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- PDB-9uaj: Ovorubin from the golden apple snail (Pomacea canaliculata) -

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Basic information

Entry
Database: PDB / ID: 9uaj
TitleOvorubin from the golden apple snail (Pomacea canaliculata)
Components
  • (Perivitellin ovorubin- ...) x 2
  • PcOvo3s
  • PcOvo5
  • Perivitellin protein
KeywordsLIPID BINDING PROTEIN / ovorubin / golden apple snail / Pomacea canaliculata
Function / homology(Z)-docos-13-enoic acid / Uncharacterized protein / Perivitellin protein / Perivitellin ovorubin-2 / Perivitellin ovorubin-1
Function and homology information
Biological speciesPomacea canaliculata (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.12 Å
AuthorsWangkanont, K. / Saw, W.-G. / Tran, B.N. / Wilasluck, P.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Other governmentChulalongkorn University Thailand
CitationJournal: Protein Sci / Year: 2026
Title: Structure of the chromoprotein ovorubin from the golden apple snail (Pomacea canaliculata).
Authors: Patcharin Wilasluck / Wuan-Geok Saw / Bich Ngoc Tran / Grzegorz Sabat / Orion Shih / Kowit Hengphasatporn / Yasuteru Shigeta / Nawaporn Vinayavekhin / Kittikhun Wangkanont /
Abstract: The golden apple snail (Pomacea canaliculata), an invasive gastropod, produces distinctly bright pink egg masses. The astaxanthin-binding ovorubin (P. canaliculata ovorubin [PcOvo]) is a 300-kDa ...The golden apple snail (Pomacea canaliculata), an invasive gastropod, produces distinctly bright pink egg masses. The astaxanthin-binding ovorubin (P. canaliculata ovorubin [PcOvo]) is a 300-kDa glycoprotein responsible for the egg coloration. Here, we determine the three-dimensional structure of PcOvo using cryo-electron microscopy (cryo-EM). PcOvo is a heterodecameric protein consisting of two copies of each PcOvo1-5 subunit. The subunits have similar repeated ferredoxin-like structures. N-linked glycosylation sites are identified. Solution x-ray scattering data support the overall architecture of the complex. PcOvo3 and PcOvo5 have hydrophobic pockets that likely bind various hydrophobic compounds. The cryo-EM map and binding experiments suggest that PcOvo5 binds astaxanthin, which is responsible for the pink color of the protein. Our structure provides molecular insights into the nature of the gastropod egg coloration and lays a foundation for further investigation of ovorubin biology and evolution.
History
DepositionApr 1, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PcOvo5
B: PcOvo3s
C: Perivitellin ovorubin-1
D: Perivitellin protein
E: Perivitellin ovorubin-2
F: PcOvo5
G: Perivitellin ovorubin-2
H: Perivitellin protein
I: Perivitellin ovorubin-1
J: PcOvo3s
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,21926
Polymers227,59410
Non-polymers6,62516
Water5,747319
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

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Protein , 3 types, 6 molecules AFBJDH

#1: Protein PcOvo5


Mass: 22841.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pomacea canaliculata (invertebrata) / References: UniProt: A0A2T7NVP5
#2: Protein PcOvo3s


Mass: 22252.473 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pomacea canaliculata (invertebrata) / References: UniProt: A0A2T7NVP5
#4: Protein Perivitellin protein


Mass: 22467.189 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pomacea canaliculata (invertebrata) / References: UniProt: A0A2T7NVP6

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Perivitellin ovorubin- ... , 2 types, 4 molecules CIEG

#3: Protein Perivitellin ovorubin-1


Mass: 22408.697 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pomacea canaliculata (invertebrata) / References: UniProt: J7I2T6
#5: Protein Perivitellin ovorubin-2


Mass: 23827.533 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pomacea canaliculata (invertebrata) / References: UniProt: J7HZ90

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Sugars , 3 types, 12 molecules

#6: Polysaccharide
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#9: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 323 molecules

#8: Chemical
ChemComp-08O / (Z)-docos-13-enoic acid


Mass: 338.568 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H42O2 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: Ovorubin / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Molecular weightValue: 0.226 MDa / Experimental value: YES
Source (natural)Organism: Pomacea canaliculata (invertebrata)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer componentConc.: 50 mM / Name: Tris
SpecimenConc.: 9.9 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 R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.5 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 magnification: 215000 X / Nominal defocus max: 1400 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6418
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2EPU3.3image acquisition
4cryoSPARC4.6.0CTF correction
7Coot0.9.8.93model fitting
9cryoSPARC4.6.0initial Euler assignment
10cryoSPARC4.6.0final Euler assignment
11cryoSPARC4.2.1classification
12cryoSPARC4.6.03D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1621962
3D reconstructionResolution: 2.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 336633 / Algorithm: FOURIER SPACE / Num. of class averages: 5 / Symmetry type: POINT
Atomic model buildingB value: 51.4 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: Other / Type: other

IDAccession codeChain-IDDetailsInitial refinement model-ID
1AF-J7I2T6-F1CAutomatic model building by Phenix using the map1
2AF-J7I2T6-F1IAutomatic model building by Phenix using the map1
3AF-J7HZ90-F1EAutomatic model building by Phenix using the map2
4AF-J7HZ90-F1GAutomatic model building by Phenix using the map2
5AF-A0A2T7NVP5-F1BAutomatic model building by Phenix using the map3
6AF-A0A2T7NVP5-F1JAutomatic model building by Phenix using the map3
7AF-A0A2T7NVP6-F1DManual model building by visual map interpretation4
8AF-A0A2T7NVP6-F1HManual model building by visual map interpretation4
9AF-A0A2T7NVP5-F1AManual model building by visual map interpretation3
10AF-A0A2T7NVP5-F1FManual model building by visual map interpretation3
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00615185
ELECTRON MICROSCOPYf_angle_d0.60920539
ELECTRON MICROSCOPYf_dihedral_angle_d7.0852580
ELECTRON MICROSCOPYf_chiral_restr0.0482387
ELECTRON MICROSCOPYf_plane_restr0.0042597

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