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- EMDB-37572: cryo-EM structure of alligator haemoglobin in oxy form -

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Basic information

Entry
Database: EMDB / ID: EMD-37572
Titlecryo-EM structure of alligator haemoglobin in oxy form
Map datasharpened map
Sample
  • Complex: alligator haemoglobin in carboxy 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


haptoglobin 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 ...haptoglobin 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
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesAlligator mississippiensis (American alligator)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.31 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-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37572.png

Downloads & links

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Map

FileDownload / File: emd_37572.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
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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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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.4995697 - 5.5919
Average (Standard dev.)0.000019667415 (±0.067399986)
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_37572_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_37572_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_37572_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : alligator haemoglobin in carboxy form

EntireName: alligator haemoglobin in carboxy form
Components
  • Complex: alligator haemoglobin in carboxy 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: alligator haemoglobin in carboxy form

SupramoleculeName: alligator haemoglobin in carboxy form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Alligator mississippiensis (American alligator)
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: Alligator mississippiensis (American alligator)
Molecular weightTheoretical: 15.891368 KDa
SequenceString:
MVLSMEDKSN VKAIWGKASG HLEEYGAEAL ERMFCAYPQT KIYFPHFDMS HNSAQIRAHG KKVFSALHEA VNHIDDLPGA LCRLSELHA HSLRVDPVNF KFLAHCVLVV FAIHHPSALS PEIHASLDKF LCAVSAVLTS 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: Alligator mississippiensis (American alligator)
Molecular weightTheoretical: 16.641213 KDa
SequenceString:
ASFDAHERKF IVDLWAKVDV AQCGADALSR MLIVYPWKRR YFEHFGKMCN AHDILHNSKV QEHGKKVLAS FGEAVKHLDN IKGHFANLS KLHCEKFHVD PENFKLLGDI IIIVLAAHHP EDFSVECHAA FQKLVRQVAA ALAAEYH

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: 208 / 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: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / 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: NONE
Final reconstructionApplied 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 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 modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8wiy:
cryo-EM structure of alligator haemoglobin in oxy form

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