7L5A

Crystal structure of the photosensory module from Xanthomonas campestris bacteriophytochrome XccBphP in the Pfr state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the Pr-Pfr long-range signaling mechanism of a full-length bacterial phytochrome at the atomic level.

Otero, L.H.Foscaldi, S.Antelo, G.T.Rosano, G.L.Sirigu, S.Klinke, S.Defelipe, L.A.Sanchez-Lamas, M.Battocchio, G.Conforte, V.Vojnov, A.A.Chavas, L.M.G.Goldbaum, F.A.Mroginski, M.A.Rinaldi, J.Bonomi, H.R.

(2021) Sci Adv 7: eabh1097-eabh1097

  • DOI: https://doi.org/10.1126/sciadv.abh1097
  • Primary Citation of Related Structures:  
    6PL0, 7L59, 7L5A

  • PubMed Abstract: 

    Phytochromes constitute a widespread photoreceptor family that typically interconverts between two photostates called Pr (red light–absorbing) and Pfr (far-red light–absorbing). The lack of full-length structures solved at the (near-)atomic level in both pure Pr and Pfr states leaves gaps in the structural mechanisms involved in the signal transmission pathways during the photoconversion. Here, we present the crystallographic structures of three versions from the plant pathogen Xanthomonas campestris virulence regulator Xcc BphP bacteriophytochrome, including two full-length proteins, in the Pr and Pfr states. The structures show a reorganization of the interaction networks within and around the chromophore-binding pocket, an α-helix/β-sheet tongue transition, and specific domain reorientations, along with interchanging kinks and breaks at the helical spine as a result of the photoswitching, which subsequently affect the quaternary assembly. These structural findings, combined with multidisciplinary studies, allow us to describe the signaling mechanism of a full-length bacterial phytochrome at the atomic level.


  • Organizational Affiliation

    Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriophytochrome517Xanthomonas campestris pv. campestris str. 8004Mutation(s): 0 
Gene Names: bphPXC_4241
UniProt
Find proteins for A0A0H2XCS3 (Xanthomonas campestris pv. campestris (strain 8004))
Explore A0A0H2XCS3 
Go to UniProtKB:  A0A0H2XCS3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2XCS3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BLA (Subject of Investigation/LOI)
Query on BLA

Download Ideal Coordinates CCD File 
B [auth A]BILIVERDINE IX ALPHA
C33 H34 N4 O6
GWZYPXHJIZCRAJ-SRVCBVSDSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.378α = 90
b = 164.378β = 90
c = 40.437γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Council (NRC, Argentina)ArgentinaPICT 2015-0621
National Research Council (NRC, Argentina)ArgentinaPICT 2016-1425

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-29
    Type: Initial release
  • Version 1.1: 2022-07-13
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description