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- EMDB-50552: Porcine Retinol-Binding Protein 3 (RBP3) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-50552
TitlePorcine Retinol-Binding Protein 3 (RBP3)
Map dataThe map with the RBP3 rigid core refined.
Sample
  • Organelle or cellular component: Retinol binding protein 3
    • Protein or peptide: Retinol binding protein 3
KeywordsRetinoids / Interphotoreceptor matrix (IPM) / Visual cycle / Shuttle / TRANSPORT PROTEIN
Function / homology
Function and homology information


interphotoreceptor matrix / retinal binding / serine-type peptidase activity / proteolysis / extracellular region
Similarity search - Function
N-terminal domain of Peptidase_S41 in eukaryotic IRBP / tail specific protease / Tail specific protease / Peptidase family S41 / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
Retinol-binding protein 3
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle 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, 2 items
OrganizationGrant numberCountry
Foundation for Polish ScienceMAB/2019/12 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 5, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50552.png

Downloads & links

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Map

FileDownload / File: emd_50552.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe map with the RBP3 rigid core refined.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 333.6 Å		0.83 Å/pix.
x 400 pix.
= 333.6 Å		0.83 Å/pix.
x 400 pix.
= 333.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.7110348 - 1.5347162
Average (Standard dev.)0.0004236992 (±0.029290654)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 333.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50552_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The joint map of the RBP3 rigid map's...

Fileemd_50552_additional_1.map
AnnotationThe joint map of the RBP3 rigid map's core and the RBP3 flexible maps' arms.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The map of the refinement focused on the flexible arms of RBP3.

Fileemd_50552_additional_2.map
AnnotationThe map of the refinement focused on the flexible arms of RBP3.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The second half map of the refinement of the RBP3 rigid core.

Fileemd_50552_half_map_1.map
AnnotationThe second half map of the refinement of the RBP3 rigid core.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The first half map of the refinement of the RBP3 rigid core.

Fileemd_50552_half_map_2.map
AnnotationThe first half map of the refinement of the RBP3 rigid core.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Retinol binding protein 3

EntireName: Retinol binding protein 3
Components
  • Organelle or cellular component: Retinol binding protein 3
    • Protein or peptide: Retinol binding protein 3

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Supramolecule #1: Retinol binding protein 3

SupramoleculeName: Retinol binding protein 3 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 135 kDa/nm

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Macromolecule #1: Retinol binding protein 3

MacromoleculeName: Retinol binding protein 3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
SequenceString: MPRKWALLLP MLLCSLTGPT HMFQSSLVLD TAKILLDNYC FPENLMGMQE AIEQATKSPE ILAITDPQT LAHVLTAGVQ NSLNDPRLII SYEPSTLEVT PKAPALRNLT LEELIEGLHN S LRHEVLEG NVGYLRVDDI PGQEVMNKLG SFLVVNVWEK LMGTSALVLD ...String:
MPRKWALLLP MLLCSLTGPT HMFQSSLVLD TAKILLDNYC FPENLMGMQE AIEQATKSPE ILAITDPQT LAHVLTAGVQ NSLNDPRLII SYEPSTLEVT PKAPALRNLT LEELIEGLHN S LRHEVLEG NVGYLRVDDI PGQEVMNKLG SFLVVNVWEK LMGTSALVLD LRHCTRGHVS GI PYVISYL HPGNTVLHVD TVYDRPSNTT TEIWTLPEVL GDRYSADKDV VVLTSSHTGG VAE DIAYIL KQMRRAIVVG ERTVGGALDL QKLRIGQSDF FLTVPVSRSL GPLGEGSQTW EGSG VLPCV GTPAEQALEK ALAILKLRRA LPGVIQRLQE VLQEYYTLVD RVPALLHHLA SMDLS SVVS EEDLVTKLNA GLQAVSEDPR LLVQVVKSKE PSSEPKDEAE EPPEVIPEVP EDEAAR RAL VDAVFQVSVL PGNVGYLRFD SFADASVLGV LAPYIVHQVW EPLQDTEHLI MDLRQNP GG PSTAVPLLLS YFQGPDPGPV RLFTTYDRRT NVTQEHYSHT ELLGQRYSTQ GGVYLLIS H RTATAAEELA FLMQSLGWAT LVGEITAGSL LHTHTVPLLE TTEGGLSLTV PVLTFIDNH GECWLGGGVV PDAIVLAEEA LDRAQEVLEF HRSLGELVEG TGHLLEAHYA RPEVVGQTGA LLRAKLAQG AYRTAVDLES LASQLTADLQ EMSGDHRLLV FHSPGEMVAE EVPPPPPVVP S PEELSYLI EALFKTEVLP GRLGYLRFDA MAELETVKAI GPQLVQLVWQ KLIDTAALVV DL RYNPGSY STAVPLLCSY FFEAEPRQHL YSVFDRATSR VMEVWTVPQV AGQRYGPQKD LYI LVSHTS GSAAEAFAHT MQDLQRATII GEPTAGGALS VGIYQVGSSP LYASMPTQMA LSAS TGEAW DLAGVEPDIT VPMSVALSTA RDIVALRAKV PTVLQTAGKL VADNYASPEM GAKIA VKLS RLQSRYARVT SEASLAEMLE ADLQLLSGDP HLKTAHIPED AKDRIPGIVP MQIPSP EVF EDLIKFSFHT NVLEGNIGYL RFDMFGDREL LTQVSELLVE HVWKKIIHTD ALIIDMR FN IGGPTSSISA LCSYFFDEGP PILLDKIYNR PNDSVSELWT HTHLTGGSYG SKKSIIIL T SSLTAGAAEE FTYIMKRLGR ALVIGEVTSG GSQPPQTYHV DDTNLYITIP TARSVGAAD GSSWEGVGVV PDVAVPAEGA LARAQEMLQH TLLRARRSLQ DHKPTLFKQE SPDRRQAFTP APFLLAKSK

UniProtKB: Retinol-binding protein 3

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.9 mg/mL
BufferpH: 8
Component:
ConcentrationName
50.0 mMHEPES
300.0 mMNaCl
1.0 mMDTT
0.01 %DDM
0.5 %CHAPSO
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 23606 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.4000000000000001 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7462000
Startup modelType of model: INSILICO MODEL
In silico model: Initial model generated by the Ab-initio job in Cryosparc.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: Local Refinement / Number images used: 611246
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC / Software - details: Hetero refinement
FSC plot (resolution estimation)

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