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Yorodumi- PDB-2o2v: Crystal Structure of the Complex of Human Mitogen Activated Prote... -
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-Basic information
Entry | Database: PDB / ID: 2o2v | ||||||
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Title | Crystal Structure of the Complex of Human Mitogen Activated Protein Kinase Kinase 5 Phox Domain (MAP2K5-phox) with Human Mitogen Activated Protein Kinase Kinase Kinase 3 (MAP3K3B-phox) | ||||||
Components |
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Keywords | TRANSFERASE / mitogen activated protein kinase kinase 5 / MAP2K5 / MEK5 / MKK5 / PRKMK5 / MAP kinase 5 / phox / phox-domain / mitogen activated protein kinase kinase kinase 3 / MEKK3 / MAPKKK3 / MAP/ERK kinase kinase 3 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information ERK5 cascade / negative regulation of chemokine (C-X-C motif) ligand 2 production / Signalling to ERK5 / positive regulation of cell proliferation in bone marrow / negative regulation of response to cytokine stimulus / negative regulation of heterotypic cell-cell adhesion / mitogen-activated protein kinase kinase kinase / negative regulation of smooth muscle cell apoptotic process / negative regulation of interleukin-8 production / mitogen-activated protein kinase kinase ...ERK5 cascade / negative regulation of chemokine (C-X-C motif) ligand 2 production / Signalling to ERK5 / positive regulation of cell proliferation in bone marrow / negative regulation of response to cytokine stimulus / negative regulation of heterotypic cell-cell adhesion / mitogen-activated protein kinase kinase kinase / negative regulation of smooth muscle cell apoptotic process / negative regulation of interleukin-8 production / mitogen-activated protein kinase kinase / cellular response to laminar fluid shear stress / negative regulation of cell migration involved in sprouting angiogenesis / positive regulation of p38MAPK cascade / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of NF-kappaB transcription factor activity / blood vessel development / negative regulation of cellular senescence / MAP kinase kinase activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / MAP kinase kinase kinase activity / positive regulation of protein metabolic process / insulin-like growth factor receptor signaling pathway / positive regulation of epithelial cell proliferation / positive regulation of MAP kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / spindle / cellular response to growth factor stimulus / Interleukin-1 signaling / MAPK cascade / heart development / positive regulation of cell growth / protein tyrosine kinase activity / positive regulation of canonical NF-kappaB signal transduction / protein autophosphorylation / protein kinase activity / intracellular signal transduction / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Filippakopoulos, P. / Savitsky, P. / Ugochukwu, E. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / von Delft, F. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Complex of Human Mitogen Activated Protein Kinase Kinase 5 Phox Domain (MAP2K5-phox) with Human Mitogen Activated Protein Kinase Kinase Kinase 3 (MAP3K3B-phox) Authors: Filippakopoulos, P. / Savitsky, P. / Ugochukwu, E. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / von Delft, F. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o2v.cif.gz | 53.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o2v.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 2o2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/2o2v ftp://data.pdbj.org/pub/pdb/validation_reports/o2/2o2v | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11941.498 Da / Num. of mol.: 1 / Fragment: MAP2K5-phox Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K5, MEK5, MKK5, PRKMK5 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 References: UniProt: Q13163, mitogen-activated protein kinase kinase |
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#2: Protein | Mass: 10484.896 Da / Num. of mol.: 1 / Fragment: MAP3K3B-phox Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K3, MAPKKK3, MEKK3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 References: UniProt: Q99759, mitogen-activated protein kinase kinase kinase |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.02M CaCl2, 0.1M Na(CH3COO), 30% MPD, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 8, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 6.1 % / Av σ(I) over netI: 12.1 / Number: 118834 / Rmerge(I) obs: 0.075 / Χ2: 1.03 / D res high: 1.83 Å / D res low: 50 Å / Num. obs: 19523 / % possible obs: 99.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.83→50 Å / Num. all: 19661 / Num. obs: 19523 / % possible obs: 99.3 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Χ2: 1.027 / Net I/σ(I): 12.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.83→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.578 / Num. unique all: 1836 / Rsym value: 0.578 / Χ2: 0.869 / % possible all: 96.5 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entries 2C60, 1WI0 Resolution: 1.83→46.83 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.099 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.12 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.491 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→46.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.876 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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