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- PDB-5dkl: Structure of the light-state dimer of the blue light photorecepto... -

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Basic information

Entry
Database: PDB / ID: 5dkl
TitleStructure of the light-state dimer of the blue light photoreceptor Aureochrome 1a LOV from P. tricornutum
ComponentsLOV domain
KeywordsSIGNALING PROTEIN / light oxygen voltage DNA binding photoreceptor blue light / FLAVOPROTEIN / transcription
Function / homology
Function and homology information


PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAS domain / Beta-Lactamase / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / LOV domain-containing protein
Similarity search - Component
Biological speciesPhaeodactylum tricornutum (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHeintz, U. / Schlichting, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationFOR526 Germany
CitationJournal: Elife / Year: 2016
Title: Blue light-induced LOV domain dimerization enhances the affinity of Aureochrome 1a for its target DNA sequence.
Authors: Udo Heintz / Ilme Schlichting /
Abstract: The design of synthetic optogenetic tools that allow precise spatiotemporal control of biological processes previously inaccessible to optogenetic control has developed rapidly over the last years. ...The design of synthetic optogenetic tools that allow precise spatiotemporal control of biological processes previously inaccessible to optogenetic control has developed rapidly over the last years. Rational design of such tools requires detailed knowledge of allosteric light signaling in natural photoreceptors. To understand allosteric communication between sensor and effector domains, characterization of all relevant signaling states is required. Here, we describe the mechanism of light-dependent DNA binding of the light-oxygen-voltage (LOV) transcription factor Aureochrome 1a from Phaeodactylum tricornutum (PtAu1a) and present crystal structures of a dark state LOV monomer and a fully light-adapted LOV dimer. In combination with hydrogen/deuterium-exchange, solution scattering data and DNA-binding experiments, our studies reveal a light-sensitive interaction between the LOV and basic region leucine zipper DNA-binding domain that together with LOV dimerization results in modulation of the DNA affinity of PtAu1a. We discuss the implications of these results for the design of synthetic LOV-based photosensors with application in optogenetics.
History
DepositionSep 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LOV domain
B: LOV domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9244
Polymers32,0112
Non-polymers9132
Water362
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-39 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.560, 108.560, 104.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein LOV domain


Mass: 16005.620 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 234-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaeodactylum tricornutum (Diatom) / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / References: UniProt: B7G9J2*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.5 M sodium formate, 0.1 M hexamine cobalt (III) chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2014
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 19785 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.01
Reflection shellResolution: 2.7→3.2 Å / Redundancy: 5 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.46 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dkk

5dkk


Resolution: 2.7→45.724 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / Phase error: 30.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 990 5 %
Rwork0.209 --
obs0.2108 19785 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→45.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 62 2 2164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092206
X-RAY DIFFRACTIONf_angle_d1.093000
X-RAY DIFFRACTIONf_dihedral_angle_d15.145796
X-RAY DIFFRACTIONf_chiral_restr0.041326
X-RAY DIFFRACTIONf_plane_restr0.007394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.84250.43181390.34912644X-RAY DIFFRACTION98
2.8425-3.02050.33361380.30462621X-RAY DIFFRACTION98
3.0205-3.25370.32861380.26952620X-RAY DIFFRACTION98
3.2537-3.5810.24661410.21112672X-RAY DIFFRACTION99
3.581-4.09890.22561400.19482673X-RAY DIFFRACTION99
4.0989-5.1630.19651450.17252737X-RAY DIFFRACTION100
5.163-45.73070.23081490.19442828X-RAY DIFFRACTION100

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