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- PDB-2vyr: Structure of human MDM4 N-terminal domain bound to a single domai... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vyr | ||||||
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Title | Structure of human MDM4 N-terminal domain bound to a single domain antibody | ||||||
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![]() | IMMUNE SYSTEM / NUCLEUS / HUMAN MDM4 / ZINC-FINGER | ||||||
Function / homology | ![]() atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / DNA damage response, signal transduction by p53 class mediator / transcription repressor complex / Stabilization of p53 / Oncogene Induced Senescence / negative regulation of protein catabolic process ...atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / DNA damage response, signal transduction by p53 class mediator / transcription repressor complex / Stabilization of p53 / Oncogene Induced Senescence / negative regulation of protein catabolic process / Regulation of TP53 Activity through Methylation / ubiquitin-protein transferase activity / Regulation of TP53 Degradation / cellular response to hypoxia / protein-containing complex assembly / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / protein stabilization / Ub-specific processing proteases / regulation of cell cycle / protein ubiquitination / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yu, G.W. / Vaysburd, M. / Allen, M.D. / Settanni, G. / Fersht, A.R. | ||||||
![]() | ![]() Title: Structure of Human Mdm4 N-Terminal Domain Bound to a Single-Domain Antibody. Authors: Yu, G.W. / Vaysburd, M. / Allen, M.D. / Settanni, G. / Fersht, A.R. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 278.9 KB | Display | ![]() |
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PDB format | ![]() | 234.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 520.4 KB | Display | ![]() |
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Full document | ![]() | 540.5 KB | Display | |
Data in XML | ![]() | 55.9 KB | Display | |
Data in CIF | ![]() | 79 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11306.168 Da / Num. of mol.: 4 / Fragment: RESIDUES 16-116 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 17041.904 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 50 % Description: STRUCTURE WAS INITIALLY SOLVED USING MAD ON A SE- MET COMPLEX CONTAINING LABELLED MDMX. THE NATIVE STRUCTURE WAS SUBSEQUENTLY DETERMINED BY MOLECULAR REPLACEMENT |
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Crystal grow | pH: 7 Details: SE-MET: 20% PEG 3350, 0.2 M MGCL2, 1MM TRIS PH 7.0, 5MM B-ME, PROTEIN 10MG/ML. NATIVE: 1.6M AMMONIUM SULPHATE, 0.5M LITHIUM CHLORIDE, 1MM TRIS, PH 7.0, 5MM B-ME, PROTEIN 10MG/ML |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 116657 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.4 |
Reflection shell | Highest resolution: 2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.3 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2→25 Å / SU ML: 0.32 / Phase error: 23.59 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.385 Å2 / ksol: 0.346 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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LS refinement shell |
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