9AYZ

T-state HbG Makassar hemoglobin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 
    0.259 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Base editing HbS to HbG-Makassar improves hemoglobin function supporting its use in sickle cell disease.

Kostamo, Z.Ortega, M.A.Xu, C.Feliciano, P.R.Budak, E.Lam, D.Winton, V.Jenkins, R.Venugopal, A.Zhang, M.Jamieson, J.Coisman, B.Goldsborough, K.Hernandez, B.Kanne, C.K.Evans, E.N.Zgodny, J.Zhang, Y.Darazim, J.Patel, A.Pendergast, M.A.Manis, J.Hartigan, A.J.Ciaramella, G.Lee, S.J.Chu, S.H.Sheehan, V.A.

(2025) Nat Commun 16: 1441-1441

  • DOI: https://doi.org/10.1038/s41467-025-56578-3
  • Primary Citation of Related Structures:  
    9AV9, 9AYZ

  • PubMed Abstract: 

    Adenine base editing can convert sickle hemoglobin (HbS, βΕ6V) to G-Makassar hemoglobin (HbG, βE6A), a naturally occurring variant that is clinically asymptomatic. However, the quality and functionality of purified HbG and of mature HbGG and HbGS red blood cells (RBC) has not been assessed. Here, we develop a mouse model to characterize HbG. Purified HbG appears normal and does not polymerize under hypoxia. The topology of the hemoglobin fold with the βΕ6Α mutation is similar to HbA in the oxy and deoxy states. However, RBC containing HbGS are dehydrated, showing altered function and increased sickling under hypoxia. Blood counts and mitochondrial retention measures place HbGS RBCs as intermediate in severity between HbAS and HbSS, while organ function is comparable to HbAS. HbGG resembles HbAA for most metrics. Our results highlight the importance of functionally assessing the mature red cell environment when evaluating novel gene editing strategies for hematologic disorders.


  • Organizational Affiliation

    Emory University School of Medicine, Department of Pediatrics, Atlanta, GA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit alpha
A, C, E, G
141Homo sapiensMutation(s): 0 
Gene Names: HBA1HBA2
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
PHAROS:  P69905
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69905
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit beta
B, D, F, H
146Homo sapiensMutation(s): 1 
Gene Names: HBB
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens)
Explore P68871 
Go to UniProtKB:  P68871
PHAROS:  P68871
GTEx:  ENSG00000244734 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68871
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free:  0.259 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.625α = 90
b = 109.187β = 90.11
c = 82.096γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release
  • Version 1.1: 2025-02-19
    Changes: Database references