[English] 日本語
Yorodumi- PDB-3ixw: Scorpion Hemocyanin activated state pseudo atomic model built bas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ixw | ||||||
---|---|---|---|---|---|---|---|
Title | Scorpion Hemocyanin activated state pseudo atomic model built based on cryo-EM density map | ||||||
Components | Hemocyanin AA6 chain | ||||||
Keywords | OXYGEN BINDING / Hemocyanin / Hc / Phenolxoidase activity / Tyrosinase (Ty) / Catecholoxidase (CO) / Enzyme / SDS / cryo-EM / single particle analysis / Copper / Metal-binding / Oxygen transport / Phosphoprotein / Secreted / Transport | ||||||
Function / homology | Function and homology information chloride ion binding / oxygen carrier activity / oxidoreductase activity / copper ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Androctonus australis (Sahara scorpion) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å | ||||||
Authors | Cong, Y. / Zhang, Q. / Woolford, D. / Schweikardt, T. / Khant, H. / Ludtke, S. / Chiu, W. / Decker, H. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Structural mechanism of SDS-induced enzyme activity of scorpion hemocyanin revealed by electron cryomicroscopy. Authors: Yao Cong / Qinfen Zhang / David Woolford / Thorsten Schweikardt / Htet Khant / Matthew Dougherty / Steven J Ludtke / Wah Chiu / Heinz Decker / Abstract: Phenoloxidases (POs) occur in all organisms and are involved in skin and hair coloring in mammals, and initiating melanization in wound healing. Mutation or overexpression of PO can cause albinism or ...Phenoloxidases (POs) occur in all organisms and are involved in skin and hair coloring in mammals, and initiating melanization in wound healing. Mutation or overexpression of PO can cause albinism or melanoma, respectively. SDS can convert inactive PO and the oxygen carrier hemocyanin (Hc) into enzymatically active PO. Here we present single-particle cryo-EM maps at subnanometer resolution and pseudoatomic models of the 24-oligomeric Hc from scorpion Pandinus imperator in resting and SDS-activated states. Our structural analyses led to a plausible mechanism of Hc enzyme PO activation: upon SDS activation, the intrinsically flexible Hc domain I twists away from domains II and III in each subunit, exposing the entrance to the active site; this movement is stabilized by enhanced interhexamer and interdodecamer interactions, particularly in the central linker subunits. This mechanism could be applicable to other type 3 copper proteins, as the active site is highly conserved. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3ixw.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ixw.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 3ixw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ixw_validation.pdf.gz | 955.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ixw_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3ixw_validation.xml.gz | 222.4 KB | Display | |
Data in CIF | 3ixw_validation.cif.gz | 325 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/3ixw ftp://data.pdbj.org/pub/pdb/validation_reports/ix/3ixw | HTTPS FTP |
-Related structure data
Related structure data | 5101MC 5100C 3ixvC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
Symmetry | Point symmetry: (Schoenflies symbol: C2 (2 fold cyclic)) |
-Components
#1: Protein | Mass: 71883.695 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Androctonus australis (Sahara scorpion) / Strain: Pandinus imperator / References: UniProt: P80476 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Hemocyanin from scorpion Pandinus imperator / Type: COMPLEX / Details: 24mer. treated by 2mM SDS to activate Hc |
---|---|
Molecular weight | Value: 1.7 MDa / Experimental value: YES |
Buffer solution | pH: 7.8 Details: 100 mM TRIS/HCL at pH 7.8, 10 mM CaCl2 and 10 mM MgCl2 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: 100 mM TRIS/HCL at pH 7.8, 10 mM CaCl2 and 10 mM MgCl2 |
Specimen support | Details: 400-mesh Quantifoil holy grid with 1.2x1.3μM hole size |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temp: 101 K / Humidity: 95 % / Method: two side bloting for 1 seconds before plunging |
-Electron microscopy imaging
Microscopy | Model: JEOL 3200FSC / Date: May 31, 2007 / Details: JEOL 3200FSC MDS low dose method |
---|---|
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 4.1 mm / Astigmatism: objective lens astigmatism correction / Camera length: 0 mm |
Specimen holder | Specimen holder model: JEOL 3200FSC CRYOHOLDER / Specimen holder type: Side Entry / Temperature: 101 K / Temperature (max): 101.2 K / Temperature (min): 101 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 18 e/Å2 / Film or detector model: KODAK SO-163 FILM |
EM imaging optics | Energyfilter name: In-column Omega Filter / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV |
-Processing
EM software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: each micrograph | ||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||
3D reconstruction | Method: reference-based refinement using 2D matching / Resolution: 8 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 13400 / Actual pixel size: 1.8 Å Details: Final refinement using FRM2D (Fast Rotational Matching) image alignment method Symmetry type: POINT | ||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL Details: METHOD--rigid body fitting, flexible fitting DETAILS--rigid body fitting followed by flexible fitting using Situs and X-plor | ||||||||||||||||||
Refinement step | Cycle: LAST
|