8VYL

The structure of Human Hemoglobin in Complex with Nanobody BtNbE11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

Starting Model: experimental
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Literature

The structure of a haemoglobin-nanobody complex reveals human beta-subunit-specific interactions.

Fox, D.R.Samuels, I.Binks, S.Grinter, R.

(2024) FEBS Lett 598: 2240-2248

  • DOI: https://doi.org/10.1002/1873-3468.14958
  • Primary Citation of Related Structures:  
    8VYL

  • PubMed Abstract: 

    Haemoglobin (Hb) is a vital oxygen carrier in vertebrates. Low blood Hb levels may indicate anaemia or genetic disorders, while its presence in the lower digestive system suggests colon cancer. Detecting and quantifying human Hb is essential for medical diagnostics. A nanobody-based sandwich-ELISA test was recently developed utilising llama-derived nanobodies NbE11 and NbB9. These nanobodies specifically bind to human Hb without cross-reacting with Hb from other vertebrates. Here, we determine the crystal structure of NbE11 in complex with human Hb. NbE11 binds Hb with high affinity, predominantly binding the β-Hb subunit. Structural differences between human Hb and other vertebrates at the NbE11 binding interface likely explain the assay's lack of cross-reactivity, providing insights for developing Hb binding diagnostics.


  • Organizational Affiliation

    Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit alphaA,
B [auth C]
142Homo sapiensMutation(s): 0 
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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit betaC [auth B],
D
147Homo sapiensMutation(s): 0 
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
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody BtNbE11E [auth F],
F [auth E]
140Escherichia coliMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 188.761α = 90
b = 74.837β = 91.44
c = 57.875γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1197376

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Database references, Structure summary