[English] 日本語
![](img/lk-miru.gif)
- PDB-3vlc: Crystal structure of S. cerevisiae Get3 in the semi open conforma... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3vlc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of S. cerevisiae Get3 in the semi open conformation in complex with Get1 cytosolic domain at 4.5 angstrom resolution | ||||||
![]() |
| ||||||
![]() | HYDROLASE/TRANSPORT PROTEIN / ATPase / membrane protein insertion / ATP binding / membrane protein binding / HYDROLASE-TRANSPORT PROTEIN complex | ||||||
Function / homology | ![]() GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to metal ion / mitophagy ...GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to metal ion / mitophagy / protein-membrane adaptor activity / protein folding chaperone / guanyl-nucleotide exchange factor activity / mitochondrial membrane / unfolded protein binding / response to heat / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kubota, K. / Yamagata, A. / Fukai, S. | ||||||
![]() | ![]() Title: Get1 stabilizes an open dimer conformation of get3 ATPase by binding two distinct interfaces Authors: Kubota, K. / Yamagata, A. / Sato, Y. / Goto-Ito, S. / Fukai, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 88 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 65.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 671.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 693.3 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3b2eSC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 39451.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: NRRL Y-53 / Plasmid: PETDuet-1 / Production host: ![]() ![]() References: UniProt: Q12154*PLUS, Hydrolases; Acting on acid anhydrides |
---|---|
#2: Protein | Mass: 11255.633 Da / Num. of mol.: 1 / Fragment: UNP residues 21-104 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: GET1, MDM39, YGL020C / Plasmid: pETDuet-1 / Production host: ![]() ![]() |
#3: Chemical | ChemComp-ADP / |
Sequence details | A SEQUENCE DATABASE REFERENCE FOR ENTITY 1 (CHAIN A) WHICH DERIVES FROM STRAIN NRRL Y-53 DOES NOT ...A SEQUENCE DATABASE REFERENCE FOR ENTITY 1 (CHAIN A) WHICH DERIVES FROM STRAIN NRRL Y-53 DOES NOT CURRENTLY EXIST. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.2 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 13.5% PEG 3350, 0.18M trisodium citrate, 9% MPD, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Feb 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4.5→50 Å / Num. obs: 3862 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Rsym value: 0.05 / Net I/σ(I): 45.8 |
Reflection shell | Resolution: 4.5→4.58 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 191 / Rsym value: 0.313 / % possible all: 98.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3B2E Resolution: 4.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 113.826 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 268.89 Å2 / Biso mean: 220.9105 Å2 / Biso min: 168.36 Å2
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.5→50 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
Xplor file |
|