[English] 日本語
Yorodumi
- EMDB-55106: Cryo-EM structure of the DDB1deltaB-CRBN-Pomalidomide complex bou... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-55106
TitleCryo-EM structure of the DDB1deltaB-CRBN-Pomalidomide complex bound to SALL4(ZF1-ZF2-Helix)
Map data
Sample
  • Complex: SALL4 bound to DDB1/CRBN in the presence of POMALIDOMIDE
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Protein cereblon
    • Protein or peptide: Sal-like protein 4
  • Ligand: ZINC ION
  • Ligand: S-Pomalidomide
KeywordsLIGASE
Function / homology
Function and homology information


POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Transcriptional regulation of pluripotent stem cells / negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / embryonic limb morphogenesis / epigenetic programming in the zygotic pronuclei / ventricular septum development / inner cell mass cell proliferation / UV-damage excision repair ...POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Transcriptional regulation of pluripotent stem cells / negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / embryonic limb morphogenesis / epigenetic programming in the zygotic pronuclei / ventricular septum development / inner cell mass cell proliferation / UV-damage excision repair / biological process involved in interaction with symbiont / limb development / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / locomotory exploration behavior / somatic stem cell population maintenance / viral release from host cell / cullin family protein binding / ectopic germ cell programmed cell death / positive regulation of viral genome replication / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / heterochromatin / proteasomal protein catabolic process / positive regulation of gluconeogenesis / Regulation of PTEN gene transcription / nucleotide-excision repair / neural tube closure / sperm end piece / positive regulation of protein-containing complex assembly / regulation of circadian rhythm / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Wnt signaling pathway / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / rhythmic process / site of double-strand break / sperm principal piece / Neddylation / sperm midpiece / Potential therapeutics for SARS / ubiquitin-dependent protein catabolic process / damaged DNA binding / transmembrane transporter binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / chromosome, telomeric region / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / : / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / membrane / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / 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) ...: / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / 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) / : / 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 / PUA-like superfamily / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA damage-binding protein 1 / Protein cereblon / Sal-like protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsGalli P / Kater L / Kempf G / Cavadini S / Thoma NH
Funding supportEuropean Union, Switzerland, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Swiss National Science Foundation Switzerland
Other private
Other private
CitationJournal: To Be Published
Title: Cryo-EM structure of the DDB1deltaB-CRBN-Pomalidomide complex bound to SALL4(ZF1-ZF2-Helix)
Authors: Galli P / Thoma NH
History
DepositionSep 19, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_55106.png

Downloads & links

-
Map

FileDownload / File: emd_55106.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 288 pix.
= 324.49 Å		1.13 Å/pix.
x 288 pix.
= 324.49 Å		1.13 Å/pix.
x 288 pix.
= 324.49 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1267 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.329
Minimum - Maximum-0.0009794846 - 1.8851583
Average (Standard dev.)0.0012096923 (±0.02611025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 324.48962 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_55106_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_55106_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_55106_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SALL4 bound to DDB1/CRBN in the presence of POMALIDOMIDE

EntireName: SALL4 bound to DDB1/CRBN in the presence of POMALIDOMIDE
Components
  • Complex: SALL4 bound to DDB1/CRBN in the presence of POMALIDOMIDE
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Protein cereblon
    • Protein or peptide: Sal-like protein 4
  • Ligand: ZINC ION
  • Ligand: S-Pomalidomide

