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Yorodumi- PDB-4n9f: Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n9f | ||||||
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Title | Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex | ||||||
Components |
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Keywords | LIGASE/VIRAL PROTEIN / Zinc Finger motif / stabilize VIf interaction with CUL5 / CUL5 / TRANSCRIPTION-VIRAL PROTEIN complex / LIGASE-VIRAL PROTEIN complex | ||||||
Function / homology | Function and homology information RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / lymphocyte differentiation ...RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / lymphocyte differentiation / ERBB2 signaling pathway / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / virion component => GO:0044423 / RUNX2 regulates genes involved in cell migration / RUNX2 regulates genes involved in differentiation of myeloid cells / Transcriptional regulation by RUNX2 / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / myeloid cell differentiation / target-directed miRNA degradation / RUNX3 Regulates Immune Response and Cell Migration / elongin complex / VCB complex / definitive hemopoiesis / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of RUNX1 Expression and Activity / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / RUNX2 regulates osteoblast differentiation / site of DNA damage / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RUNX3 regulates p14-ARF / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / cell maturation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / viral life cycle / intrinsic apoptotic signaling pathway / transcription corepressor binding / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / Transcriptional regulation of granulopoiesis / transcription elongation by RNA polymerase II / Downregulation of ERBB2 signaling / Vif-mediated degradation of APOBEC3G / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of RUNX3 expression and activity / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / calcium channel activity / Inactivation of CSF3 (G-CSF) signaling / G1/S transition of mitotic cell cycle / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / virion component / osteoblast differentiation / protein polyubiquitination / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / signaling receptor activity / Neddylation / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / sequence-specific DNA binding / Estrogen-dependent gene expression / transcription coactivator activity / host cell cytoplasm / transcription by RNA polymerase II / protein ubiquitination / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / host cell plasma membrane / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Guo, Y.Y. / Dong, L.Y. / Huang, Z.W. | ||||||
Citation | Journal: Nature / Year: 2014 Title: Structural basis for hijacking CBF-b and CUL5 E3 ligase complex by HIV-1 Vif Authors: Guo, Y.Y. / Dong, L.Y. / Qiu, X.L. / Wang, Y.S. / Zhang, B.L. / Liu, H.N. / Yu, Y. / Zang, Y. / Yang, M.J. / Huang, Z.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n9f.cif.gz | 3.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4n9f.ent.gz | 3 MB | Display | PDB format |
PDBx/mmJSON format | 4n9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n9f_validation.pdf.gz | 984.1 KB | Display | wwPDB validaton report |
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Full document | 4n9f_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4n9f_validation.xml.gz | 293.7 KB | Display | |
Data in CIF | 4n9f_validation.cif.gz | 406.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/4n9f ftp://data.pdbj.org/pub/pdb/validation_reports/n9/4n9f | HTTPS FTP |
-Related structure data
Related structure data | 4jghS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
-Components
-Protein , 3 types, 36 molecules UCIOVflrx39waFLRciou06kNbGMSdj...
#1: Protein | Mass: 36386.766 Da / Num. of mol.: 12 / Fragment: UNP residues 12-321 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CUL5, VACM1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93034 #4: Protein | Mass: 20272.629 Da / Num. of mol.: 12 / Fragment: UNP residues 1-170 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBFB, CBFbeta / Production host: Escherichia coli (E. coli) / References: UniProt: Q13951 #5: Protein | Mass: 20982.240 Da / Num. of mol.: 12 / Fragment: UNP residues 1-176 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: vif / Production host: Escherichia coli (E. coli) / References: UniProt: Q72499, UniProt: P12504*PLUS |
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-Transcription elongation factor B polypeptide ... , 2 types, 24 molecules YEKQZhntz5TBXDJPWgmsy4eH
#2: Protein | Mass: 10843.420 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15369 #3: Protein | Mass: 11488.030 Da / Num. of mol.: 12 / Fragment: UNP residues 1-102 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15370 |
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-Non-polymers , 1 types, 12 molecules
#6: Chemical | ChemComp-ZN / |
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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: 3.99 Å3/Da / Density % sol: 69.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 200 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å | |||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 27, 2013 | |||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 3.3→50 Å / Num. obs: 281473 / % possible obs: 95.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1.6 / Redundancy: 4.3 % / Net I/σ(I): 15 | |||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JGH Resolution: 3.3→49.535 Å / σ(F): 1.97 / Stereochemistry target values: ML
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Refinement step | Cycle: LAST / Resolution: 3.3→49.535 Å
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Refine LS restraints |
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Refinement TLS params. | Method: refined / Origin x: 48.2984 Å / Origin y: 5.5279 Å / Origin z: -144.855 Å
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Refinement TLS group | Selection details: all |