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- EMDB-2320: CryoEM Structure of keyhole limpet hemocyanin isoform 2 (KLH2) -

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Basic information

Entry
Database: EMDB / ID: EMD-2320
TitleCryoEM Structure of keyhole limpet hemocyanin isoform 2 (KLH2)
Map dataReconstruction of keyhole limpet hemocyanin isoform 2
Sample
  • Sample: Keyhole Limpet Hemocyanin Isoform 2 (KLH2)
  • Protein or peptide: keyhole limpet hemocyanin2
Keywordshemocyanin / respiratory protein / quaternary structure / Mollusca / keyhole limpet hemocyanin
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 / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / Di-copper centre-containing domain superfamily
Similarity search - Domain/homology
Keyhole limpet hemocyanin2
Similarity search - Component
Biological speciesMegathura crenulata (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.4 Å
AuthorsGatsogiannis C / Schnittger E / Markl SJ / Depoix F / Markl J
CitationJournal: To Be Published
Title: CryoEM Structure of keyhole limpet hemocyanin isoform 2 (KLH2)
Authors: Gatsogiannis C / Schnittger E / Markl SJ / Depoix F / Markl J
History
DepositionFeb 26, 2013-
Header (metadata) releaseApr 3, 2013-
Map releaseMar 12, 2014-
UpdateMar 12, 2014-
Current statusMar 12, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.24
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.24
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2320.png

Downloads & links

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Map

FileDownload / File: emd_2320.map.gz / Format: CCP4 / Size: 141.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of keyhole limpet hemocyanin isoform 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 336 pix.
= 504. Å		1.5 Å/pix.
x 336 pix.
= 504. Å		1.5 Å/pix.
x 336 pix.
= 504. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24 / Movie #1: 0.24
Minimum - Maximum-1.11162174 - 1.21687198
Average (Standard dev.)0.01244435 (±0.18030365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-170-170-170
Dimensions336336336
Spacing336336336
CellA=B=C: 504.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.51.51.5
M x/y/z336336336
origin x/y/z0.0000.0000.000
length x/y/z504.000504.000504.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-12-40
NX/NY/NZ732581
MAP C/R/S123
start NC/NR/NS-170-170-170
NC/NR/NS336336336
D min/max/mean-1.1121.2170.012

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Supplemental data

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Sample components

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Entire : Keyhole Limpet Hemocyanin Isoform 2 (KLH2)

EntireName: Keyhole Limpet Hemocyanin Isoform 2 (KLH2)
Components
  • Sample: Keyhole Limpet Hemocyanin Isoform 2 (KLH2)
  • Protein or peptide: keyhole limpet hemocyanin2

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Supramolecule #1000: Keyhole Limpet Hemocyanin Isoform 2 (KLH2)

SupramoleculeName: Keyhole Limpet Hemocyanin Isoform 2 (KLH2) / type: sample / ID: 1000
Oligomeric state: KLH2 is a dodecamer of a 400 kDa subunit. Each subunit is composed by 8 paralogous O2 binding functional units
Number unique components: 1
Molecular weightExperimental: 8 MDa / Theoretical: 8 MDa / Method: Predicted from the primary structure of the subunit

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Macromolecule #1: keyhole limpet hemocyanin2

MacromoleculeName: keyhole limpet hemocyanin2 / type: protein_or_peptide / ID: 1 / Name.synonym: KLH2 / Number of copies: 20 / Oligomeric state: dodecamer / Recombinant expression: No
Source (natural)Organism: Megathura crenulata (invertebrata) / synonym: Giant keyhole limpet / Tissue: hemolymph
Molecular weightExperimental: 8 MDa / Theoretical: 8 MDa
SequenceUniProtKB: Keyhole limpet hemocyanin2
InterPro: Tyrosinase copper-binding domain, Di-copper centre-containing domain superfamily

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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: 7.4 / Details: 0,05 M Tris, 0,15 M NaCl, 5 mM MgCl2, 5 mM CaCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 100 K / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TECNAI F30
DateAug 20, 2008
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Number real images: 210
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.0034 µm / Nominal defocus min: 0.0013 µm / Nominal magnification: 49000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each Particle
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC-5 / Number images used: 11379

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