[English] 日本語
Yorodumi
- PDB-7bqv: Cereblon in complex with SALL4 and (S)-5-hydroxythalidomide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bqv
TitleCereblon in complex with SALL4 and (S)-5-hydroxythalidomide
Components
  • Protein cereblon
  • Sal-like protein 4
KeywordsMETAL BINDING PROTEIN / ZINC FINGER / E3 UBIQUITIN LIGASE / COMPLEX / THALIDOMIDE
Function / homology
Function and homology information


POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / negative regulation of monoatomic ion transmembrane transport / Transcriptional regulation of pluripotent stem cells / embryonic limb morphogenesis / Cul4A-RING E3 ubiquitin ligase complex / inner cell mass cell proliferation / ventricular septum development / locomotory exploration behavior / somatic stem cell population maintenance / positive regulation of Wnt signaling pathway ...POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / negative regulation of monoatomic ion transmembrane transport / Transcriptional regulation of pluripotent stem cells / embryonic limb morphogenesis / Cul4A-RING E3 ubiquitin ligase complex / inner cell mass cell proliferation / ventricular septum development / locomotory exploration behavior / somatic stem cell population maintenance / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / heterochromatin / Regulation of PTEN gene transcription / neural tube closure / positive regulation of protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / protein ubiquitination / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily ...Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / 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
Similarity search - Domain/homology
Chem-F4U / Protein cereblon / Sal-like protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFurihata, H. / Miyauchi, Y. / Asano, A. / Tanokura, M. / Miyakawa, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP19am0101077 Japan
CitationJournal: Nat Commun / Year: 2020
Title: Structural bases of IMiD selectivity that emerges by 5-hydroxythalidomide.
Authors: Furihata, H. / Yamanaka, S. / Honda, T. / Miyauchi, Y. / Asano, A. / Shibata, N. / Tanokura, M. / Sawasaki, T. / Miyakawa, T.
History
DepositionMar 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein cereblon
B: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6077
Polymers15,0092
Non-polymers5975
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.621, 93.895, 43.682
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Protein cereblon


Mass: 12203.090 Da / Num. of mol.: 1 / Mutation: C366S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96SW2
#2: Protein/peptide Sal-like protein 4 / Zinc finger protein 797 / Zinc finger protein SALL4


Mass: 2806.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SALL4, ZNF797 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJQ4

-
Non-polymers , 4 types, 51 molecules

#3: Chemical ChemComp-F4U / 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-5-oxidanyl-isoindole-1,3-dione


Mass: 274.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10N2O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 22% PEG 4000, 0.1 M MES (pH 6.0), 0.2 M lithium sulfate

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→46.95 Å / Num. obs: 16362 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 17.34 Å2 / CC1/2: 1 / Rpim(I) all: 0.024 / Rrim(I) all: 0.088 / Net I/σ(I): 21
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 957 / CC1/2: 0.832 / Rpim(I) all: 0.373 / Rrim(I) all: 1.375 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIXVer 1.15.1_3469refinement
XDSdata reduction
Aimlessdata scaling
PHASERVer 1.15.1_3469phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BQU

7bqu


Resolution: 1.8→35.794 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 806 4.93 %
Rwork0.197 --
obs0.1983 16337 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→35.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1051 0 32 46 1129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061112
X-RAY DIFFRACTIONf_angle_d0.8581513
X-RAY DIFFRACTIONf_dihedral_angle_d12.811648
X-RAY DIFFRACTIONf_chiral_restr0.323163
X-RAY DIFFRACTIONf_plane_restr0.005183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.91280.28051210.24552568X-RAY DIFFRACTION100
1.9128-2.06050.2051390.2032525X-RAY DIFFRACTION100
2.0605-2.26780.19011420.1942541X-RAY DIFFRACTION100
2.2678-2.59590.22091340.19382579X-RAY DIFFRACTION100
2.5959-3.27020.24441360.20662596X-RAY DIFFRACTION100
3.2702-35.7940.21921340.18772722X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -27.6145 Å / Origin y: -14.6462 Å / Origin z: 0.2872 Å
111213212223313233
T0.2717 Å20.0435 Å20.0077 Å2-0.1736 Å2-0.0069 Å2--0.1734 Å2
L1.5102 °20.3863 °2-0.3065 °2-3.9243 °2-0.4282 °2--4.1759 °2
S-0.0374 Å °0.0004 Å °-0.0324 Å °-0.0579 Å °-0.0013 Å °-0.0483 Å °-0.103 Å °-0.0978 Å °0.0403 Å °
Refinement TLS groupSelection details: all

+
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