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- PDB-9frx: Porcine Retinol-Binding Protein 3 (RBP3) -

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Basic information

Entry
Database: PDB / ID: 9frx
TitlePorcine Retinol-Binding Protein 3 (RBP3)
ComponentsRetinol binding protein 3
KeywordsTRANSPORT PROTEIN / Retinoids / Interphotoreceptor matrix (IPM) / Visual cycle / Shuttle
Function / homologyN-terminal domain of Peptidase_S41 in eukaryotic IRBP / tail specific protease / Tail specific protease / Peptidase family S41 / ClpP/crotonase-like domain superfamily / serine-type peptidase activity / proteolysis / Retinol binding protein 3
Function and homology information
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsKaushik, V. / Gessa, L. / Kumar, N. / Pinkas, M. / Czarnocki-Cieciura, M. / Palczewski, K. / Novacek, J. / Fernandes, H.
Funding support Poland, European Union, 3items
OrganizationGrant numberCountry
Foundation for Polish ScienceMAB/2019/12 Poland
Foundation for Polish ScienceFENG.02.01-IP.05-T005/23 Poland
H2020 Marie Curie Actions of the European CommissionPAN.BFB.S.BDN.315.022.2022European Union
CitationJournal: Open Biol / Year: 2025
Title: CryoEM structure and small-angle X-ray scattering analyses of porcine retinol-binding protein 3.
Authors: Vineeta Kaushik / Luca Gessa / Nelam Kumar / Matyáš Pinkas / Mariusz Czarnocki-Cieciura / Krzysztof Palczewski / Jiří Nováček / Humberto Fernandes /
Abstract: The vertebrate visual cycle hinges on enzymatically converting all--retinol (at-ROL) into 11--retinal (11c-RAL), the chromophore that binds to opsins in photoreceptors, forming light-responsive ...The vertebrate visual cycle hinges on enzymatically converting all--retinol (at-ROL) into 11--retinal (11c-RAL), the chromophore that binds to opsins in photoreceptors, forming light-responsive pigments. When struck by a photon, these pigments activate the phototransduction pathway and initiate the process of vision. The enzymatic isomerization of at-ROL, crucial for restoring the visual pigments and preparing them to receive new light stimuli, relies on various enzymes found in both the photoreceptors and retinal pigment epithelium cells. To function effectively, retinoids must shuttle between these two cell types. Retinol-binding protein 3 (RBP3), located in the interphotoreceptor matrix, probably plays a pivotal role in this transport mechanism. Comprised of four retinoid-binding modules, RBP3 also binds fatty acids, potentially aiding retinal function by facilitating the loading and unloading of different retinoids at specific cell types thereby directing the cycle. In this study, we present a 3.67 Å cryoEM structure of porcine RBP3, along with molecular docking analysis and corroborative in-solution small-angle X-ray scattering data for titration of RBP3 with relevant ligands, that also give insights on RBP3 conformational adaptability.
History
DepositionJun 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinol binding protein 3


Theoretical massNumber of molelcules
Total (without water)138,6221
Polymers138,6221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Retinol binding protein 3


Mass: 138621.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: RBP3 / Production host: Sus scrofa (pig) / References: UniProt: A0A287A908
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Retinol binding protein 3 / Type: ORGANELLE OR CELLULAR COMPONENT / Details: Retinol binding protein 3 / Entity ID: all / Source: NATURAL
Molecular weightValue: 138.487 kDa/nm / Experimental value: NO
Source (natural)Organism: Sus scrofa (Pig)
Buffer solutionpH: 8
Buffer component
IDConc.NameBuffer-ID
150 mMHEPES1
2300 mMNCl1
31 mMDTT1
40.01 %DDM1
50.5 %CHAPSO1
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm / C2 aperture diameter: 30 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 23606
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameCategoryDetails
1cryoSPARCparticle selectiontemplate picker
2SerialEMimage acquisition
4CTFFINDCTF correction
12cryoSPARCclassificationHetero Refinement
13cryoSPARC3D reconstructionLocal Refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7462000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 611246 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028492
ELECTRON MICROSCOPYf_angle_d0.5111567
ELECTRON MICROSCOPYf_dihedral_angle_d3.7781167
ELECTRON MICROSCOPYf_chiral_restr0.0411371
ELECTRON MICROSCOPYf_plane_restr0.0031482

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