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- EMDB-64660: Cryo-EM structure of avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2... -

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Entry
Database: EMDB / ID: EMD-64660
TitleCryo-EM structure of avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly
Map data
Sample
  • Complex: Avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly
    • Protein or peptide: Cullin-4A
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Protein cereblon
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 D1
    • Protein or peptide: Zinc finger protein Aiolos
    • Protein or peptide: NEDD8
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed
    • Protein or peptide: Ubiquitin
  • Ligand: ZINC ION
  • Ligand: (3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione
KeywordsMolecular glue degrader / avadomide / CRL4 ubiquitin ligase / DDB1 / CRBN / Complex / LIGASE
Function / homology
Function and homology information


regulation of lymphocyte differentiation / regulation of B cell differentiation / regulation of B cell proliferation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / nucleotide-excision repair complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / Phosphorylation of the APC/C / cellular response to camptothecin ...regulation of lymphocyte differentiation / regulation of B cell differentiation / regulation of B cell proliferation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / nucleotide-excision repair complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / Phosphorylation of the APC/C / cellular response to camptothecin / negative regulation of monoatomic ion transmembrane transport / Signaling by BMP / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / cullin-RING ubiquitin ligase complex / negative regulation of mitophagy / regulation of xenophagy / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / Cul7-RING ubiquitin ligase complex / regulation of cell cycle process / neural crest cell differentiation / RNA polymerase II transcription initiation surveillance / positive regulation by virus of viral protein levels in host cell / positive regulation of protein autoubiquitination / protein neddylation / regulation of BMP signaling pathway / NEDD8 ligase activity / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / regulation of mitophagy / negative regulation of response to oxidative stress / regulation of centrosome duplication / protein K27-linked ubiquitination / UV-damage excision repair / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / E2 ubiquitin-conjugating enzyme / regulation of TOR signaling / Cul2-RING ubiquitin ligase complex / negative regulation of DNA-templated DNA replication / biological process involved in interaction with symbiont / SCF ubiquitin ligase complex / regulation of mitotic cytokinesis / regulation of DNA damage checkpoint / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / mesoderm development / regulation of mitotic cell cycle phase transition / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / WD40-repeat domain binding / Prolactin receptor signaling / Formation of the ternary complex, and subsequently, the 43S complex / regulation of cell cycle phase transition / locomotory exploration behavior / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / Regulation of APC/C activators between G1/S and early anaphase / Cul4A-RING E3 ubiquitin ligase complex / Ribosomal scanning and start codon recognition / TGF-beta receptor signaling activates SMADs / negative regulation of BMP signaling pathway / Cul4B-RING E3 ubiquitin ligase complex / Translation initiation complex formation / ubiquitin ligase complex scaffold activity / Transcriptional Regulation by VENTX / negative regulation of adipose tissue development / ubiquitin conjugating enzyme activity / T cell differentiation / regulation of proteolysis / regulation of cellular response to stress / limb development / viral release from host cell / regulation of postsynapse assembly / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / SARS-CoV-1 modulates host translation machinery / protein monoubiquitination / Peptide chain elongation / anatomical structure morphogenesis / cullin family protein binding / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / positive regulation of Wnt signaling pathway / Viral mRNA Translation / negative regulation of protein-containing complex assembly / centrosome duplication / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / regulation of DNA-templated DNA replication initiation / GTP hydrolysis and joining of the 60S ribosomal subunit / positive regulation of viral genome replication / cilium assembly
Similarity search - Function
: / Nedd8-like ubiquitin / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin protein neddylation domain ...: / Nedd8-like ubiquitin / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / Cullin alpha solenoid domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / : / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / PUA-like superfamily / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Zinc finger, C2H2 type / Ubiquitin-conjugating enzyme/RWD-like / zinc finger / Zinc finger C2H2 type domain profile. / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 D1 / E3 ubiquitin-protein ligase RBX1 / Ubiquitin-ribosomal protein eS31 fusion protein / Cullin-4A / Ubiquitin-like protein NEDD8 / DNA damage-binding protein 1 / Protein cereblon / Zinc finger protein Aiolos
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsDeng ZH / Ai HS / Liu L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22137005, 92253302, 22227810, T2488301 China
CitationJournal: To Be Published
Title: Cryo-EM structure of avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly
Authors: Deng ZH / Ai HS / Liu L
History
DepositionMay 17, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64660.png

Downloads & links

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Map

FileDownload / File: emd_64660.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.104 Å		1.06 Å/pix.
x 256 pix.
= 271.104 Å		1.06 Å/pix.
x 256 pix.
= 271.104 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.138
Minimum - Maximum-0.7330767 - 1.2940089
Average (Standard dev.)-0.00046378266 (±0.044653133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.104 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64660_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64660_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiqu...

