[English] 日本語
![](img/lk-miru.gif)
- PDB-8edi: Structure of C. elegans UNC-5 IG 1+2 Domains bound to Heparin dp4 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8edi | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of C. elegans UNC-5 IG 1+2 Domains bound to Heparin dp4 | |||||||||
![]() | Netrin receptor unc-5 | |||||||||
![]() | PROTEIN BINDING / Cell surface receptor / Axon Guidance / Signaling / Glycoprotein | |||||||||
Function / homology | ![]() distal tip cell migration / Netrin-1 signaling / positive regulation of anterior/posterior axon guidance / regulation of dorsal/ventral axon guidance / mesodermal cell migration / gonad morphogenesis / positive regulation of locomotion / nematode male tail tip morphogenesis / netrin receptor activity / dorsal/ventral axon guidance ...distal tip cell migration / Netrin-1 signaling / positive regulation of anterior/posterior axon guidance / regulation of dorsal/ventral axon guidance / mesodermal cell migration / gonad morphogenesis / positive regulation of locomotion / nematode male tail tip morphogenesis / netrin receptor activity / dorsal/ventral axon guidance / chemorepulsion of axon / netrin-activated signaling pathway / establishment or maintenance of actin cytoskeleton polarity / ventral cord development / commissural neuron axon guidance / motor neuron axon guidance / negative regulation of microtubule polymerization / positive regulation of axon extension / axonal growth cone / protein tyrosine kinase binding / membrane raft / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Priest, J.M. / Ozkan, E. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structure of C. elegans UNC-5 IG 1+2 Domains Authors: Priest, J.M. / Ozkan, E. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 214.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 144.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 23.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8edcSC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.535665366599, -0.842344850865, 0.0593107683968), (-0.841123208806, 0.526039550849, -0.125674733142), (0.0746616543779, -0.117207265831, -0.990296972732)Vector: 4. ...NCS oper: (Code: given Matrix: (-0.535665366599, -0.842344850865, 0.0593107683968), Vector: |
-
Components
#1: Protein | Mass: 23186.814 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | #3: Polysaccharide | 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)- ...4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose | Type: oligosaccharide / Mass: 1154.940 Da / Num. of mol.: 1 / Source method: isolated from a natural source #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.39 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 4% (v/v) Pentaerythritol ethoxylate (3/4 EO/OH), 0.1 M sodium acetate pH 4.6, 16% (w/v) PEG 8000, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033167 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→49.1 Å / Num. obs: 21299 / % possible obs: 58 % / Redundancy: 18.4 % / Biso Wilson estimate: 53.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.014 / Rrim(I) all: 0.061 / Rsym value: 0.059 / Net I/σ(I): 27 |
Reflection shell | Resolution: 2.11→2.3 Å / Redundancy: 14.8 % / Rmerge(I) obs: 1.66 / Mean I/σ(I) obs: 2 / Num. unique obs: 1065 / CC1/2: 0.724 / Rpim(I) all: 0.43 / Rrim(I) all: 1.72 / Rsym value: 1.66 / % possible all: 24.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 8EDC Resolution: 2.11→49.1 Å / SU ML: 0.3186 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.3254 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→49.1 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.957894604009 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
|