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Open data
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Basic information
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Title | cryo-EM structure of alligator haemoglobin in oxy form | |||||||||
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![]() | Haemoglobin / OXYGEN BINDING | |||||||||
Function / homology | ![]() haptoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle ...haptoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.31 Å | |||||||||
![]() | Takahashi K / Lee Y / Fago A / Bautista NM / Kawamoto A / Kurisu G / Storz J / Nishizawa T / Tame JRH | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The unique allosteric property of crocodilian haemoglobin elucidated by cryo-EM. Authors: Katsuya Takahashi / Yongchan Lee / Angela Fago / Naim M Bautista / Jay F Storz / Akihiro Kawamoto / Genji Kurisu / Tomohiro Nishizawa / Jeremy R H Tame / ![]() ![]() ![]() Abstract: The principal effect controlling the oxygen affinity of vertebrate haemoglobins (Hbs) is the allosteric switch between R and T forms with relatively high and low oxygen affinity respectively. ...The principal effect controlling the oxygen affinity of vertebrate haemoglobins (Hbs) is the allosteric switch between R and T forms with relatively high and low oxygen affinity respectively. Uniquely among jawed vertebrates, crocodilians possess Hb that shows a profound drop in oxygen affinity in the presence of bicarbonate ions. This allows them to stay underwater for extended periods by consuming almost all the oxygen present in the blood-stream, as metabolism releases carbon dioxide, whose conversion to bicarbonate and hydrogen ions is catalysed by carbonic anhydrase. Despite the apparent universal utility of bicarbonate as an allosteric regulator of Hb, this property evolved only in crocodilians. We report here the molecular structures of both human and a crocodilian Hb in the deoxy and liganded states, solved by cryo-electron microscopy. We reveal the precise interactions between two bicarbonate ions and the crocodilian protein at symmetry-related sites found only in the T state. No other known effector of vertebrate Hbs binds anywhere near these sites. | |||||||||
History |
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | |||
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Header (meta data) | ![]() | |||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8wiyMC ![]() 37571 ![]() 37573 ![]() 37574 ![]() 37575 ![]() 37576 ![]() 8wixC ![]() 8wizC ![]() 8wj0C ![]() 8wj1C ![]() 8wj2C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.02 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : alligator haemoglobin in carboxy form
Entire | Name: alligator haemoglobin in carboxy form |
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Components |
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-Supramolecule #1: alligator haemoglobin in carboxy form
Supramolecule | Name: alligator haemoglobin in carboxy form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 100 KDa |
-Macromolecule #1: Hemoglobin subunit alpha
Macromolecule | Name: Hemoglobin subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 15.891368 KDa |
Sequence | String: MVLSMEDKSN VKAIWGKASG HLEEYGAEAL ERMFCAYPQT KIYFPHFDMS HNSAQIRAHG KKVFSALHEA VNHIDDLPGA LCRLSELHA HSLRVDPVNF KFLAHCVLVV FAIHHPSALS PEIHASLDKF LCAVSAVLTS KYR UniProtKB: Hemoglobin subunit alpha |
-Macromolecule #2: Hemoglobin subunit beta
Macromolecule | Name: Hemoglobin subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 16.641213 KDa |
Sequence | String: ASFDAHERKF IVDLWAKVDV AQCGADALSR MLIVYPWKRR YFEHFGKMCN AHDILHNSKV QEHGKKVLAS FGEAVKHLDN IKGHFANLS KLHCEKFHVD PENFKLLGDI IIIVLAAHHP EDFSVECHAA FQKLVRQVAA ALAAEYH UniProtKB: Hemoglobin subunit beta |
-Macromolecule #3: PROTOPORPHYRIN IX CONTAINING FE
Macromolecule | Name: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 3 / Number of copies: 2 / Formula: HEM |
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Molecular weight | Theoretical: 616.487 Da |
Chemical component information | ![]() ChemComp-HEM: |
-Macromolecule #4: OXYGEN MOLECULE
Macromolecule | Name: OXYGEN MOLECULE / type: ligand / ID: 4 / Number of copies: 2 / Formula: OXY |
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Molecular weight | Theoretical: 31.999 Da |
Chemical component information | ![]() ChemComp-O2: |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 208 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 372582 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1) |
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Output model | ![]() PDB-8wiy: |