|Entry||Database: EMDB / ID: EMD-3488|
|Title||CryoEM structure of haemoglobin at 3.2 A determined with the Volta phase plate|
|Function / homology|
Function and homology information
Chaperone Mediated Autophagy / Microautophagy / Neutrophil degranulation / Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Scavenging of heme from plasma / Factors involved in megakaryocyte development and platelet production / nitric oxide transport / hemoglobin binding / hemoglobin alpha binding ...Chaperone Mediated Autophagy / Microautophagy / Neutrophil degranulation / Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Scavenging of heme from plasma / Factors involved in megakaryocyte development and platelet production / nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / cellular oxidant detoxification / oxygen transport / hemoglobin complex / endocytic vesicle lumen / positive regulation of cell death / platelet aggregation / hydrogen peroxide catabolic process / cytosolic small ribosomal subunit / regulation of blood pressure / response to hydrogen peroxide / oxygen carrier activity / bicarbonate transport / receptor-mediated endocytosis / oxygen binding / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / ficolin-1-rich granule lumen / blood microparticle / blood coagulation / iron ion binding / neutrophil degranulation / heme binding / extracellular space / extracellular exosome / membrane / extracellular region / metal ion binding / cytosol
Globin family profile. / Haemoglobin, beta-type / Haemoglobin, alpha-type / Haemoglobin, pi / Globin-like superfamily / Globin/Protoglobin / Globin / Globin
Hemoglobin subunit beta / Hemoglobin subunit alpha
|Biological species||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.2 Å|
|Authors||Khoshouei M / Radjainia R / Baumeister W / Danev R|
|Citation||Journal: Nat Commun / Year: 2017|
Title: Cryo-EM structure of haemoglobin at 3.2 Å determined with the Volta phase plate.
Authors: Maryam Khoshouei / Mazdak Radjainia / Wolfgang Baumeister / Radostin Danev /
Abstract: With the advent of direct electron detectors, the perspectives of cryo-electron microscopy (cryo-EM) have changed in a profound way. These cameras are superior to previous detectors in coping with ...With the advent of direct electron detectors, the perspectives of cryo-electron microscopy (cryo-EM) have changed in a profound way. These cameras are superior to previous detectors in coping with the intrinsically low contrast and beam-induced motion of radiation-sensitive organic materials embedded in amorphous ice, and hence they have enabled the structure determination of many macromolecular assemblies to atomic or near-atomic resolution. Nevertheless, there are still limitations and one of them is the size of the target structure. Here, we report the use of a Volta phase plate in determining the structure of human haemoglobin (64 kDa) at 3.2 Å. Our results demonstrate that this method can be applied to complexes that are significantly smaller than those previously studied by conventional defocus-based approaches. Cryo-EM is now close to becoming a fast and cost-effective alternative to crystallography for high-resolution protein structure determination.
|Validation Report||PDB-ID: 5ni1|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_3488.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.05 Å|
|Symmetry||Space group: 1|
CCP4 map header:
|Entire||Name: HaemoglobinHemoglobin / Number of components: 1|
-Component #1: protein, Haemoglobin
|Protein||Name: HaemoglobinHemoglobin / Recombinant expression: No|
|Mass||Theoretical: 64 kDa|
|Source||Species: Homo sapiens (human)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 7.4|
|Vitrification||Cryogen name: OTHER|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: OTHER|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 175300|
|3D reconstruction||Software: RELION / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF|
|FSC plot (resolution estimation)|
-Atomic model buiding
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