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- PDB-9dz3: Photoactivation in Bacteriophytochromes, reference (dark) structu... -

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Basic information

Entry
Database: PDB / ID: 9dz3
TitlePhotoactivation in Bacteriophytochromes, reference (dark) structure for the 3 ps time point
ComponentsPhotoreceptor-histidine kinase BphP
KeywordsSIGNALING PROTEIN / Red-light receptor enzyme Bacteriophytochrome Myxobacteria Photosensory Core Domain
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / histidine kinase / phosphorelay sensor kinase activity / protein kinase activator activity / photoreceptor activity / regulation of DNA-templated transcription
Similarity search - Function
Phytochrome / : / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain ...Phytochrome / : / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Chem-3Q8 / BENZAMIDINE / histidine kinase
Similarity search - Component
Biological speciesStigmatella aurantiaca (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsMalla, T.N. / Stojkovic, E.A. / Schmidt, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
National Science Foundation (NSF, United States)2423601 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM105549 United States
Citation
Journal: Commun Chem / Year: 2025
Title: Observation of early events in the photoactivation of Myxobacterial phytochrome using time-resolved serial femtosecond crystallography.
Authors: Malla, T.N. / Aldama, L. / Leon, V. / Feliz, D. / Hu, H. / Thomas, I. / Cellini, A. / Wahlgren, W.Y. / Nimmrich, A. / Botha, S. / Sierra, R. / Hunter, M.S. / Poitevin, F. / Lisova, S. / ...Authors: Malla, T.N. / Aldama, L. / Leon, V. / Feliz, D. / Hu, H. / Thomas, I. / Cellini, A. / Wahlgren, W.Y. / Nimmrich, A. / Botha, S. / Sierra, R. / Hunter, M.S. / Poitevin, F. / Lisova, S. / Batyuk, A. / Gate, G. / Jernigan, R. / Kupitz, C.J. / Maj, P. / Meszaros, P. / Kurttila, M. / Monrroy, L. / Luo, F. / Owada, S. / Kang, J. / Slavov, C. / Maj, M. / Gautier, C. / Kashipathy, M. / Tolstikova, A. / Mariani, V. / Barty, A. / Moss, F. / Schwander, P. / Liu, H. / Boutet, S. / Fromme, P. / Takala, H. / Ihalainen, J.A. / Weierstall, U. / Westenhoff, S. / Stojkovic, E.A. / Schmidt, M.
#1: Journal: Sci Adv / Year: 2024
Title: Photoreception and signaling in bacterial phytochrome revealed by single-particle cryo-EM.
Authors: Tek Narsingh Malla / Carolina Hernandez / Srinivasan Muniyappan / David Menendez / Dorina Bizhga / Joshua H Mendez / Peter Schwander / Emina A Stojković / Marius Schmidt /
Abstract: Phytochromes are red-light photoreceptors discovered in plants with homologs in bacteria and fungi that regulate a variety of physiological responses. They display a reversible photocycle between two ...Phytochromes are red-light photoreceptors discovered in plants with homologs in bacteria and fungi that regulate a variety of physiological responses. They display a reversible photocycle between two distinct states: a red-light-absorbing Pr state and a far-red light-absorbing Pfr state. The photoconversion regulates the activity of an enzymatic domain, usually a histidine kinase (HK). The molecular mechanism that explains how light controls the HK activity is not understood because structures of unmodified bacterial phytochromes with HK activity are missing. Here, we report three cryo-electron microscopy structures of a wild-type bacterial phytochrome with HK activity determined as Pr and Pfr homodimers and as a Pr/Pfr heterodimer with individual subunits in distinct states. We propose that the Pr/Pfr heterodimer is a physiologically relevant signal transduction intermediate. Our results offer insight into the molecular mechanism that controls the enzymatic activity of the HK as part of a bacterial two-component system that perceives and transduces light signals.
History
DepositionOct 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photoreceptor-histidine kinase BphP
B: Photoreceptor-histidine kinase BphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2615
Polymers103,9632
Non-polymers1,2983
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-12 kcal/mol
Surface area41990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.580, 83.040, 86.790
Angle α, β, γ (deg.)90.000, 107.740, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Photoreceptor-histidine kinase BphP / PCM Myxobacterial Phytochrome


Mass: 51981.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stigmatella aurantiaca (bacteria) / Gene: STIAU_8420 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09E27
#2: Chemical ChemComp-3Q8 / 3-[2-[[5-[[(3E,4S)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 291 K / Method: batch mode
Details: Hampton Crystal Screen Cryo HR2-122, #9 (PEG 4000), benzamidine HCl (3%)

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: in vacuum / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.3 Å
DetectorType: SLAC ePix10k 2M / Detector: PIXEL / Date: Feb 25, 2022
RadiationMonochromator: no monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.3→30.5 Å / Num. obs: 50738 / % possible obs: 100 % / Redundancy: 963 % / Biso Wilson estimate: 63.63 Å2 / CC1/2: 0.99 / R split: 0.095 / Net I/σ(I): 5.8
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 664 % / Mean I/σ(I) obs: 0.22 / Num. unique obs: 5042 / CC1/2: 0.11 / % possible all: 100
Serial crystallography measurementFocal spot size: 5 µm2 / Pulse duration: 40 fsec. / Pulse energy: 1 µJ / Pulse photon energy: 9.3 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryDescription: Superlube (viscous media) / Method: injection
Serial crystallography sample delivery injectionDescription: viscous media injector

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
CrystFELdata reduction
CrystFELdata scaling
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→27.3 Å / SU ML: 0.4266 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 32.4888
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2509 2222 5.08 %
Rwork0.1908 41487 -
obs0.1939 43709 86.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.67 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7322 0 95 61 7478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00837597
X-RAY DIFFRACTIONf_angle_d1.099710371
X-RAY DIFFRACTIONf_chiral_restr0.04971173
X-RAY DIFFRACTIONf_plane_restr0.01111365
X-RAY DIFFRACTIONf_dihedral_angle_d17.53162789
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.41711210.3931898X-RAY DIFFRACTION64.53
2.35-2.40.4157980.36422102X-RAY DIFFRACTION70.15
2.4-2.460.39191020.33392172X-RAY DIFFRACTION72.72
2.46-2.530.41971210.32512175X-RAY DIFFRACTION73.45
2.53-2.610.44021180.34422276X-RAY DIFFRACTION76.22
2.61-2.690.3951320.31662358X-RAY DIFFRACTION79.86
2.69-2.790.351450.2712520X-RAY DIFFRACTION84.1
2.79-2.90.31131640.24392570X-RAY DIFFRACTION88.48
2.9-3.030.30631590.25112703X-RAY DIFFRACTION90.77
3.03-3.190.29211490.24282810X-RAY DIFFRACTION94.18
3.19-3.390.28421630.19212871X-RAY DIFFRACTION97.09
3.39-3.650.26311310.1853001X-RAY DIFFRACTION98.8
3.65-4.020.22451420.16272968X-RAY DIFFRACTION98.82
4.02-4.590.19711620.15253006X-RAY DIFFRACTION99.65
4.59-5.780.22761400.16313008X-RAY DIFFRACTION99.62
5.78-27.30.20721750.16583049X-RAY DIFFRACTION99.23

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