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Yorodumi- EMDB-1078: Lumbricus terrestris hemoglobin--the architecture of linker chain... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1078 | |||||||||
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Title | Lumbricus terrestris hemoglobin--the architecture of linker chains and structural variation of the central toroid. | |||||||||
Map data | Whole structure of Lumbricus terrestris hemoglobin | |||||||||
Sample |
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Biological species | Lumbricus terrestris (common earthworm) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 14.9 Å | |||||||||
Authors | Mouche F / Boisset N / Penczek PA | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1078.map.gz | 1.7 MB | EMDB map data format | |
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Header (meta data) | emd-1078-v30.xml emd-1078.xml | 9.6 KB 9.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_1078_fsc.xml | 8.5 KB | Display | FSC data file |
Images | 1078.gif | 83.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1078 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1078 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1078.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Whole structure of Lumbricus terrestris hemoglobin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.76 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Lumbricus terrestris hemoglobin
Entire | Name: Lumbricus terrestris hemoglobin |
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Components |
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-Supramolecule #1000: Lumbricus terrestris hemoglobin
Supramolecule | Name: Lumbricus terrestris hemoglobin / type: sample / ID: 1000 / Oligomeric state: 12 x 12 mer / Number unique components: 1 |
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Molecular weight | Theoretical: 3.6 MDa |
-Macromolecule #1: Lumbricus terrestris hemoglobin
Macromolecule | Name: Lumbricus terrestris hemoglobin / type: protein_or_peptide / ID: 1 / Number of copies: 144 / Oligomeric state: 12 x 12 mer / Recombinant expression: No |
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Source (natural) | Organism: Lumbricus terrestris (common earthworm) / synonym: earthworm / Tissue: blood |
Molecular weight | Experimental: 3.6 MDa |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.2 / Details: 50 mM Tris-HCl, 50 mM MgCl2, 10 mM CaCl2 |
Staining | Type: NEGATIVE / Details: NO STAIN Cryo-electron microscopy |
Grid | Details: 400 mesh gold grid |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home made / Method: Single side blotting and rapid plunging |
-Electron microscopy
Microscope | JEOL 2010F |
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Temperature | Min: 86 K / Max: 86 K / Average: 86 K |
Alignment procedure | Legacy - Electron beam tilt params: 0 |
Date | Oct 17, 1999 |
Image recording | Category: 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 min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated 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 stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |