9S0C | pdb_00009s0c

10 ns Intermediate-state of CBD of TtCarH at 12 mJ/cm2 laser fluence (TR-SFX, SACLA), refined against extrapolated structure factors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 
    0.298 (Depositor), 0.299 (DCC) 
  • R-Value Work: 
    0.253 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 
    0.255 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Integrated structural dynamics uncover a new B 12 photoreceptor activation mode.

Rios-Santacruz, R.Poddar, H.Pounot, K.Heyes, D.J.Coquelle, N.Mackintosh, M.J.Johannissen, L.O.Schianchi, S.Jeffreys, L.N.De Zitter, E.Munro, R.Appleby, M.Axford, D.Beale, E.V.Cliff, M.J.Davila-Miliani, M.C.Engilberge, S.Gotthard, G.Hadjidemetriou, K.Hardman, S.J.O.Horrell, S.Hub, J.S.Ishihara, K.Jaho, S.Karras, G.Kataoka, M.Kawakami, R.Mason, T.Okumura, H.Owada, S.Owen, R.L.Royant, A.Saaret, A.Sakuma, M.Shanmugam, M.Sugimoto, H.Tono, K.Zala, N.Beale, J.H.Tosha, T.Colletier, J.P.Levantino, M.Hay, S.Kozlowski, P.M.Leys, D.Scrutton, N.S.Weik, M.Schiro, G.

(2026) Nature 650: 1045-1052

  • DOI: https://doi.org/10.1038/s41586-025-10074-2
  • Primary Citation of Related Structures:  
    9S06, 9S07, 9S08, 9S09, 9S0A, 9S0B, 9S0C, 9S0D, 9S0E, 9S0F, 9S0G, 9S0H, 9S0I, 9S0J

  • PubMed Abstract: 

    Photoreceptor proteins regulate fundamental biological processes such as vision, photosynthesis and circadian rhythms 1 . A large photoreceptor subfamily uses vitamin B 12 derivatives for light sensing 2 , contrasting with the well-established mode of action of these organometallic derivatives in thermally activated enzymatic reactions 3 . The exact molecular mechanism of B 12 photoreception and how this differs from the thermal pathways remains unknown. Here we provide a detailed description of photoactivation in the prototypical B 12 photoreceptor CarH 4,5 from nanoseconds to seconds, combining time-resolved and temperature-resolved structural and spectroscopic methods with quantum chemical calculations. Building on the crystal structures of the initial tetrameric dark and final monomeric light-activated states 5 , our structural snapshots of key intermediates in the truncated B 12 -binding domain illustrate how photocleavage of a cobalt-carbon (Co-C) bond within the B 12 chromophore adenosylcobalamin triggers a series of structural changes that propagate throughout CarH. Breakage of the photolabile Co-C5' bond leads to the formation of a previously unknown adduct that links the C4' position of the adenosyl moiety to the Co ion and can subsequently be cleaved thermally over longer timescales to allow release of the adenosyl group, ultimately causing tetramer dissociation 4,5 . This adduct, which differentiates CarH from thermally activated B 12 enzymes, steers the photoactivation pathway and acts as the molecular bridge between photochemical and photobiological timescales. The biological relevance of our study is corroborated by kinetic data on full-length CarH in the presence of DNA. Our results offer a spatiotemporal understanding of CarH photoactivation and pave the way for designing B 12 -dependent photoreceptors for optogenetic applications.


  • Organizational Affiliation
    • University of Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, Grenoble, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable transcriptional regulator
A, B, C, D
215Thermus thermophilusMutation(s): 0 
Gene Names: TT_P0056
UniProt
Find proteins for Q746J7 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q746J7 
Go to UniProtKB:  Q746J7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ746J7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B12 (Subject of Investigation/LOI)
Query on B12

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
5AD (Subject of Investigation/LOI)
Query on 5AD

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.298 (Depositor), 0.299 (DCC) 
  • R-Value Work:  0.253 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 0.255 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.8α = 90
b = 71.08β = 90
c = 207.27γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FrancePhotoGene
Centre National de la Recherche Scientifique (CNRS)FranceGoToXFEL
Agence Nationale de la Recherche (ANR)FranceBioXFEL

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-28
    Type: Initial release
  • Version 1.1: 2026-02-18
    Changes: Database references
  • Version 1.2: 2026-03-11
    Changes: Database references