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- EMDB-1628: 8-A cryoEM structure and molecular model of the myriapod (Scutige... -

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Basic information

Entry
Database: EMDB / ID: EMD-1628
Title8-A cryoEM structure and molecular model of the myriapod (Scutigera) 6x6mer hemocyanin: understanding a giant oxygen transport protein
Map dataHemocyanin from the myriapod Scutigera
Sample
  • Sample: Scutigera hemocyanin
  • Protein or peptide: Scutigera hemocyanin
Keywordshemocyanin / 3D electron microscopy / molecular model / allostery / Myriapoda
Biological speciesScutigera coleoptrata (house centipede)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 8.0 Å
AuthorsMarkl J / Moeller A / Martin AG / Rheinbay J / Gebauer W / Depoix F
CitationJournal: J Mol Biol / Year: 2009
Title: 10-A cryoEM structure and molecular model of the Myriapod (Scutigera) 6x6mer hemocyanin: understanding a giant oxygen transport protein.
Authors: Jürgen Markl / Arne Moeller / Andreas G Martin / Judith Rheinbay / Wolfgang Gebauer / Frank Depoix /
Abstract: Oxygen transport in Myriapoda is maintained by a unique 6x6mer hemocyanin, that is, 36 subunits arranged as six hexamers (1x6mers). In the sluggish diplopod Spirostreptus, the 1x6mers seem to operate ...Oxygen transport in Myriapoda is maintained by a unique 6x6mer hemocyanin, that is, 36 subunits arranged as six hexamers (1x6mers). In the sluggish diplopod Spirostreptus, the 1x6mers seem to operate as almost or fully independent allosteric units (h approximately 1.3; P(50) approximately 5 torr), whereas in the swift centipede Scutigera, they intensively cooperate allosterically (h approximately 10; P(50) approximately 50 torr). Here, we show the chemomechanical basis of this differential behavior as deduced from hybrid 6x6mer structures, obtained by single-particle cryo-electron microscopy of the Scutigera 6x6mer (10.0 A resolution according to the 0.5 criterion) and docking of homology-modeled subunits from Scutigera and two diplopods, Spirostreptus and Polydesmus. The Scutigera 6x6mer hemocyanin is a trigonal antiprism assembled from six smaller trigonal antiprisms (1x6mers), thereby exhibiting D3 point group symmetry. It can be described as two staggered 3x6mers or three oblique 2x6mers. Topologically, the 6x6mer is subdivided into six subunit zones, thereby exhibiting a mantle (24 subunits) and a core (12 subunits). The six hexamers are linked by 21 bridges, subdivided into five types: two within each 3x6mer and three between both 3x6mers. The molecular models of the 6x6mer reveal intriguing amino acid appositions at these inter-hexamer interfaces. Besides opportunities for salt bridges, we found pairs of carboxylate residues for possible bridging via a Ca(2+) or Mg(2+) ion. Moreover, we detected histidine clusters, notably in Scutigera, allowing us to advance hypotheses as to how the hexamers are allosterically coupled in centipede hemocyanin and why they act more independently in diplopod hemocyanin.
History
DepositionJun 22, 2009-
Header (metadata) releaseApr 26, 2011-
Map releaseApr 26, 2011-
UpdateApr 26, 2011-
Current statusApr 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0012
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

em1628.png

Downloads & links

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Map

FileDownload / File: emd_1628.map.gz / Format: CCP4 / Size: 146.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHemocyanin from the myriapod Scutigera
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 340 pix.
= 340. Å		1 Å/pix.
x 340 pix.
= 340. Å		1 Å/pix.
x 340 pix.
= 340. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.0012 / Movie #1: 0.0012
Minimum - Maximum-0.0127973 - 0.0186785
Average (Standard dev.)0.00013993 (±0.00129549)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 340 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z340.000340.000340.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.0130.0190.000

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Supplemental data

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Sample components

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Entire : Scutigera hemocyanin

EntireName: Scutigera hemocyanin
Components
  • Sample: Scutigera hemocyanin
  • Protein or peptide: Scutigera hemocyanin

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Supramolecule #1000: Scutigera hemocyanin

SupramoleculeName: Scutigera hemocyanin / type: sample / ID: 1000 / Oligomeric state: 6x6mer / Number unique components: 1
Molecular weightTheoretical: 2.7 MDa

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Macromolecule #1: Scutigera hemocyanin

MacromoleculeName: Scutigera hemocyanin / type: protein_or_peptide / ID: 1 / Name.synonym: ScoHc / Oligomeric state: 6x6mer / Recombinant expression: No
Source (natural)Organism: Scutigera coleoptrata (house centipede) / Tissue: Hemolymph
Molecular weightExperimental: 2.7 MDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4 / Details: 50mM Tris/HCl, 150mM NaCl
StainingType: NEGATIVE / Details: cryo EM, no stain
GridDetails: 400 mesh copper
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Homebuilt

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD
Sample stageSpecimen holder: ST cryo holder / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CTFFIND3 and transfer IMAGIC-5
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: OTHER / Software - Name: IMAGIC-5 / Number images used: 6484

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