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- EMDB-5586: An asymmetric unit map from Electron cryo-microscopy of Haliotis ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5586
TitleAn asymmetric unit map from Electron cryo-microscopy of Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1)
Map dataAsymmetric unit map segmented from the reconstruction of isolated Haliotis diversicolor molluscan hemocyanin isoform 1
Sample
  • Sample: An asymmetry unit of Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1)
  • Protein or peptide: hemocyanin isoform 1
KeywordsCryo-EM / molluscan hemocyanin / Allosteric
Function / homology
Function and homology information


oxygen carrier activity / oxidoreductase activity / metal ion binding
Similarity search - Function
Haemocyanin beta-sandwich domain / Haemocyanin C-terminal domain superfamily / Haemocyanin beta-sandwich / Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily
Similarity search - Domain/homology
Hemocyanin isoform 1
Similarity search - Component
Biological speciesHaliotis diversicolor (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsZhang Q / Dai X / Cong Y / Zhang J / Chen DH / Dougherty M / Wang J / Ludtke S / Schmid MF / Chiu W
CitationJournal: Structure / Year: 2013
Title: Cryo-EM structure of a molluscan hemocyanin suggests its allosteric mechanism.
Authors: Qinfen Zhang / Xinghong Dai / Yao Cong / Junjie Zhang / Dong-Hua Chen / Matthew T Dougherty / Jiangyong Wang / Steven J Ludtke / Michael F Schmid / Wah Chiu /
Abstract: Hemocyanins are responsible for transporting O2 in the arthropod and molluscan hemolymph. Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1) is an 8 MDa oligomer. Each subunit is made up of ...Hemocyanins are responsible for transporting O2 in the arthropod and molluscan hemolymph. Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1) is an 8 MDa oligomer. Each subunit is made up of eight functional units (FUs). Each FU contains two Cu ions, which can reversibly bind an oxygen molecule. Here, we report a 4.5 A° cryo-EM structure of HdH1. The structure clearly shows ten asymmetric units arranged with D5 symmetry. Each asymmetric unit contains two structurally distinct but chemically identical subunits. The map is sufficiently resolved to trace the entire subunit Ca backbone and to visualize densities corresponding to some large side chains, Cu ion pairs, and interaction networks of adjacent subunits. A FU topology path intertwining between the two subunits of the asymmetric unit is unambiguously determined. Our observations suggest a structural mechanism for the stability of the entire hemocyanin didecamer and 20 ‘‘communication clusters’’ across asymmetric units responsible for its allosteric property upon oxygen binding.
History
DepositionFeb 19, 2013-
Header (metadata) releaseApr 10, 2013-
Map releaseApr 17, 2013-
UpdateMay 29, 2013-
Current statusMay 29, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j32
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5586_1.png

Downloads & links

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Map

FileDownload / File: emd_5586.map.gz / Format: CCP4 / Size: 804.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAsymmetric unit map segmented from the reconstruction of isolated Haliotis diversicolor molluscan hemocyanin isoform 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 600 pix.
= 612. Å		1.02 Å/pix.
x 600 pix.
= 612. Å		1.02 Å/pix.
x 600 pix.
= 612. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-0.07149746 - 11.358547209999999
Average (Standard dev.)0.00563778 (±0.11131296)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-300-300-300
Dimensions600600600
Spacing600600600
CellA=B=C: 612.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.021.021.02
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z612.000612.000612.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS-300-300-300
NC/NR/NS600600600
D min/max/mean-0.07111.3590.006

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Supplemental data

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Sample components

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Entire : An asymmetry unit of Haliotis diversicolor molluscan hemocyanin i...

EntireName: An asymmetry unit of Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1)
Components
  • Sample: An asymmetry unit of Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1)
  • Protein or peptide: hemocyanin isoform 1

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Supramolecule #1000: An asymmetry unit of Haliotis diversicolor molluscan hemocyanin i...

SupramoleculeName: An asymmetry unit of Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1)
type: sample / ID: 1000 / Oligomeric state: one asymmetric unit contains two subunits / Number unique components: 1
Molecular weightExperimental: 800 KDa / Theoretical: 800 KDa

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Macromolecule #1: hemocyanin isoform 1

MacromoleculeName: hemocyanin isoform 1 / type: protein_or_peptide / ID: 1 / Name.synonym: HdH1 / Number of copies: 1 / Oligomeric state: Dimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Haliotis diversicolor (invertebrata) / synonym: mollusca / Tissue: lymph
Molecular weightExperimental: 800 KDa / Theoretical: 800 KDa

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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

BufferpH: 7.5 / Details: 0.2M NaCl, 50mM Tris-HCl, 5mM CaCl2, 5mM MgCl2
GridDetails: 400 mesh copper 1.2/1.3 quantifoil grid with continuous carbon support, glow discharged.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III / Method: Blot for 2 seconds before plunging.

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureMin: 80 K / Max: 100 K / Average: 88 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 400,000 nominal magnification
Specialist opticsEnergy filter - Name: in column omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DetailsMDS
DateJul 7, 2008
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: 784 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Sample stageSpecimen holder: liquid N2 cooled / Specimen holder model: JEOL 3200FSC CRYOHOLDER

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Image processing

DetailsProcessed with EMAN1 followed by segmentation of asymmetric unit.
CTF correctionDetails: each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN1 / Number images used: 28641

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