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- EMDB-37575: cryo-EM structure of human haemoglobin in oxy form -

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Basic information

Entry
Database: EMDB / ID: EMD-37575
Titlecryo-EM structure of human haemoglobin in oxy form
Map datasharpened map
Sample
  • Complex: human haemoglobin in oxy form
    • Protein or peptide: Hemoglobin subunit alpha
    • Protein or peptide: Hemoglobin subunit beta
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: OXYGEN MOLECULE
  • Ligand: water
KeywordsHaemoglobin / OXYGEN BINDING
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / 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 / carbon dioxide transport / response to hydrogen peroxide / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / 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 / inflammatory response / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.27 Å
AuthorsTakahashi K / Lee Y / Fago A / Bautista NM / Kawamoto A / Kurisu G / Storz J / Nishizawa T / Tame JRH
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Commun / Year: 2024
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
DepositionSep 25, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37575.png

Downloads & links

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Map

FileDownload / File: emd_37575.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 256 pix.
= 261.12 Å		1.02 Å/pix.
x 256 pix.
= 261.12 Å		1.02 Å/pix.
x 256 pix.
= 261.12 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-5.152731 - 7.680479
Average (Standard dev.)-0.0008277873 (±0.10707446)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 261.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37575_msk_1.map
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AxesZYX

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Histogram

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Half map: half map B

Fileemd_37575_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_37575_half_map_2.map
Annotationhalf map A
Projections & Slices
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Sample components

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Entire : human haemoglobin in oxy form

EntireName: human haemoglobin in oxy form
Components
  • Complex: human haemoglobin in oxy form
    • Protein or peptide: Hemoglobin subunit alpha
    • Protein or peptide: Hemoglobin subunit beta
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: OXYGEN MOLECULE
  • Ligand: water

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Supramolecule #1: human haemoglobin in oxy form

SupramoleculeName: human haemoglobin in oxy form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: Hemoglobin subunit alpha

MacromoleculeName: Hemoglobin subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.28155 KDa
SequenceString:
MVLSPADKTN VKAAWGKVGA HAGEYGAEAL ERMFLSFPTT KTYFPHFDLS HGSAQVKGHG KKVADALTNA VAHVDDMPNA LSALSDLHA HKLRVDPVNF KLLSHCLLVT LAAHLPAEFT PAVHASLDKF LASVSTVLTS KYR

UniProtKB: Hemoglobin subunit alpha

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Macromolecule #2: Hemoglobin subunit beta

MacromoleculeName: Hemoglobin subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.021396 KDa
SequenceString:
MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK VKAHGKKVLG AFSDGLAHLD NLKGTFATL SELHCDKLHV DPENFRLLGN VLVCVLAHHF GKEFTPPVQA AYQKVVAGVA NALAHKYH

UniProtKB: Hemoglobin subunit beta

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Macromolecule #3: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 3 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #4: OXYGEN MOLECULE

MacromoleculeName: OXYGEN MOLECULE / type: ligand / ID: 4 / Number of copies: 2 / Formula: OXY
Molecular weightTheoretical: 31.999 Da
Chemical component information

ChemComp-O2:
OXYGEN MOLECULE

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 123 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageSpecimen 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 modelType of model: PDB ENTRY
PDB model - PDB ID:

2dn1

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 550843
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2dn1


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8wj1:
cryo-EM structure of human haemoglobin in oxy form

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