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- EMDB-6185: Electron cryo-microscopy of Melanoides tuberculata mega-hemocyanin -

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Basic information

Entry
Database: EMDB / ID: EMD-6185
TitleElectron cryo-microscopy of Melanoides tuberculata mega-hemocyanin
Map dataReconstruction of Melanoides tuberculata mega-hemocyanin
Sample
  • Sample: Melanoides tuberculata Mega-Hemocyanin (MtH)
  • Protein or peptide: mega-hemocyanin, strain MtH400
  • Protein or peptide: mega-hemocyanin, strain MtH550
Keywordsoxygen transport / origami
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
Mega-hemocyanin / Mega-hemocyanin
Similarity search - Component
Biological speciesMelanoides tuberculata (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.2 Å
AuthorsGatsogiannis C / Hofnagel O / Markl J / Raunser S
CitationJournal: Structure / Year: 2015
Title: Structure of mega-hemocyanin reveals protein origami in snails.
Authors: Christos Gatsogiannis / Oliver Hofnagel / Jürgen Markl / Stefan Raunser /
Abstract: Mega-hemocyanin is a 13.5 MDa oxygen transporter found in the hemolymph of some snails. Similar to typical gastropod hemocyanins, it is composed of 400 kDa building blocks but has additional ...Mega-hemocyanin is a 13.5 MDa oxygen transporter found in the hemolymph of some snails. Similar to typical gastropod hemocyanins, it is composed of 400 kDa building blocks but has additional 550 kDa subunits. Together, they form a large, completely filled cylinder. The structural basis for this highly complex protein packing is not known so far. Here, we report the electron cryomicroscopy (cryo-EM) structure of mega-hemocyanin complexes from two different snail species. The structures reveal that mega-hemocyanin is composed of flexible building blocks that differ in their conformation, but not in their primary structure. Like a protein origami, these flexible blocks are optimally packed, implementing different local symmetries and pseudosymmetries. A comparison between the two structures suggests a surprisingly simple evolutionary mechanism leading to these large oxygen transporters.
History
DepositionNov 17, 2014-
Header (metadata) releaseDec 24, 2014-
Map releaseDec 31, 2014-
UpdateJan 14, 2015-
Current statusJan 14, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 12.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 12.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6185.jpg

Downloads & links

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Map

FileDownload / File: emd_6185.map.gz / Format: CCP4 / Size: 28.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Melanoides tuberculata mega-hemocyanin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.64 Å/pix.
x 196 pix.
= 713.44 Å		3.64 Å/pix.
x 196 pix.
= 713.44 Å		3.64 Å/pix.
x 196 pix.
= 713.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 12.4 / Movie #1: 12.4
Minimum - Maximum-10.541213040000001 - 34.951896669999996
Average (Standard dev.)0.82119966 (±3.32889986)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 713.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.643.643.64
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z713.440713.440713.440
α/β/γ90.00090.00090.000
start NX/NY/NZ-72-72-72
NX/NY/NZ145145145
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS196196196
D min/max/mean-10.54134.9520.821

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Supplemental data

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Sample components

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Entire : Melanoides tuberculata Mega-Hemocyanin (MtH)

EntireName: Melanoides tuberculata Mega-Hemocyanin (MtH)
Components
  • Sample: Melanoides tuberculata Mega-Hemocyanin (MtH)
  • Protein or peptide: mega-hemocyanin, strain MtH400
  • Protein or peptide: mega-hemocyanin, strain MtH550

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Supramolecule #1000: Melanoides tuberculata Mega-Hemocyanin (MtH)

SupramoleculeName: Melanoides tuberculata Mega-Hemocyanin (MtH) / type: sample / ID: 1000
Oligomeric state: Two peripheral decamers of the MtH400 subunit bind to a central decamer of the MtH550 subunit.
Number unique components: 2
Molecular weightExperimental: 13.5 MDa / Theoretical: 13.5 MDa

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Macromolecule #1: mega-hemocyanin, strain MtH400

MacromoleculeName: mega-hemocyanin, strain MtH400 / type: protein_or_peptide / ID: 1 / Name.synonym: MtH400 / Number of copies: 2 / Oligomeric state: Decamer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Melanoides tuberculata (invertebrata) / synonym: red-rimmed melania
Molecular weightExperimental: 4 MDa / Theoretical: 4 MDa
SequenceUniProtKB: Mega-hemocyanin

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Macromolecule #2: mega-hemocyanin, strain MtH550

MacromoleculeName: mega-hemocyanin, strain MtH550 / type: protein_or_peptide / ID: 2 / Name.synonym: MtH550 / Number of copies: 1 / Oligomeric state: Decamer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Melanoides tuberculata (invertebrata) / synonym: red-rimmed melania
Molecular weightExperimental: 5.5 MDa / Theoretical: 5.5 MDa
SequenceUniProtKB: Mega-hemocyanin

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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

Concentration0.2 mg/mL
BufferpH: 7.4
Details: 50 mM Tris-HCl, 150 mM NaCl, 5 mM CaCl2, 5 mM MgCl2
GridDetails: C-Flat 2/1-4C copper 400 mesh, with additional thin carbon support
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 100 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 3 seconds before plunging.

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Electron microscopy

MicroscopeJEOL 3200FSC
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification.
Specialist opticsEnergy filter - Name: in-column Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 15.0 eV
DateJun 7, 2011
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 652 / Average electron dose: 15 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 170978 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 80000
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER

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Image processing

DetailsC5 symmetry was imposed locally after each iteration during the refinement.
CTF correctionDetails: each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.2 Å / Resolution method: OTHER / Software - Name: SPARX / Number images used: 6764

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