EntireName: Avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly
Components
  • Complex: Avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly
    • Protein or peptide: Cullin-4A
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Protein cereblon
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 D1
    • Protein or peptide: Zinc finger protein Aiolos
    • Protein or peptide: NEDD8
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed
    • Protein or peptide: Ubiquitin
  • Ligand: ZINC ION
  • Ligand: (3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione

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Supramolecule #1: Avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiqu...

SupramoleculeName: Avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cullin-4A

MacromoleculeName: Cullin-4A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.368867 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPGSGWSHPQ FEKGSGSADE APRKGSFSAL VGRTNGLTKP AALAAAPAKP GGAGGSKKLV IKNFRDRPRL PDNYTQDTWR KLHEAVRAV QSSTSIRYNL EELYQAVENL CSHKVSPMLY KQLRQACEDH VQAQILPFRE DSLDSVLFLK KINTCWQDHC R QMIMIRSI ...String:
GPGSGWSHPQ FEKGSGSADE APRKGSFSAL VGRTNGLTKP AALAAAPAKP GGAGGSKKLV IKNFRDRPRL PDNYTQDTWR KLHEAVRAV QSSTSIRYNL EELYQAVENL CSHKVSPMLY KQLRQACEDH VQAQILPFRE DSLDSVLFLK KINTCWQDHC R QMIMIRSI FLFLDRTYVL QNSTLPSIWD MGLELFRTHI ISDKMVQSKT IDGILLLIER ERSGEAVDRS LLRSLLGMLS DL QVYKDSF ELKFLEETNC LYAAEGQRLM QEREVPEYLN HVSKRLEEEG DRVITYLDHS TQKPLIACVE KQLLGEHLTA ILQ KGLDHL LDENRVPDLA QMYQLFSRVR GGQQALLQHW SEYIKTFGTA IVINPEKDKD MVQDLLDFKD KVDHVIEVCF QKNE RFVNL MKESFETFIN KRPNKPAELI AKHVDSKLRA GNKEATDEEL ERTLDKIMIL FRFIHGKDVF EAFYKKDLAK RLLVG KSAS VDAEKSMLSK LKHECGAAFT SKLEGMFKDM ELSKDIMVHF KQHMQNQSDS GPIDLTVNIL TMGYWPTYTP MEVHLT PEM IKLQEVFKAF YLGKHSGRKL QWQTTLGHAV LKAEFKEGKK EFQVSLFQTL VLLMFNEGDG FSFEEIKMAT GIEDSEL RR TLQSLACGKA RVLIKSPKGK EVEDGDKFIF NGEFKHKLFR IKINQIQMKE TVEEQVSTTE RVFQDRQYQI DAAIVRIM K MRKTLGHNLL VSELYNQLKF PVKPGDLKKR IESLIDRDYM ERDKDNPNQY HYVA

UniProtKB: Cullin-4A

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Macromolecule #2: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 127.097469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK ...String:
MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK FLYGCQAPTI CFVYQDPQGR HVKTYEVSLR EKEFNKGPWK QENVEAEASM VIAVPEPFGG AIIIGQESIT YH NGDKYLA IAPPIIKQST IVCHNRVDPN GSRYLLGDME GRLFMLLLEK EEQMDGTVTL KDLRVELLGE TSIAECLTYL DNG VVFVGS RLGDSQLVKL NVDSNEQGSY VVAMETFTNL GPIVDMCVVD LERQGQGQLV TCSGAFKEGS LRIIRNGIGI HEHA SIDLP GIKGLWPLRS DPNRETDDTL VLSFVGQTRV LMLNGEEVEE TELMGFVDDQ QTFFCGNVAH QQLIQITSAS VRLVS QEPK ALVSEWKEPQ AKNISVASCN SSQVVVAVGR ALYYLQIHPQ ELRQISHTEM EHEVACLDIT PLGDSNGLSP LCAIGL WTD ISARILKLPS FELLHKEMLG GEIIPRSILM TTFESSHYLL CALGDGALFY FGLNIETGLL SDRKKVTLGT QPTVLRT FR SLSTTNVFAC SDRPTVIYSS NHKLVFSNVN LKEVNYMCPL NSDGYPDSLA LANNSTLTIG TIDEIQKLHI RTVPLYES P RKICYQEVSQ CFGVLSSRIE VQDTSGGTTA LRPSASTQAL SSSVSSSKLF SSSTAPHETS FGEEVEVHNL LIIDQHTFE VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE AEPKQGRIVV FQYSDGKLQT VAEKEVKGAV YSMVEFNGKL LASINSTVR LYEWTTEKEL RTECNHYNNI MALYLKTKGD FILVGDLMRS VLLLAYKPME GNFEEIARDF NPNWMSAVEI L DDDNFLGA ENAFNLFVCQ KDSAATTDEE RQHLQEVGLF HLGEFVNVFC HGSLVMQNLG ETSTPTQGSV LFGTVNGMIG LV TSLSESW YNLLLDMQNR LNKVIKSVGK IEHSFWRSFH TERKTEPATG FIDGDLIESF LDISRPKMQE VVANLQYDDG SGM KREATA DDLIKVVEEL TRIH