-
Supramolecule #1: SALL4 bound to DDB1/CRBN in the presence of POMALIDOMIDE

SupramoleculeName: SALL4 bound to DDB1/CRBN in the presence of POMALIDOMIDE
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.425586 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGSSHHHHHH SAAHIVMVDA YKPTKGGRMS YNYVVTAQKP TAVNGCVTGH FTSAEDLNLL IAKNTRLEIY VVTAEGLRPV KEVGMYGKI AVMELFRPKG ESKDLLFILT AKYNACILEY KQSGESIDII TRAHGNVQDR IGRPSETGII GIIDPECRMI G LRLYDGLF ...String:
MGSSHHHHHH SAAHIVMVDA YKPTKGGRMS YNYVVTAQKP TAVNGCVTGH FTSAEDLNLL IAKNTRLEIY VVTAEGLRPV KEVGMYGKI AVMELFRPKG ESKDLLFILT AKYNACILEY KQSGESIDII TRAHGNVQDR IGRPSETGII GIIDPECRMI G LRLYDGLF KVIPLDRDNK ELKAFNIRLE ELHVIDVKFL YGCQAPTICF VYQDPQGRHV KTYEVSLREK EFNKGPWKQE NV EAEASMV IAVPEPFGGA IIIGQESITY HNGDKYLAIA PPIIKQSTIV CHNRVDPNGS RYLLGDMEGR LFMLLLEKEE QMD GTVTLK DLRVELLGET SIAECLTYLD NGVVFVGSRL GDSQLVKLNV DSNEQGSYVV AMETFTNLGP IVDMCVVDLE RQGQ GQLVT CSGAFKEGSL RIIRNGIGGN GNSGEIQKLH IRTVPLYESP RKICYQEVSQ CFGVLSSRIE VQDTSGGTTA LRPSA STQA LSSSVSSSKL FSSSTAPHET SFGEEVEVHN LLIIDQHTFE VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMV YPE EAEPKQGRIV VFQYSDGKLQ TVAEKEVKGA VYSMVEFNGK LLASINSTVR LYEWTTEKEL RTECNHYNNI MALYLKT KG DFILVGDLMR SVLLLAYKPM EGNFEEIARD FNPNWMSAVE ILDDDNFLGA ENAFNLFVCQ KDSAATTDEE RQHLQEVG L FHLGEFVNVF CHGSLVMQNL GETSTPTQGS VLFGTVNGMI GLVTSLSESW YNLLLDMQNR LNKVIKSVGK IEHSFWRSF HTERKTEPAT GFIDGDLIES FLDISRPKMQ EVVANLQYDD GSGMKREATA DDLIKVVEEL TRIH

UniProtKB: DNA damage-binding protein 1, DNA damage-binding protein 1

-
Macromolecule #2: Protein cereblon

MacromoleculeName: Protein cereblon / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.290535 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGSSHHHHHH SAVDENLYFQ GGGRMAGEGD QQDAAHNMGN HLPLLPAESE EEDEMEVEDQ DSKEAKKPNI INFDTSLPTS HTYLGADME EFHGRTLHDD DSCQVIPVLP QVMMILIPGQ TLPLQLFHPQ EVSMVRNLIQ KDRTFAVLAY SNVQEREAQF G TTAEIYAY ...String:
MGSSHHHHHH SAVDENLYFQ GGGRMAGEGD QQDAAHNMGN HLPLLPAESE EEDEMEVEDQ DSKEAKKPNI INFDTSLPTS HTYLGADME EFHGRTLHDD DSCQVIPVLP QVMMILIPGQ TLPLQLFHPQ EVSMVRNLIQ KDRTFAVLAY SNVQEREAQF G TTAEIYAY REEQDFGIEI VKVKAIGRQR FKVLELRTQS DGIQQAKVQI LPECVLPSTM SAVQLESLNK CQIFPSKPVS RE DQCSYKW WQKYQKRKFH CANLTSWPRW LYSLYDAETL MDRIKKQLRE WDENLKDDSL PSNPIDFSYR VAACLPIDDV LRI QLLKIG SAIQRLRCEL DIMNKCTSLC CKQCQETEIT TKNEIFSLSL CGPMAAYVNP HGYVHETLTV YKACNLNLIG RPST EHSWF PGYAWTVAQC KICASHIGWK FTATKKDMSP QKFWGLTRSA LLPTIPDTED EISPDKVILC L

UniProtKB: Protein cereblon

-
Macromolecule #3: Sal-like protein 4

MacromoleculeName: Sal-like protein 4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.486793 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDWSHPQFEK SAVDENLYFQ GGGRGKPPNI SAVDVKPKDE AALYKHKCKY CSKVFGTDSS LQIHLRSHTG ERPFVCSVCG HRFTTKGNL KVHFHRHPQV KANPQLFAEF QDKVAAGNGI PYALSVPDPI DEPSLSLDSK PVLVTTSVGL PQNLSSGTNP K DLTGGSLP ...String:
MDWSHPQFEK SAVDENLYFQ GGGRGKPPNI SAVDVKPKDE AALYKHKCKY CSKVFGTDSS LQIHLRSHTG ERPFVCSVCG HRFTTKGNL KVHFHRHPQV KANPQLFAEF QDKVAAGNGI PYALSVPDPI DEPSLSLDSK PVLVTTSVGL PQNLSSGTNP K DLTGGSLP GDLQPGPSPE SEGGPTLPGV GPNYNSPRAG GFQGSGTPEP GSETLKLQQL VENIDKATTD PNECLICHRV LS CQSSLKM HYRTHTGE

UniProtKB: Sal-like protein 4

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #5: S-Pomalidomide

MacromoleculeName: S-Pomalidomide / type: ligand / ID: 5 / Number of copies: 1 / Formula: Y70
Molecular weightTheoretical: 273.244 Da
Chemical component information

ChemComp-Y70:
S-Pomalidomide

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 280439
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more