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Yorodumi- PDB-3zkj: Crystal Structure of Ankyrin Repeat and Socs Box-Containing Prote... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 3zkj | |||||||||
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| Title | Crystal Structure of Ankyrin Repeat and Socs Box-Containing Protein 9 (Asb9) in Complex with Elonginb and Elonginc | |||||||||
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Keywords | TRANSCRIPTION / TRANSCRIPTION REGULATION / AUTOANTIBODY | |||||||||
| Function / homology | Function and homology informationtarget-directed miRNA degradation / elongin complex / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript ...target-directed miRNA degradation / elongin complex / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / 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 / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / positive regulation of protein catabolic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular signal transduction / protein ubiquitination / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / cytosol Similarity search - Function | |||||||||
| Biological species | HOMO SAPIENS (human) | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å | |||||||||
Authors | Muniz, J.R.C. / Guo, K. / Zhang, Y. / Ayinampudi, V. / Savitsky, P. / Keates, T. / Filippakopoulos, P. / Vollmar, M. / Yue, W.W. / Krojer, T. ...Muniz, J.R.C. / Guo, K. / Zhang, Y. / Ayinampudi, V. / Savitsky, P. / Keates, T. / Filippakopoulos, P. / Vollmar, M. / Yue, W.W. / Krojer, T. / Ugochukwu, E. / von Delft, F. / Knapp, S. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2013Title: Molecular Architecture of the Ankyrin Socs Box Family of Cul5-Dependent E3 Ubiquitin Ligases Authors: Muniz, J.R.C. / Guo, K. / Kershaw, N.J. / Ayinampudi, V. / von Delft, F. / Babon, J.J. / Bullock, A.N. | |||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 3zkj.cif.gz | 340.6 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb3zkj.ent.gz | 279.6 KB | Display | PDB format |
| PDBx/mmJSON format | 3zkj.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/3zkj ftp://data.pdbj.org/pub/pdb/validation_reports/zk/3zkj | HTTPS FTP |
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-Related structure data
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Links
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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| 2 | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
NCS oper: (Code: given Matrix: (0.0843, -0.0303, -0.996), Vector: |
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Components
-Protein , 1 types, 2 molecules AD
| #1: Protein | Mass: 28559.803 Da / Num. of mol.: 2 / Fragment: RESIDUES 35-294 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Organ: KIDNEY / Plasmid: P11 / Production host: ![]() |
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-TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE ... , 2 types, 4 molecules BECF
| #2: Protein | Mass: 10843.420 Da / Num. of mol.: 2 / Fragment: RESIDUES 17-112 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Organ: KIDNEY / Plasmid: P11 / Production host: ![]() #3: Protein | Mass: 13147.781 Da / Num. of mol.: 2 / Fragment: RESIDUES 221-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Organ: KIDNEY / Plasmid: P11 / Production host: ![]() |
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-Non-polymers , 4 types, 67 molecules 






| #4: Chemical | | #5: Chemical | ChemComp-PEG / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 3.81 Å3/Da / Density % sol: 67.78 % / Description: NONE |
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| Crystal grow | Details: 0.2M NA2SO4, 0.1M BTPROP 6.5, 20% PEG 3350, 10% ETGLY |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
| Detector | Date: Feb 27, 2010 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
| Reflection | Resolution: 2.58→50.47 Å / Num. obs: 41297 / % possible obs: 99.7 % / Observed criterion σ(I): 2.1 / Redundancy: 6.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.7 |
| Reflection shell | Resolution: 2.58→2.72 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→50.47 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / SU B: 23.907 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOODDetails: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 74.17 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.58→50.47 Å
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| Refine LS restraints |
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HOMO SAPIENS (human)
X-RAY DIFFRACTION
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