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- PDB-3ixw: Scorpion Hemocyanin activated state pseudo atomic model built bas... -

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Basic information

Entry
Database: PDB / ID: 3ixw
TitleScorpion Hemocyanin activated state pseudo atomic model built based on cryo-EM density map
ComponentsHemocyanin AA6 chain
KeywordsOXYGEN 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
Arthropod hemocyanins / insect LSPs signature 1. / Arthropod hemocyanins / insect LSPs signature 2. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin, C-terminal domain superfamily / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, copper containing domain / Hemocyanin, ig-like domain ...Arthropod hemocyanins / insect LSPs signature 1. / Arthropod hemocyanins / insect LSPs signature 2. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin, C-terminal domain superfamily / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, copper containing domain / Hemocyanin, ig-like domain / Hemocyanin/hexamerin / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / Immunoglobulin E-set
Similarity search - Domain/homology
Hemocyanin AA6 chain
Similarity search - Component
Biological speciesAndroctonus australis (Sahara scorpion)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å
AuthorsCong, Y. / Zhang, Q. / Woolford, D. / Schweikardt, T. / Khant, H. / Ludtke, S. / Chiu, W. / Decker, H.
CitationJournal: 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
DepositionFeb 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_imaging_optics / em_software
Item: _em_imaging_optics.energyfilter_name / _em_software.image_processing_id / _em_software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Hemocyanin AA6 chain
C: Hemocyanin AA6 chain
D: Hemocyanin AA6 chain
E: Hemocyanin AA6 chain
F: Hemocyanin AA6 chain
G: Hemocyanin AA6 chain
H: Hemocyanin AA6 chain
I: Hemocyanin AA6 chain
J: Hemocyanin AA6 chain
K: Hemocyanin AA6 chain
L: Hemocyanin AA6 chain
M: Hemocyanin AA6 chain


Theoretical massNumber of molelcules
Total (without water)862,60412
Polymers862,60412
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))

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Components

#1: Protein
Hemocyanin AA6 chain


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Hemocyanin from scorpion Pandinus imperator / Type: COMPLEX / Details: 24mer. treated by 2mM SDS to activate Hc
Molecular weightValue: 1.7 MDa / Experimental value: YES
Buffer solutionpH: 7.8
Details: 100 mM TRIS/HCL at pH 7.8, 10 mM CaCl2 and 10 mM MgCl2
SpecimenConc.: 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 supportDetails: 400-mesh Quantifoil holy grid with 1.2x1.3μM hole size
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temp: 101 K / Humidity: 95 % / Method: two side bloting for 1 seconds before plunging

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC / Date: May 31, 2007 / Details: JEOL 3200FSC MDS low dose method
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / 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 holderSpecimen 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 recordingElectron dose: 18 e/Å2 / Film or detector model: KODAK SO-163 FILM
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV

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Processing

EM software
IDNameCategory
1MODELLERmodel fitting
2Situsmodel fitting
3UCSF Chimeramodel fitting
4X-PLORmodel fitting
5EMAN3D reconstruction
CTF correctionDetails: each micrograph
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionMethod: 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 buildingProtocol: 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 stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms74208 0 0 0 74208

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