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- EMDB-1078: Lumbricus terrestris hemoglobin--the architecture of linker chain... -

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Basic information

Entry
Database: EMDB / ID: EMD-1078
TitleLumbricus terrestris hemoglobin--the architecture of linker chains and structural variation of the central toroid.
Map dataWhole structure of Lumbricus terrestris hemoglobin
Sample
  • Sample: Lumbricus terrestris hemoglobin
  • Protein or peptide: Lumbricus terrestris hemoglobin
Biological speciesLumbricus terrestris (common earthworm)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 14.9 Å
AuthorsMouche F / Boisset N / Penczek PA
CitationJournal: J Struct Biol / Year: 2001
Title: Lumbricus terrestris hemoglobin--the architecture of linker chains and structural variation of the central toroid.
Authors: F Mouche / N Boisset / P A Penczek /
Abstract: The extracellular giant hemoglobin from the earthworm Lumbricus terrestris was reconstructed at 14.9-A resolution from cryo-electron microscope images, using a new procedure for estimating parameters ...The extracellular giant hemoglobin from the earthworm Lumbricus terrestris was reconstructed at 14.9-A resolution from cryo-electron microscope images, using a new procedure for estimating parameters of the contrast transfer (CTF) function. In this approach, two important CTF parameters, defocus and amplitude contrast ratio, can be refined iteratively within the framework of 3D projection alignment procedure, using minimization of sign disagreement between theoretical CTF and cross-resolution curves. The 3D cryo-EM map is in overall good agreement with the recent X-ray crystallography map of Royer et al. (2000, Proc. Natl. Acad. Sci. USA 97, 7107-7111), and it reveals the local threefold arrangement of the three linker chains present within each 1/12 of the complex. The 144 globin chains and 36 linker chains within the complex are clearly visible, and the interdigitation of the 12 coiled-coil helical spokes forming the central toroidal piece is confirmed. Based on these findings, two mechanisms of the dodecameric unit assembly are proposed and termed "zigzag" and "pairwise" polymerizations. However, the detection by cryo-EM of 12 additional rod-like bodies within the toroid raises the possibility that the architecture of the toroid is more complex than previously thought or that yet unknown ligands or allosteric effectors for this oxygen carrier are present.
History
DepositionMay 7, 2004-
Header (metadata) releaseMay 7, 2004-
Map releaseMay 7, 2004-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.47
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.47
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1078.gif

Downloads & links

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Map

FileDownload / File: emd_1078.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationWhole structure of Lumbricus terrestris hemoglobin
Voxel sizeX=Y=Z: 3.76 Å
Density
Contour Level1: 0.559 / Movie #1: 0.47
Minimum - Maximum0.0 - 1.0
Average (Standard dev.)0.341941 (±0.099831)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-40-40-40
Dimensions818181
Spacing818181
CellA=B=C: 304.56 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.763.763.76
M x/y/z818181
origin x/y/z0.0000.0000.000
length x/y/z304.560304.560304.560
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS818181
D min/max/mean0.0001.0000.342

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Supplemental data

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Sample components

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Entire : Lumbricus terrestris hemoglobin

EntireName: Lumbricus terrestris hemoglobin
Components
  • Sample: Lumbricus terrestris hemoglobin
  • Protein or peptide: Lumbricus terrestris hemoglobin

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Supramolecule #1000: Lumbricus terrestris hemoglobin

SupramoleculeName: Lumbricus terrestris hemoglobin / type: sample / ID: 1000 / Oligomeric state: 12 x 12 mer / Number unique components: 1
Molecular weightTheoretical: 3.6 MDa

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Macromolecule #1: Lumbricus terrestris hemoglobin

MacromoleculeName: Lumbricus terrestris hemoglobin / type: protein_or_peptide / ID: 1 / Number of copies: 144 / Oligomeric state: 12 x 12 mer / Recombinant expression: No
Source (natural)Organism: Lumbricus terrestris (common earthworm) / synonym: earthworm / Tissue: blood
Molecular weightExperimental: 3.6 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

Concentration0.5 mg/mL
BufferpH: 7.2 / Details: 50 mM Tris-HCl, 50 mM MgCl2, 10 mM CaCl2
StainingType: NEGATIVE / Details: NO STAIN Cryo-electron microscopy
GridDetails: 400 mesh gold grid
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home made / Method: Single side blotting and rapid plunging

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Electron microscopy

MicroscopeJEOL 2010F
TemperatureMin: 86 K / Max: 86 K / Average: 86 K
Alignment procedureLegacy - Electron beam tilt params: 0
DateOct 17, 1999
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OPTRONICS / Digitization - Sampling interval: 2.5 µm / Number real images: 16 / Details: Rotating drum microdensitometer / Od range: 1 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 66489 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.0 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 60000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsImages recorded at 200 kV with a magnification of x60000 on a Jeol JEM2010F. Condensor aperture 150 um. Objective aperture 60 um. Defocus within a range of 1.3 to 3.2 um.
CTF correctionDetails: Wiener filtering on volumes
Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Details: SIRT on single 2D-projections / Number images used: 7770
Final angle assignmentDetails: SPIDER: theta 90 degrees, phi 60 degrees
FSC plot (resolution estimation)

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