+Open data
-Basic information
Entry | Database: PDB / ID: 4a0c | ||||||
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Title | Structure of the CAND1-CUL4B-RBX1 complex | ||||||
Components |
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Keywords | CELL CYCLE / TRANSCRIPTION / LIGASE / UBIQUITIN / DNA DAMAGE REPAIR | ||||||
Function / homology | Function and homology information Prolactin receptor signaling / SCF complex assembly / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Dual incision in TC-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER ...Prolactin receptor signaling / SCF complex assembly / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Dual incision in TC-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of DVL / Orc1 removal from chromatin / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Hedgehog 'on' state / Degradation of beta-catenin by the destruction complex / eukaryotic initiation factor 4E binding / Interleukin-1 signaling / anaphase-promoting complex / KEAP1-NFE2L2 pathway / cullin-RING-type E3 NEDD8 transferase / GLI3 is processed to GLI3R by the proteasome / negative regulation of catalytic activity / cullin-RING ubiquitin ligase complex / Neddylation / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul7-RING ubiquitin ligase complex / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of protein autoubiquitination / VCB complex / Cul4-RING E3 ubiquitin ligase complex / protein neddylation / UV-damage excision repair / astrocyte differentiation / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-ubiquitin ligase activity / Cul4A-RING E3 ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / protein monoubiquitination / cullin family protein binding / protein K48-linked ubiquitination / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of RNA polymerase II transcription preinitiation complex assembly / ubiquitin ligase complex / positive regulation of TORC1 signaling / TBP-class protein binding / T cell activation / proteasomal protein catabolic process / Recognition of DNA damage by PCNA-containing replication complex / cellular response to amino acid stimulus / Iron uptake and transport / DNA Damage Recognition in GG-NER / G1/S transition of mitotic cell cycle / protein catabolic process / RING-type E3 ubiquitin transferase / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein polyubiquitination / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / neuron projection development / cellular response to UV / ubiquitin protein ligase activity / ribosome biogenesis / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / gene expression / Neddylation / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / ficolin-1-rich granule lumen / RNA polymerase II-specific DNA-binding transcription factor binding / molecular adaptor activity / cell differentiation / protein ubiquitination / DNA repair / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / Golgi apparatus / extracellular exosome / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Scrima, A. / Fischer, E.S. / Faty, M. / Gut, H. / Thoma, N.H. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2011 Title: The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation Authors: Scrima, A. / Fischer, E.S. / Iwai, S. / Gut, H. / Thoma, N.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a0c.cif.gz | 755.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a0c.ent.gz | 604 KB | Display | PDB format |
PDBx/mmJSON format | 4a0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/4a0c ftp://data.pdbj.org/pub/pdb/validation_reports/a0/4a0c | HTTPS FTP |
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-Related structure data
Related structure data | 4a08C 4a09C 4a0aC 4a0bC 4a0kC 4a0lC 4a11C 1u6gS 2hyeS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 139226.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q86VP6 #2: Protein | Mass: 86961.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q13620 #3: Protein | Mass: 11330.942 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PFASTBAC DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) References: UniProt: P62878, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #4: Chemical | ChemComp-ZN / Sequence details | CHAINS A AND B CONTAINS NATURAL VARIANT A952V | |
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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: 3.52 Å3/Da / Density % sol: 65.08 % Description: CAND1 USED AS MODEL FROM 1U6G, CUL4B MODEL GENERATED USING MODELLER BASED ON CUL4A FROM 2HYE |
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Crystal grow | pH: 6.3 / Details: 100 MM MES PH 6.3, 30% PEG 200, 2% PEG 8000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. obs: 59850 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 3.8→3.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1U6G, 2HYE Resolution: 3.8→47.76 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.882 / SU B: 56.264 / SU ML: 0.797 / Cross valid method: THROUGHOUT / ESU R Free: 0.906 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 128.578 Å2
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Refinement step | Cycle: LAST / Resolution: 3.8→47.76 Å
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