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- PDB-8wix: cryo-EM structure of alligator haemoglobin in carbonmonoxy form -

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Basic information

Entry
Database: PDB / ID: 8wix
Titlecryo-EM structure of alligator haemoglobin in carbonmonoxy form
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN BINDING / Haemoglobin
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesAlligator mississippiensis (American alligator)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsTakahashi, K. / Lee, Y. / Fago, A. / Bautista, N.M. / Kawamoto, A. / Kurisu, G. / Storz, J. / Nishizawa, T. / Tame, J.R.H.
Funding support Japan, 1items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.0Aug 14, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 14, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 14, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Aug 14, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 14, 2024Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 14, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Data collection / Derived calculations / Structure summary
Category: em_admin / pdbx_entry_details ...em_admin / pdbx_entry_details / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8226
Polymers32,5332
Non-polymers1,2894
Water2,108117
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules

A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,64312
Polymers65,0654
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-1), (-1), (1)261.12, 261.12

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Components

#1: Protein Hemoglobin subunit alpha / Alpha-globin / Hemoglobin alpha chain


Mass: 15891.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Alligator mississippiensis (American alligator)
References: UniProt: P01999
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 16641.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Alligator mississippiensis (American alligator)
References: UniProt: P02130
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: alligator haemoglobin in carbonmonoxy form / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 0.1 MDa / Experimental value: NO
Source (natural)Organism: Alligator mississippiensis (American alligator)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4cryoSPARC4.2.1CTF correction
7Coot0.9.8.8model fitting
8ISOLDE1.6model fitting
9UCSF ChimeraX1.6.1model fitting
11cryoSPARC4.2.1initial Euler assignment
12cryoSPARC4.2.1final Euler assignment
14cryoSPARC4.2.13D reconstruction
15Servalcat0.2.85model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 751964 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementResolution: 2.29→2.29 Å / Cor.coef. Fo:Fc: 0.867 / SU B: 3.598 / SU ML: 0.081 / ESU R: 0.132
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.31114 --
obs0.31114 83558 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 54.974 Å2
Refinement stepCycle: 1 / Total: 2490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0110.0122448
ELECTRON MICROSCOPYr_bond_other_d00.0162252
ELECTRON MICROSCOPYr_angle_refined_deg1.8631.7183335
ELECTRON MICROSCOPYr_angle_other_deg0.6421.6325174
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.3595285
ELECTRON MICROSCOPYr_dihedral_angle_2_deg8.869510
ELECTRON MICROSCOPYr_dihedral_angle_3_deg20.33210392
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.1050.2343
ELECTRON MICROSCOPYr_gen_planes_refined0.0110.022848
ELECTRON MICROSCOPYr_gen_planes_other0.0070.02582
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it7.2025.1941148
ELECTRON MICROSCOPYr_mcbond_other7.1975.1891147
ELECTRON MICROSCOPYr_mcangle_it9.4439.3421429
ELECTRON MICROSCOPYr_mcangle_other9.4459.3521430
ELECTRON MICROSCOPYr_scbond_it9.4836.1231300
ELECTRON MICROSCOPYr_scbond_other9.4796.1221298
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other13.6910.7091906
ELECTRON MICROSCOPYr_long_range_B_refined17.7765.8210541
ELECTRON MICROSCOPYr_long_range_B_other17.78165.7810497
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork2.081 6175 -
obs--100 %

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