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Yorodumi- EMDB-12978: structure of human haemoglobin obtained via cryoelectron microsco... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12978 | |||||||||
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Title | structure of human haemoglobin obtained via cryoelectron microscopy at 200 kV | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / 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 / platelet aggregation / oxygen binding / regulation of blood pressure / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.04 Å | |||||||||
Authors | Mann D / Sachse C | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: To Be Published 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12978.map.gz | 59.8 MB | EMDB map data format | |
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Header (meta data) | emd-12978-v30.xml emd-12978.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12978_fsc.xml | 8.9 KB | Display | FSC data file |
Images | emd_12978.png | 68.3 KB | ||
Masks | emd_12978_msk_1.map | 64 MB | Mask map | |
Others | emd_12978_half_map_1.map.gz emd_12978_half_map_2.map.gz | 59.2 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12978 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12978 | HTTPS FTP |
-Related structure data
Similar structure data | |
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EM raw data | EMPIAR-10721 (Title: CryoEM single particle analysis of 65 kDa human haemoglobin using a 200 kV Talos Arctica Data size: 1.5 TB Data #1: Unaligned movies (tiff) and aligned micrographs (mrc) of hHGB in vitreous ice [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12978.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 | emd_12978_msk_1.map | ||||||||||||
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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 |
-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: Bos taurus (cattle) |
-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: Bos taurus (cattle) |
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: Bos taurus (cattle) |
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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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | TFS TALOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / 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 |
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 |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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