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Yorodumi- PDB-2g5b: Crystal Structure of the anti-Bax monoclonal antibody 6A7 and a B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g5b | |||||||||
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Title | Crystal Structure of the anti-Bax monoclonal antibody 6A7 and a Bax peptide. | |||||||||
Components |
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Keywords | APOPTOSIS / 6A7 / Bax / Fab / Antibody / Fab-Peptide Complex | |||||||||
Function / homology | Function and homology information T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation ...T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation / Activation, translocation and oligomerization of BAX / positive regulation of B cell apoptotic process / development of secondary sexual characteristics / NTRK3 as a dependence receptor / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / B cell homeostatic proliferation / glycosphingolipid metabolic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell negative selection / BAK complex / apoptotic process involved in blood vessel morphogenesis / mitochondrial fragmentation involved in apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / apoptotic process involved in embryonic digit morphogenesis / Release of apoptotic factors from the mitochondria / mitochondrial permeability transition pore complex / post-embryonic camera-type eye morphogenesis / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / Transcriptional regulation by RUNX2 / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / B cell apoptotic process / positive regulation of endoplasmic reticulum unfolded protein response / endoplasmic reticulum calcium ion homeostasis / fertilization / immunoglobulin complex / positive regulation of epithelial cell apoptotic process / calcium ion transport into cytosol / motor neuron apoptotic process / channel activity / mitochondrial fusion / Bcl-2 family protein complex / epithelial cell apoptotic process / myeloid cell homeostasis / BH domain binding / execution phase of apoptosis / hypothalamus development / positive regulation of calcium ion transport into cytosol / thymocyte apoptotic process / pore complex / odontogenesis of dentin-containing tooth / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / germ cell development / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / vagina development / B cell homeostasis / negative regulation of mitochondrial membrane potential / negative regulation of apoptotic signaling pathway / intrinsic apoptotic signaling pathway by p53 class mediator / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / immunoglobulin mediated immune response / response to axon injury / blood vessel remodeling / ectopic germ cell programmed cell death / cellular response to unfolded protein / Pyroptosis / supramolecular fiber organization / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / ovarian follicle development / release of sequestered calcium ion into cytosol / extrinsic apoptotic signaling pathway in absence of ligand / homeostasis of number of cells within a tissue / response to salt stress / Hsp70 protein binding / intrinsic apoptotic signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / negative regulation of protein binding / kidney development / antigen binding / response to gamma radiation / apoptotic signaling pathway / neuron migration / positive regulation of protein-containing complex assembly / response to toxic substance / cellular response to virus / cerebral cortex development Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Peyerl, F.W. / Dai, S. / Murphy, G.A. / Marrack, P. / Kappler, J.W. | |||||||||
Citation | Journal: Cell Death Differ. / Year: 2007 Title: Elucidation of some Bax conformational changes through crystallization of an antibody-peptide complex. Authors: Peyerl, F.W. / Dai, S. / Murphy, G.A. / Crawford, F. / White, J. / Marrack, P. / Kappler, J.W. | |||||||||
History |
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Remark 999 | SEQUENCE There is no suitable sequence database reference available. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g5b.cif.gz | 349.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g5b.ent.gz | 290.5 KB | Display | PDB format |
PDBx/mmJSON format | 2g5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/2g5b ftp://data.pdbj.org/pub/pdb/validation_reports/g5/2g5b | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein/peptide , 1 types, 4 molecules IJKL
#3: Protein/peptide | Mass: 760.790 Da / Num. of mol.: 4 / Fragment: Bax peptide fragment / Source method: obtained synthetically / Details: This sequence occurs naturally in mice and humans / References: UniProt: Q07812*PLUS |
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-Antibody , 2 types, 8 molecules ACEGBDFH
#1: Antibody | Mass: 24086.699 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / References: UniProt: Q58EU4 #2: Antibody | Mass: 23928.721 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / References: UniProt: P84751 |
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-Sugars , 3 types, 4 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 2 types, 429 molecules
#7: Chemical | ChemComp-SO4 / #8: 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: 2.63 Å3/Da / Density % sol: 53.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.35 Details: 20% PEG 8000, 0.1 M Tris-HCl, pH 7.35, 0.4 M lithium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.58 Å / Num. all: 106760 / Num. obs: 91909 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 5.71 % / Rmerge(I) obs: 0.106 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 5.68 % / Rmerge(I) obs: 0.63 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 25.899 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.683 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Xplor file |
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