7LHO | pdb_00007lho

Crystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A mutant of cellular retinol binding protein II complex with all-trans-retinal in the dark

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.196 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 

Literature

Photoisomerization detected in a fully wavelength-tunable rhodopsin mimic system.

Ehyaei, N., Bingham, C., Silva, K., Nossoni, Z., Gavgani, H.N., Nosrati, M., Eaves, J., Akhdar, M., Vasileiou, C., Borhan, B., Geiger, J.H.

(2026) Acta Crystallogr D Struct Biol 82: 664-671

  • DOI: https://doi.org/10.1107/S2059798326003839
  • Primary Citation Related Structures: 
    7LHM, 7LHN, 7LHO, 9PN1

  • PubMed Abstract: 

    We describe the photoisomerization of the retinylidene protonated Schiff base in human retinol-binding protein II (hCRBPII) and the role of water molecules in this process. We characterize the photoisomerization of the 15-cis/all-trans retinylidene protonated Schiff base in this system using UV-visible spectroscopy and atomic-resolution X-ray crystallography. We further demonstrate a process where the pK a of the protonated Schiff base is substantially altered by light-induced dehydration of the binding pocket, suggesting novel pathways of photoswitching that rely not on isomerization or conformational change of the chromophore but rather on light-induced reorganization of the protein environment.

    • Organizational Affiliation: 
    • Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA.

Macromolecule Content 

  • Total Structure Weight: 31.84 kDa 
  • Atom Count: 2,536 
  • Modeled Residue Count: 266 
  • Deposited Residue Count: 266 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Retinol-binding protein 2
A, B
133Homo sapiensMutation(s): 8 
Gene Names: RBP2, CRBP2
UniProt & NIH Common Fund Data Resources
Find proteins for P50120 (Homo sapiens)
Explore P50120 
Go to UniProtKB:  P50120
PHAROS:  P50120
GTEx:  ENSG00000114113 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50120
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.196 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.842α = 85.95
b = 35.918β = 86.434
c = 64.062γ = 65.334
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary
  • Version 1.3: 2026-06-10
    Changes: Database references