+Open data
-Basic information
Entry | Database: PDB / ID: 5hxb | ||||||
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Title | Cereblon in complex with DDB1, CC-885, and GSPT1 | ||||||
Components |
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Keywords | LIGASE / E3 / ubiquitin / DCAF / cereblon / DDB1 / CRL4 / cullin / IMiD / GSPT1 / CRBN | ||||||
Function / homology | Function and homology information translation release factor complex / negative regulation of monoatomic ion transmembrane transport / translation release factor activity / regulation of translational termination / positive regulation by virus of viral protein levels in host cell / protein methylation / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair ...translation release factor complex / negative regulation of monoatomic ion transmembrane transport / translation release factor activity / regulation of translational termination / positive regulation by virus of viral protein levels in host cell / protein methylation / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / Cul4A-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 / cullin family protein binding / Eukaryotic Translation Termination / viral release from host cell / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death / proteasomal protein catabolic process / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / translational termination / positive regulation of gluconeogenesis / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / DNA Damage Recognition in GG-NER / positive regulation of protein-containing complex assembly / regulation of circadian rhythm / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / G1/S transition of mitotic cell cycle / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / protein-macromolecule adaptor activity / Neddylation / site of double-strand break / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / Potential therapeutics for SARS / chromosome, telomeric region / damaged DNA binding / protein ubiquitination / translation / DNA repair / GTPase activity / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / GTP binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein-containing complex / DNA binding / RNA binding / extracellular space / extracellular exosome / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | ||||||
Authors | Chamberlain, P.P. / Matyskiela, M. / Pagarigan, B. | ||||||
Citation | Journal: Nature / Year: 2016 Title: A novel cereblon modulator recruits GSPT1 to the CRL4(CRBN) ubiquitin ligase. Authors: Matyskiela, M.E. / Lu, G. / Ito, T. / Pagarigan, B. / Lu, C.C. / Miller, K. / Fang, W. / Wang, N.Y. / Nguyen, D. / Houston, J. / Carmel, G. / Tran, T. / Riley, M. / Nosaka, L. / Lander, G.C. ...Authors: Matyskiela, M.E. / Lu, G. / Ito, T. / Pagarigan, B. / Lu, C.C. / Miller, K. / Fang, W. / Wang, N.Y. / Nguyen, D. / Houston, J. / Carmel, G. / Tran, T. / Riley, M. / Nosaka, L. / Lander, G.C. / Gaidarova, S. / Xu, S. / Ruchelman, A.L. / Handa, H. / Carmichael, J. / Daniel, T.O. / Cathers, B.E. / Lopez-Girona, A. / Chamberlain, P.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hxb.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5hxb.ent.gz | 981.5 KB | Display | PDB format |
PDBx/mmJSON format | 5hxb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hxb_validation.pdf.gz | 956.1 KB | Display | wwPDB validaton report |
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Full document | 5hxb_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5hxb_validation.xml.gz | 126.7 KB | Display | |
Data in CIF | 5hxb_validation.cif.gz | 169.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/5hxb ftp://data.pdbj.org/pub/pdb/validation_reports/hx/5hxb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Details | trimeric as determined by electron microscopy |
-Components
#1: Protein | Mass: 21995.799 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSPT1, ERF3A / Production host: Escherichia coli (E. coli) / References: UniProt: P15170 #2: Protein | Mass: 127097.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531 #3: Protein | Mass: 46596.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96SW2 #4: Chemical | #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.89 Å3/Da / Density % sol: 68.37 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / Details: 200mM Sodium Citrate, Tris pH 8.5, 18% PEG 3350 / PH range: 8.4 - 8.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. obs: 66582 / % possible obs: 94.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.198 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 3.6→3.66 Å / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3343 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TZ4, 3E1Y Resolution: 3.6→50 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.858 / SU B: 64.833 / SU ML: 0.536 / Cross valid method: THROUGHOUT / ESU R Free: 0.644 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 112.3 Å2
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Refinement step | Cycle: LAST / Resolution: 3.6→50 Å
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Refine LS restraints |
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