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- PDB-9vid: cryo-EM structure of alligator haemoglobin in the R conformation -

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Basic information

Entry
Database: PDB / ID: 9vid
Titlecryo-EM structure of alligator haemoglobin in the R conformation
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN BINDING / haemoglobin
Function / homology
Function and homology information


haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding ...haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / 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 / Globin / Globin domain profile. / 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: 2.22 Å
AuthorsTakahashi, K. / Lee, Y. / Nishizawa, T. / Tame, J.R.H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Biorxiv / Year: 2025
Title: Conformational analysis of liganded human hemoglobin by cryo electron microscopy
Authors: Takahashi, K. / Lee, Y. / Nishizawa, T. / Tame, J.R.H.
History
DepositionJun 18, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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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
Water00
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
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: obtained synthetically / 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 / Feature type: SUBJECT OF INVESTIGATION
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 carboxy 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 type: Quantifoil
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: TFS 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
1cryoSPARC4.6.2particle selection
2REFMAC5.8.0419model refinement
5cryoSPARC4.6.2CTF correction
10cryoSPARC4.6.2initial Euler assignment
11cryoSPARC4.6.2final Euler assignment
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 371597 / Symmetry type: POINT
Atomic model buildingPDB-ID: 8WIX

8wix


Accession code: 8WIX / Source name: PDB / Type: experimental model
RefinementResolution: 2.22→2.22 Å / Cor.coef. Fo:Fc: 0.849 / SU B: 3.455 / SU ML: 0.078 / ESU R: 0.127
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.32166 --
obs0.32166 89772 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 47.332 Å2
Refinement stepCycle: 1 / Total: 2373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.0122448
ELECTRON MICROSCOPYr_bond_other_d00.0162252
ELECTRON MICROSCOPYr_angle_refined_deg1.7231.7183335
ELECTRON MICROSCOPYr_angle_other_deg0.6171.6325174
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.0785285
ELECTRON MICROSCOPYr_dihedral_angle_2_deg10.397510
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.53410392
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.1040.2343
ELECTRON MICROSCOPYr_gen_planes_refined0.010.022848
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_it5.4044.21148
ELECTRON MICROSCOPYr_mcbond_other5.4024.1951147
ELECTRON MICROSCOPYr_mcangle_it7.4457.5891429
ELECTRON MICROSCOPYr_mcangle_other7.4487.5971430
ELECTRON MICROSCOPYr_scbond_it7.9345.0921300
ELECTRON MICROSCOPYr_scbond_other7.8995.0881298
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other12.3528.8341906
ELECTRON MICROSCOPYr_long_range_B_refined15.13353.3410119
ELECTRON MICROSCOPYr_long_range_B_other15.1253.3310117
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 -
Rwork2.317 6629 -
obs--100 %

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