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- PDB-4aiz: Crystallographic structure of 3mJL2 from the germinal line lambda 3 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4aiz | ||||||
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Title | Crystallographic structure of 3mJL2 from the germinal line lambda 3 | ||||||
![]() | (V2-17 PROTEIN) x 2 | ||||||
![]() | IMMUNE SYSTEM / AMYLOIDOSIS | ||||||
Function / homology | ![]() regulation of complement activation / complement activation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / leukocyte migration / Fc-gamma receptor signaling pathway involved in phagocytosis / Fc-epsilon receptor signaling pathway / FCGR activation / regulation of immune response ...regulation of complement activation / complement activation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / leukocyte migration / Fc-gamma receptor signaling pathway involved in phagocytosis / Fc-epsilon receptor signaling pathway / FCGR activation / regulation of immune response / 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 / receptor-mediated endocytosis / complement activation, classical pathway / 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 / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Villalba, M.I. / Luna, O.D. / Rudino-Pinera, E. / Sanchez, R. / Sanchez-Lopez, R. / Rojas-Trejo, S. / Olamendi-Portugal, T. / Fernandez-Velasco, D.A. / Becerril, B. | ||||||
![]() | ![]() Title: Site-Directed Mutagenesis Reveals Regions Implicated in the Stability and Fiber Formation of Human Lambda3R Light Chains. Authors: Villalba, M.I. / Canul-Tec, J.C. / Luna-Martinez, O.D. / Sanchez-Alcala, R. / Olamendi-Portugal, T. / Rudino-Pinera, E. / Rojas, S. / Sanchez-Lopez, R. / Fernandez-Velasco, D.A. / Becerril, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.3 KB | Display | ![]() |
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PDB format | ![]() | 81.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 798 KB | Display | ![]() |
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Full document | ![]() | 805.7 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 33.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4aixC ![]() 4aj0C ![]() 1lilS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Antibody , 2 types, 4 molecules ACDB
#1: Antibody | Mass: 11517.674 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | | Mass: 11515.701 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 409 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/88Q.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/88Q.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-CIT / | #5: Chemical | ChemComp-88Q / | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | 88Q WAS CONSTRUCTED BASED ON THE ELECTRON DENSITY IN THE POSITION, HOWEVER WE WERE NOT ABLE TO FIND ...88Q WAS CONSTRUCTE |
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Sequence details | THIS DEPOSIT IS THE FIRST REFERENCE TO THE SEQUENCE OF 3MJL2. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.33 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.2 M SODIUM CITRATE, 0.1 M HEPES, 30 % MPD, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 1, 2011 Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING. |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. obs: 31323 / % possible obs: 79.4 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 17.22 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 74.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LIL Resolution: 1.75→34.224 Å / SU ML: 0.38 / σ(F): 1.38 / Phase error: 23.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.115 Å2 / ksol: 0.404 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→34.224 Å
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Refine LS restraints |
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LS refinement shell |
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