Dark, Room Temperature, PCM Myxobacterial Phytochrome, P2, Wild Type

Experimental Data Snapshot

  • Resolution: 2.10 Å

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures.

Sanchez, J.C.Carrillo, M.Pandey, S.Noda, M.Aldama, L.Feliz, D.Claesson, E.Wahlgren, W.Y.Tracy, G.Duong, P.Nugent, A.C.Field, A.Srajer, V.Kupitz, C.Iwata, S.Nango, E.Tanaka, R.Tanaka, T.Fangjia, L.Tono, K.Owada, S.Westenhoff, S.Schmidt, M.Stojkovic, E.A.

(2019) Struct Dyn 6: 054701-054701

  • DOI: https://doi.org/10.1063/1.5120527
  • Primary Citation of Related Structures:  
    6PTQ, 6PTX, 6PU2

  • PubMed Abstract: 

    Phytochromes (PHYs) are photoreceptor proteins first discovered in plants, where they control a variety of photomorphogenesis events. PHYs as photochromic proteins can reversibly switch between two distinct states: a red light (Pr) and a far-red light (Pfr) absorbing form. The discovery of Bacteriophytochromes (BphPs) in nonphotosynthetic bacteria has opened new frontiers in our understanding of the mechanisms by which these natural photoswitches can control single cell development, although the role of BphPs in vivo remains largely unknown. BphPs are dimeric proteins that consist of a photosensory core module (PCM) and an enzymatic domain, often a histidine kinase. The PCM is composed of three domains (PAS, GAF, and PHY). It holds a covalently bound open-chain tetrapyrrole (biliverdin, BV) chromophore. Upon absorption of light, the double bond between BV rings C and D isomerizes and reversibly switches the protein between Pr and Pfr states. We report crystal structures of the wild-type and mutant (His275Thr) forms of the canonical BphP from the nonphotosynthetic myxobacterium Stigmatella aurantiaca ( Sa BphP2) in the Pr state. Structures were determined at 1.65 Å and 2.2 Å (respectively), the highest resolution of any PCM construct to date. We also report the room temperature wild-type structure of the same protein determined at 2.1 Å at the SPring-8 Angstrom Compact free electron LAser (SACLA), Japan. Our results not only highlight and confirm important amino acids near the chromophore that play a role in Pr-Pfr photoconversion but also describe the signal transduction into the PHY domain which moves across tens of angstroms after the light stimulus.

  • Organizational Affiliation

    Department of Biology, Northeastern Illinois University, 5500 N. St. Louis Ave., Chicago, Illinois 60625, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photoreceptor-histidine kinase BphP
A, B
482Stigmatella aurantiaca DW4/3-1Mutation(s): 0 
Gene Names: STIAU_8420
Find proteins for Q09E27 (Stigmatella aurantiaca (strain DW4/3-1))
Explore Q09E27 
Go to UniProtKB:  Q09E27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09E27
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EL5 (Subject of Investigation/LOI)
Query on EL5

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid
C33 H36 N4 O6
Query on BEN

Download Ideal Coordinates CCD File 
C7 H8 N2
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.69α = 90
b = 83.4β = 107.63
c = 86.87γ = 90
Software Package:
Software NamePurpose
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.2: 2023-05-24
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references
  • Version 1.4: 2024-01-31
    Changes: Structure summary