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Yorodumi- PDB-5xp1: Structure of monomeric mutant of REI immunoglobulin light chain v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xp1 | |||||||||
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Title | Structure of monomeric mutant of REI immunoglobulin light chain variable domain crystallized at pH 6 | |||||||||
Components | Immunoglobulin kappa variable 1D-33 | |||||||||
Keywords | IMMUNE SYSTEM / Immunoglobulin | |||||||||
Function / homology | Function and homology information CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / antigen binding / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / blood microparticle / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å | |||||||||
Authors | Mine, S. / Nakamura, T. / Uegaki, K. / Hamada, D. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: FEBS J. / Year: 2017 Title: Heat-induced native dimerization prevents amyloid formation by variable domain from immunoglobulin light-chain REI Authors: Nawata, M. / Tsutsumi, H. / Kobayashi, Y. / Unzai, S. / Mine, S. / Nakamura, T. / Uegaki, K. / Kamikubo, H. / Kataoka, M. / Hamada, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xp1.cif.gz | 174.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xp1.ent.gz | 140.1 KB | Display | PDB format |
PDBx/mmJSON format | 5xp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/5xp1 ftp://data.pdbj.org/pub/pdb/validation_reports/xp/5xp1 | HTTPS FTP |
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-Related structure data
Related structure data | 5xqyC 2q20S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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6 |
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7 |
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8 |
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Unit cell |
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-Components
#1: Antibody | Mass: 11946.266 Da / Num. of mol.: 8 / Fragment: UNP residues 22-117 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGKV1D-33 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01593 #2: Water | ChemComp-HOH / | Sequence details | Authors state that the structure was based on the sequence of UNP P01607 as well as the structure ...Authors state that the structure was based on the sequence of UNP P01607 as well as the structure 1REI, which is updated by P01593 at present. Therefore, the structure has a mutation Y96K. Other conflicts are due to sequence conflicts of P01607. | |
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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: 4.22 Å3/Da / Density % sol: 70.61 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M BIS-TRIS pH 6.0, 18% POLYETHYLENE GLYCOL 3350, 0.12M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 27, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→17.961 Å / Num. obs: 35217 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 65.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.88→2.93 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 5 / Num. unique obs: 5153 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Q20 Resolution: 2.88→17.961 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.88→17.961 Å
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Refine LS restraints |
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LS refinement shell |
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