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Yorodumi- PDB-4qr9: Crystal structure of two HMGB1 Box A domains cooperating to under... -
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-Basic information
Entry | Database: PDB / ID: 4qr9 | ||||||
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Title | Crystal structure of two HMGB1 Box A domains cooperating to underwind and kink a DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / HMG-box / HMGB1 / Box A domain / High mobility group / DNA-binding / bend DNA / kink DNA / architectural factor / minor groove / chromatin / Nucleus | ||||||
Function / homology | Function and homology information male-specific defense response to bacterium / positive regulation of myeloid progenitor cell differentiation / open form four-way junction DNA binding / calcium-dependent protein kinase regulator activity / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / plasmacytoid dendritic cell activation / regulation of tolerance induction / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair ...male-specific defense response to bacterium / positive regulation of myeloid progenitor cell differentiation / open form four-way junction DNA binding / calcium-dependent protein kinase regulator activity / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / plasmacytoid dendritic cell activation / regulation of tolerance induction / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / positive regulation of toll-like receptor 2 signaling pathway / negative regulation of apoptotic cell clearance / positive regulation of myeloid cell differentiation / negative regulation of RNA polymerase II transcription preinitiation complex assembly / DNA geometric change / positive regulation of macrophage inflammatory protein 1 alpha production / myeloid dendritic cell activation / T-helper 1 cell activation / T-helper 1 cell differentiation / C-X-C chemokine binding / bent DNA binding / positive regulation of glycogen catabolic process / glycolipid binding / positive regulation of dendritic cell differentiation / negative regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of toll-like receptor 9 signaling pathway / neutrophil clearance / endothelial cell chemotaxis / positive regulation of DNA ligation / eye development / positive regulation of interleukin-1 production / RAGE receptor binding / induction of positive chemotaxis / bubble DNA binding / alphav-beta3 integrin-HMGB1 complex / regulation of nucleotide-excision repair / V(D)J recombination / myeloid progenitor cell differentiation / myeloid cell differentiation / macrophage activation involved in immune response / positive regulation of innate immune response / positive regulation of monocyte chemotactic protein-1 production / positive regulation of chemokine (C-X-C motif) ligand 2 production / inflammatory response to antigenic stimulus / supercoiled DNA binding / endothelial cell proliferation / cellular response to interleukin-7 / positive regulation of monocyte chemotaxis / glycogen catabolic process / apoptotic cell clearance / myoblast proliferation / DNA binding, bending / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / phosphatidylserine binding / positive regulation of wound healing / protein kinase activator activity / negative regulation of DNA replication / positive regulation of activated T cell proliferation / positive regulation of sprouting angiogenesis / response to type II interferon / positive regulation of smooth muscle cell migration / negative regulation of blood vessel endothelial cell migration / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / negative regulation of type II interferon production / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of blood vessel endothelial cell migration / positive regulation of myoblast differentiation / cellular response to interleukin-1 / response to glucose / DNA polymerase binding / heterochromatin formation / positive regulation of autophagy / four-way junction DNA binding / condensed chromosome / response to glucocorticoid / transcription repressor complex / activation of innate immune response / positive regulation of interferon-beta production / positive regulation of interleukin-12 production / positive regulation of mitotic cell cycle / positive regulation of interleukin-1 beta production / cytokine activity / positive regulation of interleukin-8 production / lipopolysaccharide binding / peptide binding / lung development / positive regulation of JNK cascade / base-excision repair / response to insulin / cell morphogenesis / positive regulation of neuron projection development / autophagy / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / circadian rhythm / neuron projection development / transcription corepressor activity Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sanchez-Giraldo, R. / Acosta-Reyes, F.J. / Malarkey, C.S. / Saperas, N. / Churchill, M.E.A. / Campos, J.L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Two high-mobility group box domains act together to underwind and kink DNA. Authors: Sanchez-Giraldo, R. / Acosta-Reyes, F.J. / Malarkey, C.S. / Saperas, N. / Churchill, M.E. / Campos, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qr9.cif.gz | 120.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qr9.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 4qr9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/4qr9 ftp://data.pdbj.org/pub/pdb/validation_reports/qr/4qr9 | HTTPS FTP |
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-Related structure data
Related structure data | 1cktS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 5 - 79 / Label seq-ID: 1 - 75
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-Components
#1: Protein | Mass: 8949.302 Da / Num. of mol.: 2 / Fragment: Residues 8-81 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hmgb1, Hmg-1, Hmg1 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLySS / References: UniProt: P63159 #2: DNA chain | Mass: 3043.029 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-MG / | #4: 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: 2.82 Å3/Da / Density % sol: 56.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.025M Sodium Cacodylate 0.020M Magnesium Chloride 2.5% MPD (equilibrated against 40% MPD), pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2013 / Details: Mirrors |
Radiation | Monochromator: Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2→42.12 Å / Num. all: 23702 / Num. obs: 23441 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 16.025 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2162 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1CKT Resolution: 2→42.12 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.442 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.15 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.412 Å2
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Refinement step | Cycle: LAST / Resolution: 2→42.12 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 3839 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.001→2.053 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 |
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