+
Open data
-
Basic information
Entry | Database: PDB / ID: 1kcq | ||||||
---|---|---|---|---|---|---|---|
Title | Human Gelsolin Domain 2 with a Cd2+ bound | ||||||
![]() | GELSOLIN | ||||||
![]() | STRUCTURAL PROTEIN / alpha-beta structure / actin-binding protein / familial amyloidosis--Finnish type / cadmium binding / metal binding | ||||||
Function / homology | ![]() striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway ...striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / actin cap / regulation of podosome assembly / sequestering of actin monomers / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / actin filament depolymerization / barbed-end actin filament capping / actin polymerization or depolymerization / cardiac muscle cell contraction / cell projection assembly / podosome / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / cortical actin cytoskeleton / phagocytosis, engulfment / hepatocyte apoptotic process / sarcoplasm / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / phagocytic vesicle / actin filament polymerization / central nervous system development / actin filament organization / protein destabilization / cellular response to type II interferon / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / amyloid fibril formation / blood microparticle / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kazmirski, S.L. / Isaacson, R.L. / An, C. / Buckle, A. / Johnson, C.M. / Daggett, V. / Fersht, A.R. | ||||||
![]() | ![]() Title: Loss of a metal-binding site in gelsolin leads to familial amyloidosis-Finnish type. Authors: Kazmirski, S.L. / Isaacson, R.L. / An, C. / Buckle, A. / Johnson, C.M. / Daggett, V. / Fersht, A.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 38.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 24.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 420.4 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 10.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1d0nS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 | ![]()
| ||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 11592.965 Da / Num. of mol.: 1 / Fragment: DOMAIN 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
---|---|---|---|
#2: Chemical | ChemComp-CD / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.43 % | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 400, cadmium chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP at 290K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 4, 2000 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→43.033 Å / Num. obs: 14799 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.174 / % possible all: 94.6 |
Reflection | *PLUS Lowest resolution: 43 Å / Num. obs: 13093 / Num. measured all: 44277 |
Reflection shell | *PLUS % possible obs: 94.6 % / Mean I/σ(I) obs: 3.5 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: Residues 151-266 from PDB ENTRY 1D0N Resolution: 1.65→22.25 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.2 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→22.25 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: ![]() | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.18 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.2 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.9 |