTLSKAAFL LTVLSERPEH HNLAFRVGMF ALELQRPPAS TKALEVKLAY QESEVAALL KKIPLGPSEM STMRCRAEEL REGTLCDYRP VLPLMLASFI FDVLCAPGSR PPSRNWNSET PGDEELGFEA A VAALGMKT TVSEAEHPLL CEGTRREKGD LALALMITYK DDQAKLKKIL DKLLDRESQT HKPQTLSSFY SSSRPTTASQ RS PSKHGGP SAPGALQPLT SGSAGPAQPG SVAGAGPGPT EGFTEKNVPE SSPHSPCEGL PSEAALTPRP EGKVPSRLAL GSR GGYNGR GWGSPGRPKK KHTGMASIDS SAPETTSDSS PTLSRRPLRG GWAPTSWGRG QDSDSISSSS SDSLGSSSSS GSRR ASASG GARAKTVEVG RYKGRRPESH APHVPNQPSE AAAHFYFELA KTVLIKAGGN SSTSIFTHPS SSGGHQGPHR NLHLC AFEI GLYALGLHNF VSPNWLSRTY SSHVSWITGQ AMEIGSAALT ILVECWDGHL TPPEVASLAD RASRARDSNM VRAAAE LAL SCLPHAHALN PNEIQRALVQ CKEQDNLMLE KACMAVEEAA KGGGVYPEVL FEVAHQWFWL YEQTAGGSST AREGATS CS ASGIRAGGEA GRGMPEGRGG PGTEPVTVAA AAVTAAATVV PVISVGSSLY PGPGLGHGHS PGLHPYTALQ PHLPCSPQ Y LTHPAHPAHP MPHMPRPAVF PVPSSAYPQG VHPAFLGAQY PYSVTPPSLA ATAVSFPVPS MAPITVHPYH TEPGLPLPT SVACELWGQG TVSSVHPAST FPAIQGASLP ALTTQPSPLV SGGFPPPEEE THSQPVNPHS LHHLHAAYRV GMLALEMLGR RAHNDHPNN FSRSPPYTDD VKWLLGLAAK LGVNYVHQFC VGAAKGVLSP FVLQEIVMET LQRLSPAHAH NHLRAPAFHQ L VQRCQQAY MQYIHHRLIH LTPADYDDFV NAIRSARSAF CLTPMGMMQF NDILQNLKRS KQTKELWQRV SLEMATFSPG WS HPQFEKG GGSGGGSGGS AWSHPQFEK

UniProtKB: Zinc finger SWIM domain-containing protein 8

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Macromolecule #4: miR-7

MacromoleculeName: miR-7 / type: rna / ID: 4 / Details: 5' terminus is phosphorylated / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.69052 KDa
SequenceString:
UGGAAGACUA GUGAUUUUGU UGUU

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Macromolecule #6: CYRANO trigger RNA

MacromoleculeName: CYRANO trigger RNA / type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.577793 KDa
SequenceString:
GGGACAAAUG UUACAAGUUG UUUAAGAACA ACAAAAUCAC CAAUGUCUUC CAUUUUGAGA UGUGUAUAGU UUUGUAAGCA UUAGUGCUU GGUAGCAUAU UGUAGUGCCA UGUUAGAAAA A

GENBANK: GENBANK: XR_002136808.2

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.8 / Details: 25 mM HEPES, 50 mM NaCl, 1 mM TCEP, pH 7.8
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 58.0 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 / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Screening dataset derived map was used as an initial model.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 230859
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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