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Basic information

Entry
Database: PDB / ID: 9naa
TitleUnusual structure of a bacteriophytochrome fragment derived from full length SaBphP2
Componentshistidine kinase
KeywordsSIGNALING PROTEIN / phytochrome / myxobacteria / biliverdin
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / phosphorelay sensor kinase activity / histidine kinase / protein kinase activator activity / photoreceptor activity / regulation of DNA-templated transcription
Similarity search - Function
Phytochrome / : / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain ...Phytochrome / : / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / 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-EL5 / histidine kinase
Similarity search - Component
Biological speciesStigmatella aurantiaca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchmidt, M. / Prabin, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
National Science Foundation (NSF, United States)2423601 United States
CitationJournal: Struct Dyn / Year: 2025
Title: Structures of myxobacterial phytochrome revealed by cryo-EM using the Spotiton technique and with x-ray crystallography.
Authors: Prabin Karki / David Menendez / William Budell / Shishir Dangi / Carolina Hernandez / Joshua Mendez / Srinivasan Muniyappan / Shibom Basu / Peter Schwander / Tek N Malla / Emina A Stojković / Marius Schmidt /
Abstract: Phytochromes are red-light photoreceptors first identified in plants, with homologs found in bacteria and fungi, that regulate a variety of critical physiological processes. They undergo a reversible ...Phytochromes are red-light photoreceptors first identified in plants, with homologs found in bacteria and fungi, that regulate a variety of critical physiological processes. They undergo a reversible photocycle between two distinct states: a red-light-absorbing Pr form and a far-red light-absorbing Pfr form. This Pr/Pfr photoconversion controls the activity of a C-terminal enzymatic domain, typically a histidine kinase (HK). However, the molecular mechanisms underlying light-induced regulation of HK activity in bacteria remain poorly understood, as only a few structures of unmodified bacterial phytochromes with HK activity are known. Recently, cryo-EM structures of a wild-type bacterial phytochrome with HK activity are solved that reveal homodimers in both the Pr and Pfr states, as well as a heterodimer with individual monomers in distinct Pr and Pfr states. Cryo-EM structures of a truncated version of the same phytochrome-lacking the HK domain-also show a homodimer in the Pfr state and a Pr/Pfr heterodimer. Here, we describe in detail how structural information is obtained from cryo-EM data on a full-length intact bacteriophytochrome, and how the cryo-EM structure can contribute to the understanding of the function of the phytochrome. In addition, we compare the cryo-EM structure to an unusual x-ray structure that is obtained from a fragmented full-length phytochrome crystallized in the Pr-state.
History
DepositionFeb 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: histidine kinase
B: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1164
Polymers64,9472
Non-polymers1,1692
Water6,918384
1
A: histidine kinase
B: histidine kinase
hetero molecules

A: histidine kinase
B: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,2338
Polymers129,8944
Non-polymers2,3394
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3_555-x,y+1/2,-z+1/21
Buried area1360 Å2
ΔGint-13 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.760, 101.140, 103.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 9 through 115 or resid 137 through 306 or resid 401))
d_2ens_1chain "B"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASPASPPROPROAA9 - 1151 - 107
d_12GLYGLYARGARGAA137 - 306129 - 298
d_13BLABLABLABLAAC401
d_21ASPASPARGARGBB9 - 3061 - 298
d_22BLABLABLABLABD401

NCS oper: (Code: givenMatrix: (-0.999936129899, -0.0108053239384, -0.00331377371132), (0.0108079738086, -0.999941285747, -0.000782790429716), (-0.0033051208414, -0.000818555612292, 0.999994203055) ...NCS oper: (Code: given
Matrix: (-0.999936129899, -0.0108053239384, -0.00331377371132), (0.0108079738086, -0.999941285747, -0.000782790429716), (-0.0033051208414, -0.000818555612292, 0.999994203055)
Vector: 0.494708773602, -8.80977555242, 0.0160725688642)

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Components

#1: Protein histidine kinase


Mass: 32473.533 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, histidine kinase
#2: Chemical ChemComp-EL5 / 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 / biliverdin, bound form at Pfr state


Mass: 584.662 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H36N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.1 M TAPS, 0.1 M Mg(NO3)2, 24% PEG 20000, pH 9

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.1→38.87 Å / Num. obs: 35675 / % possible obs: 99.4 % / Redundancy: 5 % / Biso Wilson estimate: 39.7 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.089 / Net I/σ(I): 5
Reflection shellResolution: 2.1→2.13 Å / Redundancy: 5 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1 / Num. unique obs: 2963 / CC1/2: 0.62 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→38.87 Å / SU ML: 0.2808 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 35.6083
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2602 3343 5.09 %
Rwork0.2273 62286 -
obs0.229 35585 91.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.14 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4254 0 86 384 4724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814436
X-RAY DIFFRACTIONf_angle_d1.13566053
X-RAY DIFFRACTIONf_chiral_restr0.0526687
X-RAY DIFFRACTIONf_plane_restr0.0097790
X-RAY DIFFRACTIONf_dihedral_angle_d19.11231647
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.985212528032 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.46621400.40992632X-RAY DIFFRACTION93.24
2.13-2.160.44911160.38932710X-RAY DIFFRACTION94.26
2.16-2.20.39231730.3752635X-RAY DIFFRACTION93.57
2.2-2.230.33441440.35092637X-RAY DIFFRACTION93.83
2.23-2.270.38491530.34582652X-RAY DIFFRACTION92.76
2.27-2.310.33461210.33182680X-RAY DIFFRACTION93.27
2.31-2.360.36381530.31732634X-RAY DIFFRACTION92.71
2.36-2.40.30971380.30072635X-RAY DIFFRACTION92.9
2.4-2.460.35271120.28612664X-RAY DIFFRACTION92.6
2.46-2.510.40771320.28742599X-RAY DIFFRACTION91.61
2.51-2.580.29191520.27232576X-RAY DIFFRACTION90.96
2.58-2.650.30181550.27332535X-RAY DIFFRACTION89.4
2.65-2.720.24671600.25692549X-RAY DIFFRACTION91
2.72-2.810.311510.25562622X-RAY DIFFRACTION92.65
2.81-2.910.25851450.23492633X-RAY DIFFRACTION92.63
2.91-3.030.29031430.22812639X-RAY DIFFRACTION92.39
3.03-3.170.24581420.21712595X-RAY DIFFRACTION91.81
3.17-3.330.26071540.20692599X-RAY DIFFRACTION91.71
3.33-3.540.21141270.19082576X-RAY DIFFRACTION90.8
3.54-3.810.22941440.18312576X-RAY DIFFRACTION90.88
3.82-4.20.21611490.18152514X-RAY DIFFRACTION89.09
4.2-4.80.15941210.16672490X-RAY DIFFRACTION87.09
4.81-6.050.25731210.20042466X-RAY DIFFRACTION85.92
6.05-38.870.2002970.18822438X-RAY DIFFRACTION85.04

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