9H41 | pdb_00009h41

Apo-Helical Carotenoid Protein 4 (HCP4) from Anabaena G152C mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 
    0.242 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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Literature

The apo-HCP4 structure reveals facets of carotenoid uptake.

Sklyar, J.Glaser, F.Adir, N.

(2025) Int J Biol Macromol 315: 144290-144290

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.144290
  • Primary Citation of Related Structures:  
    9H41

  • PubMed Abstract: 

    Photosynthetic organisms employ sophisticated mechanisms to mitigate photodamage caused by excessive light energy. Among these, proteins such as the Orange Carotenoid Protein (OCP) and the Helical Carotenoid Protein 4 (HCP4) play a central role in non-photochemical quenching (NPQ), by dissipating excess energy. OCP consists of two domains: the N-terminal domain (NTD), which serves as the effector domain, and the C-terminal domain (CTD), which acts as the regulatory domain. The HCPs, which are homologs of the NTD, perform carotenoid-driven energy quenching, carotenoid transport and reactive oxygen species scavenging in cyanobacteria. CTD homologs (CTDH) are involved in carotenoid uptake and delivery. This study presents the first crystal structure of an apo-HCP4 from Anabaena sp. PCC 7120 at a resolution of 3.1 Å, revealing significant structural differences from the previously determined carotenoid bound form (holo-HCP4). The ligand-binding cavity in apo-HCP4 is occluded by dynamic loops, that must move to afford carotenoid transfer from a transiently bound holo-CTDH. The predicted conformational changes of HCP4 loops and the mobility of CTDH residues create a favorable environment for efficient ligand transfer. Our structural analysis identified HCP4 Tyr48 as a key gating residue, regulating cavity accessibility during carotenoid uptake. Biolayer interferometry experiments demonstrated that apo-HCP4 requires interaction with holo-CTDH for effective carotenoid transfer, emphasizing the interplay between these proteins in the carotenoid transport mechanism. Our findings provide insights into the structural and functional differences between apo- and holo-HCP4, elucidating the regulatory mechanisms underlying carotenoid transport and energy quenching in cyanobacteria. This study advances our understanding of carotenoid-mediated photoprotection and transport.


  • Organizational Affiliation
    • Schulich Faculty of Chemistry, Technion, Haifa 3200003, Israel.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orange carotenoid-binding domain-containing protein169Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 1 
Gene Names: all4941
UniProt
Find proteins for Q8YMJ2 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore Q8YMJ2 
Go to UniProtKB:  Q8YMJ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8YMJ2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free:  0.242 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.871α = 90
b = 60.871β = 90
c = 112.389γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael1596/21

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release