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- EMDB-6186: Electron cryo-microscopy of Terebralia palustris mega-hemocyanin -

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Basic information

Entry
Database: EMDB / ID: EMD-6186
TitleElectron cryo-microscopy of Terebralia palustris mega-hemocyanin
Map dataReconstruction of Terebralia palustris mega-hemocyanin
Sample
  • Sample: Terebralia palustris Mega-Hemocyanin (TpH)
  • Protein or peptide: Mega-hemocyanin long-chain
  • Protein or peptide: Mega-hemocyanin short-chain
Keywordsoxygen transport / origami
Biological speciesTerebralia palustris (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.4 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: 8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6186.jpg

Downloads & links

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Map

FileDownload / File: emd_6186.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Terebralia palustris mega-hemocyanin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.51 Å/pix.
x 300 pix.
= 753. Å		2.51 Å/pix.
x 300 pix.
= 753. Å		2.51 Å/pix.
x 300 pix.
= 753. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.51 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.0 / Movie #1: 8
Minimum - Maximum-12.9912653 - 29.262863159999998
Average (Standard dev.)0.50509101 (±2.30213332)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 753.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.512.512.51
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z753.000753.000753.000
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/NS300300300
D min/max/mean-12.99129.2630.505

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Supplemental data

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Sample components

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Entire : Terebralia palustris Mega-Hemocyanin (TpH)

EntireName: Terebralia palustris Mega-Hemocyanin (TpH)
Components
  • Sample: Terebralia palustris Mega-Hemocyanin (TpH)
  • Protein or peptide: Mega-hemocyanin long-chain
  • Protein or peptide: Mega-hemocyanin short-chain

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Supramolecule #1000: Terebralia palustris Mega-Hemocyanin (TpH)

SupramoleculeName: Terebralia palustris Mega-Hemocyanin (TpH) / type: sample / ID: 1000
Oligomeric state: Two peripheral decamers of the short TpH subunit with 8FUs bind to a central decamer of the long TpH subunit with 11 FUs.
Number unique components: 2
Molecular weightExperimental: 13 MDa / Theoretical: 13 MDa

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Macromolecule #1: Mega-hemocyanin long-chain

MacromoleculeName: Mega-hemocyanin long-chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: Decamer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Terebralia palustris (invertebrata)
Molecular weightExperimental: 5 MDa / Theoretical: 5 MDa

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Macromolecule #2: Mega-hemocyanin short-chain

MacromoleculeName: Mega-hemocyanin short-chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Oligomeric state: Decamer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Terebralia palustris (invertebrata)
Molecular weightExperimental: 4 MDa / Theoretical: 4 MDa

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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
DateMar 10, 2012
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 1636 / Average electron dose: 15 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 124472 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 60000
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: 10.4 Å / Resolution method: OTHER / Software - Name: SPARX / Number images used: 30527

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