+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2627 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Electron cryo-microscopy of Lumbricus terrestris hemoglobin | |||||||||
Map data | single particle reconstruction of Lumbricus terrestris hemoglobin in oxygenated state | |||||||||
Sample |
| |||||||||
Keywords | Lumbricus terrestris / hemoglobin | |||||||||
Function / homology | Function and homology information hemoglobin complex / oxygen carrier activity / oxygen binding / response to hypoxia / iron ion binding / heme binding / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Lumbricus terrestris (common earthworm) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.1 Å | |||||||||
Authors | Chen WT / Chen YC / Liou HH / Chao CY | |||||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Structural basis for cooperative oxygen binding and bracelet-assisted assembly of Lumbricus terrestris hemoglobin. Authors: Wei-Ting Chen / Yu-Chuen Chen / Horng-Huei Liou / Chih-Yu Chao / Abstract: The iron-containing hemoglobins (Hbs) are essential proteins to serve as oxygen transporters in the blood. Among various kinds of Hbs, the earthworm Hbs are the champions in carrying oxygen due to ...The iron-containing hemoglobins (Hbs) are essential proteins to serve as oxygen transporters in the blood. Among various kinds of Hbs, the earthworm Hbs are the champions in carrying oxygen due to not only their large size but also the unusually high cooperativity of ligand binding. However, the cooperative oxygen binding mechanisms are still mostly unknown. Here we report the cryo-electron microscopy structure of Lumbricus terrestris Hb in its native, oxygenated state at 9.1 Å resolution, showing remarkable differences from the carbon monoxide-binding X-ray structure. Our structural analysis first indicates that the cooperative ligand binding of L. terrestris Hb requires tertiary and quaternary transitions in the heme pocket and a global subunit movement facilitated by intra-ring and inter-ring contacts. Moreover, the additional sinusoidal bracelet provides the confirmation for the long-standing debate about the additional electron densities absent in the X-ray crystal structure. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2627.map.gz | 98.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-2627-v30.xml emd-2627.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | emd_2627.tif | 735.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2627 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2627 | HTTPS FTP |
-Validation report
Summary document | emd_2627_validation.pdf.gz | 257 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_2627_full_validation.pdf.gz | 256.1 KB | Display | |
Data in XML | emd_2627_validation.xml.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2627 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2627 | HTTPS FTP |
-Related structure data
Related structure data | 4v93MC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_2627.map.gz / Format: CCP4 / Size: 238.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | single particle reconstruction of Lumbricus terrestris hemoglobin in oxygenated state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Lumbricus terrestris hemoglobin
Entire | Name: Lumbricus terrestris hemoglobin |
---|---|
Components |
|
-Supramolecule #1000: Lumbricus terrestris hemoglobin
Supramolecule | Name: Lumbricus terrestris hemoglobin / type: sample / ID: 1000 / Oligomeric state: 12 mer / Number unique components: 1 |
---|---|
Molecular weight | Theoretical: 3.6 MDa |
-Macromolecule #1: Lumbricus terrestris hemoglobin
Macromolecule | Name: Lumbricus terrestris hemoglobin / type: protein_or_peptide / ID: 1 / Oligomeric state: 12 mer / Recombinant expression: No |
---|---|
Source (natural) | Organism: Lumbricus terrestris (common earthworm) / synonym: common earthworm |
Molecular weight | Theoretical: 3.6 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
---|---|
Buffer | pH: 7.2 / Details: 50 mM Tris-HCl, 10 mM CaCl2, 10 mM MgCl2 |
Grid | Details: Holy carbon on top of 200 mesh copper grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Date | Oct 15, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 250 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 80000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: micrograph |
---|---|
Final reconstruction | Applied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: OTHER / Software - Name: EMAN2, IMAGIC / Number images used: 4500 |