[English] 日本語
![](img/lk-miru.gif)
- PDB-3a4u: Crystal structure of MCFD2 in complex with carbohydrate recogniti... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3a4u | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of MCFD2 in complex with carbohydrate recognition domain of ERGIC-53 | ||||||
![]() |
| ||||||
![]() | PROTEIN TRANSPORT / LECTIN / ERGIC / ER / GOLGI / TRANSPORT / Disulfide bond / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Membrane / Transmembrane / Disease mutation | ||||||
Function / homology | ![]() Transport to the Golgi and subsequent modification / positive regulation of organelle organization / negative regulation of protein targeting to mitochondrion / Cargo concentration in the ER / endoplasmic reticulum organization / RHOD GTPase cycle / COPII-mediated vesicle transport / RHOC GTPase cycle / COPII-coated ER to Golgi transport vesicle / Golgi organization ...Transport to the Golgi and subsequent modification / positive regulation of organelle organization / negative regulation of protein targeting to mitochondrion / Cargo concentration in the ER / endoplasmic reticulum organization / RHOD GTPase cycle / COPII-mediated vesicle transport / RHOC GTPase cycle / COPII-coated ER to Golgi transport vesicle / Golgi organization / D-mannose binding / endoplasmic reticulum-Golgi intermediate compartment / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / sarcomere / endoplasmic reticulum-Golgi intermediate compartment membrane / ER to Golgi transport vesicle membrane / blood coagulation / unfolded protein binding / protein transport / protein folding / collagen-containing extracellular matrix / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / extracellular exosome / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nishio, M. / Kamiya, Y. / Mizushima, T. / Wakatsuki, S. / Sasakawa, H. / Yamamoto, K. / Uchiyama, S. / Noda, M. / McKay, A.R. / Fukui, K. ...Nishio, M. / Kamiya, Y. / Mizushima, T. / Wakatsuki, S. / Sasakawa, H. / Yamamoto, K. / Uchiyama, S. / Noda, M. / McKay, A.R. / Fukui, K. / Hauri, H.P. / Kato, K. | ||||||
![]() | ![]() Title: Structural basis for the cooperative interplay between the two causative gene products of combined factor V and factor VIII deficiency. Authors: Nishio, M. / Kamiya, Y. / Mizushima, T. / Wakatsuki, S. / Sasakawa, H. / Yamamoto, K. / Uchiyama, S. / Noda, M. / McKay, A.R. / Fukui, K. / Hauri, H.P. / Kato, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 81.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 58.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 444.3 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1r1zS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 28039.068 Da / Num. of mol.: 1 / Fragment: Carbohydrate Recognition Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Protein | Mass: 16316.842 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.14 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% PEG 3350, 0.2M sodium tartrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2008 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→49.81 Å / Num. obs: 36530 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.84 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.188 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.84→1.94 Å / Redundancy: 7 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 6.1 / Num. unique all: 5229 / Rsym value: 0.188 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1R1Z Resolution: 1.84→49.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.975 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.197 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→49.81 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.838→1.886 Å / Total num. of bins used: 20
|