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Yorodumi- PDB-1lve: STRUCTURE OF THE VARIABLE DOMAIN OF HUMAN IMMUNOGLOBULIN K-4 LIGH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lve | |||||||||
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Title | STRUCTURE OF THE VARIABLE DOMAIN OF HUMAN IMMUNOGLOBULIN K-4 LIGHT CHAIN LEN | |||||||||
Components | LEN, A VARIABLE DOMAIN FROM KAPPA-4 TYPE | |||||||||
Keywords | IMMUNOGLOBULIN / BENCE-JONES PROTEIN | |||||||||
Function / homology | Function and homology information CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / 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 / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / 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 / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / 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 region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Schiffer, M. / Huang, D.-B. / Chang, C.-H. | |||||||||
Citation | Journal: Mol.Immunol. / Year: 1997 Title: Variable domain structure of kappaIV human light chain Len: high homology to the murine light chain McPC603. Authors: Huang, D.B. / Chang, C.H. / Ainsworth, C. / Johnson, G. / Solomon, A. / Stevens, F.J. / Schiffer, M. #1: Journal: Acta Crystallogr.,Sect.A / Year: 1996 Title: Structure of the Variable Domain of Human Immunoglobulin Kappa-Iv Light Chain Len Authors: Huang, D.-B. / Ainsworth, C. / Chang, C.-H. / Stevens, F.J. / Schiffer, M. #2: Journal: Protein Sci. / Year: 1995 Title: Recombinant Immunoglobulin Variable Domains Generated from Synthetic Genes Provide a System for in Vitro Characterization of Light-Chain Amyloid Proteins Authors: Stevens, P.W. / Raffen, R. / Hanson, D.K. / Deng, Y.L. / Berrios-Hammond, M. / Westholm, F.A. / Murphy, C. / Eulitz, M. / Wetzel, R. / Solomon, A. / Schiffer, M. / Stevens, F.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lve.cif.gz | 37.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lve.ent.gz | 25.5 KB | Display | PDB format |
PDBx/mmJSON format | 1lve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lve_validation.pdf.gz | 423.1 KB | Display | wwPDB validaton report |
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Full document | 1lve_full_validation.pdf.gz | 431.6 KB | Display | |
Data in XML | 1lve_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 1lve_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/1lve ftp://data.pdbj.org/pub/pdb/validation_reports/lv/1lve | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 13422.900 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01625, UniProt: P06312*PLUS |
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#2: 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: 1.84 Å3/Da / Density % sol: 33 % | |||||||||||||||
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Crystal grow | pH: 7 / Details: 1.5 M AMMONIUM SULFATE, PH 7.0 | |||||||||||||||
Crystal grow | *PLUS Method: batch | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: PICKER / Detector: DIFFRACTOMETER / Date: 1990 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→23.4 Å / Num. obs: 7471 / % possible obs: 99 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: WAT (MONOMER 2) Resolution: 1.95→10 Å / σ(F): 3
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Displacement parameters | Biso mean: 16.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rwork: 0.222 / Num. reflection obs: 793 |