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- EMDB-5101: 24-meric Scorpion Hemocyanin Activated State cryo-EM Density Map ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5101
Title24-meric Scorpion Hemocyanin Activated State cryo-EM Density Map at 8 Angstrom Resolution
Map dataThis is the Hemocyanin activated cryo-EM density map
Sample
  • Sample: Hemocyanin from scorpion Pandinus imperator (Activated State)
  • Protein or peptide: Pandinus imperator
KeywordsHemocyanin / Hc / Phenolxoidase activity / Tyrosinase (Ty) / Catecholoxidase (CO) / Enzyme / SDS / cryo-EM / single particle analysis
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/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, copper containing 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/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 speciesunidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 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 10, 2009-
Header (metadata) releaseFeb 20, 2009-
Map releaseMay 26, 2009-
UpdateJul 8, 2011-
Current statusJul 8, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.16
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.16
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3ixw
  • Surface level: 1.16
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5101_1.png

Downloads & links

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Map

FileDownload / File: emd_5101.map.gz / Format: CCP4 / Size: 33.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the Hemocyanin activated cryo-EM density map
Voxel sizeX=Y=Z: 1.8 Å
Density
Contour Level1: 1.16 / Movie #1: 1.16
Minimum - Maximum-0.472771 - 1.66289
Average (Standard dev.)0.0736112 (±0.264247)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-104-104-104
Dimensions208208208
Spacing208208208
CellA=B=C: 374.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.81.81.8
M x/y/z208208208
origin x/y/z0.0000.0000.000
length x/y/z374.400374.400374.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-20-28-19
NX/NY/NZ415638
MAP C/R/S123
start NC/NR/NS-104-104-104
NC/NR/NS208208208
D min/max/mean-0.4731.6630.074

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Supplemental data

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Sample components

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Entire : Hemocyanin from scorpion Pandinus imperator (Activated State)

EntireName: Hemocyanin from scorpion Pandinus imperator (Activated State)
Components
  • Sample: Hemocyanin from scorpion Pandinus imperator (Activated State)
  • Protein or peptide: Pandinus imperator

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Supramolecule #1000: Hemocyanin from scorpion Pandinus imperator (Activated State)

SupramoleculeName: Hemocyanin from scorpion Pandinus imperator (Activated State)
type: sample / ID: 1000 / Details: treated by 2mM SDS to activate Hc / Oligomeric state: 24-mer / Number unique components: 1
Molecular weightExperimental: 1.7 MDa / Theoretical: 1.7 MDa / Method: Sedimentation

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Macromolecule #1: Pandinus imperator

MacromoleculeName: Pandinus imperator / type: protein_or_peptide / ID: 1 / Name.synonym: scorpion / Number of copies: 1 / Oligomeric state: 24-mer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: unidentified (others) / Location in cell: hemolymph
Molecular weightExperimental: 1.7 MDa / Theoretical: 1.7 MDa
SequenceGO: oxygen carrier activity / InterPro: Hemocyanin/hexamerin middle domain

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.8
Details: 100 mM TRIS/HCL at pH 7.8, 10 mM CaCl2 and 10 mM MgCl2
GridDetails: 200 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 101 K / Instrument: OTHER / Details: Vitrification instrument: FEI vitrobot / Method: two side blotting for 1 second before plunging

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Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 4.1 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Specialist opticsEnergy filter - Name: in-column omega energy filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder: Side Entry / Specimen holder model: JEOL 3200FSC CRYOHOLDER
TemperatureMin: 101 K / Max: 101.2 K / Average: 101 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism correction
DetailsJEOL 3200FSC MDS low dose method
DateMay 31, 2007
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 200 / Average electron dose: 18 e/Å2
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN
Details: Final refinement using FRM2D (Fast Rotational Matching) image alignment method
Number images used: 13400

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