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Open data
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Basic information
Entry | Database: PDB / ID: 1qp1 | ||||||
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Title | KAPPA VARIABLE LIGHT CHAIN | ||||||
![]() | BENCE-JONES KAPPA I ANTIBODY BRE (LIGHT CHAIN) | ||||||
![]() | IMMUNE SYSTEM / BETA SANDWICH / DOUBLE SPIRAL | ||||||
Function / homology | ![]() 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 / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Steinrauf, L.K. | ||||||
![]() | ![]() Title: Molecular structure of the amyloid-forming protein kappa I Bre. Authors: Steinrauf, L.K. / Chiang, M.Y. / Shiuan, D. #1: ![]() Title: Structure of an Immunoglubulin Kappa Variable Light Chain Associated with Primary Amyloidosis Authors: Steinrauf, L.K. / Hamilton, J.A. / Clawson, D. / Liepnieks, J. / Murrell, J. / Benson, M.D. #2: ![]() Title: Tertiary Structure of an Amyloid Immunoglobulin Light Chain Protein: A Proposed Model for Amyloid Fibril Formation Authors: Schormann, N. / Murrell, J.R. / Liepnieks, J.R. / Benson, M.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.5 KB | Display | ![]() |
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PDB format | ![]() | 58.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.3 KB | Display | ![]() |
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Full document | ![]() | 429.5 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 11787.930 Da / Num. of mol.: 3 / Fragment: IMMUNOGLOBULIN FRAGMENT, VARIABLE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.24 % | ||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: AMMONIUM SULFATE, CITRATE BUFFER, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 11, 1992 |
Radiation | Monochromator: BENT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→60 Å / Num. all: 89999 / Num. obs: 22485 / % possible obs: 68.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.06→2.18 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 1.92 / % possible all: 50.25 |
Reflection shell | *PLUS % possible obs: 50.2 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: THE BENCE-JONES PROTEINS ROY: COLMAN, SCHRAMM, GURS J. MOL. BIOL. 116, 73, 1977 AND REI: EPP, COLMAN, FEHLHAMMER, BODE, SCHIFFER, HUBER, AND PALM EUR. J. BIOCHEM. 45, 513 1974 Resolution: 2.06→20 Å / Num. parameters: 1040 / Num. restraintsaints: 984 / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2708 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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