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- EMDB-12978: structure of human haemoglobin obtained via cryoelectron microsco... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12978 | |||||||||
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Title | structure of human haemoglobin obtained via cryoelectron microscopy at 200 kV | |||||||||
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Function / homology | ![]() nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.04 Å | |||||||||
![]() | Mann D / Sachse C | |||||||||
Funding support | ![]()
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![]() | ![]() Title: structure of human haemoglobin obtained via cryoelectron microscopy at 200 kV Authors: Mann D / Sachse C | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.8 KB 14.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.9 KB | Display | ![]() |
Images | ![]() | 68.3 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Others | ![]() ![]() | 59.2 MB 59.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 409.6 KB | Display | ![]() |
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Full document | ![]() | 408.7 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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EM raw data | ![]() Data size: 1.5 TB Data #1: Unaligned movies (tiff) and aligned micrographs (mrc) of hHGB in vitreous ice [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8389 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12978_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12978_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : tetrameric complex of human haemoglobin alpha and beta subunits
Entire | Name: tetrameric complex of human haemoglobin alpha and beta subunits |
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Components |
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-Supramolecule #1: tetrameric complex of human haemoglobin alpha and beta subunits
Supramolecule | Name: tetrameric complex of human haemoglobin alpha and beta subunits type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: haemoglobin subunit alpha
Macromolecule | Name: haemoglobin subunit alpha / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SVSTVLTSKY R |
-Macromolecule #2: haemoglobin subunit beta
Macromolecule | Name: haemoglobin subunit beta / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK EFTPPVQAAY QKVVAGVANA LAHKYH |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.6 / Component - Formula: TRIS / Component - Name: TRIS buffer |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV |
Details | obtained lyophilized from commercial source (Sigma-Aldrich), dissolved in 50 mM TRIS buffer |
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Electron microscopy
Microscope | TFS TALOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 1400 / Average electron dose: 65.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 100000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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