9VID | pdb_00009vid

cryo-EM structure of alligator haemoglobin in the R conformation

• PDB DOI: https://doi.org/10.2210/pdb9VID/pdb
• EM Map EMD-65084: EMDB EMDataResource

• Classification: OXYGEN BINDING
• Organism(s): Alligator mississippiensis
• Mutation(s): No 


• Deposited: 2025-06-18 Released: 2025-07-23 
• Deposition Author(s): Takahashi, K., Lee, Y., Nishizawa, T., Tame, J.R.H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Conformational analysis of liganded human hemoglobin by cryo electron microscopy

Takahashi, K., Lee, Y., Nishizawa, T., Tame, J.R.H.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2025.07.07.661630

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 33.82 kDa 
• Atom Count: 2,373 
• Modeled Residue Count: 287 
• Deposited Residue Count: 288 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A	142	Alligator mississippiensis	Mutation(s): 0
UniProt
Find proteins for P01999 (Alligator mississippiensis) Explore P01999  Go to UniProtKB:  P01999

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B	146	Alligator mississippiensis	Mutation(s): 0
UniProt
Find proteins for P02130 (Alligator mississippiensis) Explore P02130  Go to UniProtKB:  P02130

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CMO (Subject of Investigation/LOI)	D [auth A], F [auth B]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	REFMAC	5.8.0419
RECONSTRUCTION	cryoSPARC	4.6.2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Takahashi, K., Lee, Y., Nishizawa, T., Tame, J.R.H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release