6G20

Crystal structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in its functional Meta-F intermediate state.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural snapshot of a bacterial phytochrome in its functional intermediate state.

Schmidt, A.Sauthof, L.Szczepek, M.Lopez, M.F.Escobar, F.V.Qureshi, B.M.Michael, N.Buhrke, D.Stevens, T.Kwiatkowski, D.von Stetten, D.Mroginski, M.A.Krauss, N.Lamparter, T.Hildebrandt, P.Scheerer, P.

(2018) Nat Commun 9: 4912-4912

  • DOI: https://doi.org/10.1038/s41467-018-07392-7
  • Primary Citation of Related Structures:  
    6G1Y, 6G1Z, 6G20

  • PubMed Abstract: 

    Phytochromes are modular photoreceptors of plants, bacteria and fungi that use light as a source of information to regulate fundamental physiological processes. Interconversion between the active and inactive states is accomplished by a photoinduced reaction sequence which couples the sensor with the output module. However, the underlying molecular mechanism is yet not fully understood due to the lack of structural data of functionally relevant intermediate states. Here we report the crystal structure of a Meta-F intermediate state of an Agp2 variant from Agrobacterium fabrum. This intermediate, the identity of which was verified by resonance Raman spectroscopy, was formed by irradiation of the parent Pfr state and displays significant reorientations of almost all amino acids surrounding the chromophore. Structural comparisons allow identifying structural motifs that might serve as conformational switch for initiating the functional secondary structure change that is linked to the (de-)activation of these photoreceptors.


  • Organizational Affiliation

    Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, Berlin, D-10117, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriophytochrome protein
A, B
509Agrobacterium fabrum str. C58Mutation(s): 24 
Gene Names: SY94_2021
EC: 2.7.13.3
UniProt
Find proteins for A9CI81 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore A9CI81 
Go to UniProtKB:  A9CI81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9CI81
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EL5
Query on EL5

Download Ideal Coordinates CCD File 
C [auth A],
T [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
SNHIGJASYQUMKZ-IDFYGOSVSA-N
ETE
Query on ETE

Download Ideal Coordinates CCD File 
JA [auth B],
S [auth A]
2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C9 H20 O5
ZNYRFEPBTVGZDN-UHFFFAOYSA-N
PG0
Query on PG0

Download Ideal Coordinates CCD File 
IA [auth B]2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
R [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
D [auth A]
DA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
D [auth A],
DA [auth B],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
FA [auth B]
GA [auth B]
HA [auth B]
O [auth A]
P [auth A]
FA [auth B],
GA [auth B],
HA [auth B],
O [auth A],
P [auth A],
Q [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
EA [auth B],
N [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.114α = 90
b = 183.114β = 90
c = 179.655γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
GermanySFB1078

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 1.1: 2018-12-05
    Changes: Data collection, Database references
  • Version 1.2: 2023-05-24
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description, Structure summary
  • Version 1.4: 2024-10-23
    Changes: Structure summary