UniProtKB: DNA damage-binding protein 1

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Macromolecule #3: Protein cereblon

MacromoleculeName: Protein cereblon / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.874941 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSSHHHHHHH HSSGLEVLFQ GPGSSAKKPN IINFDTSLPT SHTYLGADME EFHGRTLHDD DSCQVIPVLP QVMMILIPGQ TLPLQLFHP QEVSMVRNLI QKDRTFAVLA YSNVQEREAQ FGTTAEIYAY REEQDFGIEI VKVKAIGRQR FKVLELRTQS D GIQQAKVQ ...String:
GSSHHHHHHH HSSGLEVLFQ GPGSSAKKPN IINFDTSLPT SHTYLGADME EFHGRTLHDD DSCQVIPVLP QVMMILIPGQ TLPLQLFHP QEVSMVRNLI QKDRTFAVLA YSNVQEREAQ FGTTAEIYAY REEQDFGIEI VKVKAIGRQR FKVLELRTQS D GIQQAKVQ ILPECVLPST MSAVQLESLN KCQIFPSKPV SREDQCSYKW WQKYQKRKFH CANLTSWPRW LYSLYDAETL MD RIKKQLR EWDENLKDDS LPSNPIDFSY RVAACLPIDD VLRIQLLKIG SAIQRLRCEL DIMNKCTSLC CKQCQETEIT TKN EIFSLS LCGPMAAYVN PHGYVHETLT VYKACNLNLI GRPSTEHSWF PGYAWTVAQC KICASHIGWK FTATKKDMSP QKFW GLTRS ALLPTIPDTE DEISPDKVIL CL

UniProtKB: Protein cereblon

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Macromolecule #4: Ubiquitin-conjugating enzyme E2 D1

MacromoleculeName: Ubiquitin-conjugating enzyme E2 D1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.490812 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ALKRIQKELS DLQRDPPAHC SAGPVGDDLF HWQATIMGPP DSAYQGGVFF LTVHFPTDYP FKPPKIAFTT KIYHPNINSN GSICLDILR SQWSPALTVS KVLLSICSLL CDPNPDDPLV PDIAQIYKSD KEKYNRHARE WTQKYAM

UniProtKB: Ubiquitin-conjugating enzyme E2 D1

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Macromolecule #5: Zinc finger protein Aiolos

MacromoleculeName: Zinc finger protein Aiolos / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.549474 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPGERPFQCN QCGASFTQKG NLLRHICLHT GEKPFKCHLC NYATQRRDAL TGHLRTHS

UniProtKB: Zinc finger protein Aiolos

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Macromolecule #6: NEDD8

MacromoleculeName: NEDD8 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.573978 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLIKVKTLTG KEIEIDIEPT DKVERIKERV EEKEGIPPQQ QRLIYSGKQM NDEKTAADYK ILGGSVLHLV LALRGG

UniProtKB: Ubiquitin-like protein NEDD8

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Macromolecule #7: E3 ubiquitin-protein ligase RBX1, N-terminally processed

MacromoleculeName: E3 ubiquitin-protein ligase RBX1, N-terminally processed
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.457076 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPGSAAAMDV DTPSGTNSGA GKKRFEVKKW NAVALWAWDI VVDNCAICRN HIMDLCIECQ ANQASATSEE CTVAWGVCNH AFHFHCISR WLKTRQVCPL DNREWEFQKY GH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #8: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Ubiquitin-ribosomal protein eS31 fusion protein

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #10: (3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperid...

MacromoleculeName: (3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione
type: ligand / ID: 10 / Number of copies: 1 / Formula: 835
Molecular weightTheoretical: 286.286 Da
Chemical component information

ChemComp-835:
(3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 60674
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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