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- EMDB-63984: Ovorubin from the golden apple snail (Pomacea canaliculata) -

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Basic information

Entry
Database: EMDB / ID: EMD-63984
TitleOvorubin from the golden apple snail (Pomacea canaliculata)
Map data
Sample
  • Complex: Ovorubin
    • Protein or peptide: PcOvo5
    • Protein or peptide: PcOvo3s
    • Protein or peptide: Perivitellin ovorubin-1
    • Protein or peptide: Perivitellin protein
    • Protein or peptide: Perivitellin ovorubin-2
  • Ligand: (Z)-docos-13-enoic acid
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
Keywordsovorubin / golden apple snail / Pomacea canaliculata / LIPID BINDING PROTEIN
Function / homologyUncharacterized protein / Perivitellin protein / Perivitellin ovorubin-2 / Perivitellin ovorubin-1
Function and homology information
Biological speciesPomacea canaliculata (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.12 Å
AuthorsWangkanont K / Saw W-G / Tran BN / Wilasluck P
Funding support Thailand, 1 items
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, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63984.png

Downloads & links

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Map

FileDownload / File: emd_63984.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.58 Å/pix.
x 320 pix.
= 185.6 Å		0.58 Å/pix.
x 320 pix.
= 185.6 Å		0.58 Å/pix.
x 320 pix.
= 185.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.58 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0605
Minimum - Maximum-0.09006565 - 0.24487132
Average (Standard dev.)0.0016652402 (±0.012428447)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 185.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63984_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Sharpen map from deepEMhancer

Fileemd_63984_additional_1.map
AnnotationSharpen map from deepEMhancer
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_63984_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63984_half_map_2.map
Projections & Slices
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Sample components

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Entire : Ovorubin

EntireName: Ovorubin
Components
  • Complex: Ovorubin
    • Protein or peptide: PcOvo5
    • Protein or peptide: PcOvo3s
    • Protein or peptide: Perivitellin ovorubin-1
    • Protein or peptide: Perivitellin protein
    • Protein or peptide: Perivitellin ovorubin-2
  • Ligand: (Z)-docos-13-enoic acid
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Ovorubin

SupramoleculeName: Ovorubin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Pomacea canaliculata (invertebrata)
Molecular weightTheoretical: 226 KDa

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Macromolecule #1: PcOvo5

MacromoleculeName: PcOvo5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pomacea canaliculata (invertebrata)
Molecular weightTheoretical: 22.841211 KDa
SequenceString: MLVATLTLVA LSAVFTNVYG SDQYTILDVY KASNVSVEDY KDLLKDLDVV HSFKVLGSSR VIFVVKMRED SYEKLSKINL PGDVYSIPA GDLSDKMQSV GVEWKRWDDL PDANLTLFER TLELKGEPLE GLASHMKAFG EKVSHVMELY PNKGFYLLGR T PPKAFVIV ...String:
MLVATLTLVA LSAVFTNVYG SDQYTILDVY KASNVSVEDY KDLLKDLDVV HSFKVLGSSR VIFVVKMRED SYEKLSKINL PGDVYSIPA GDLSDKMQSV GVEWKRWDDL PDANLTLFER TLELKGEPLE GLASHMKAFG EKVSHVMELY PNKGFYLLGR T PPKAFVIV SLPFRCRQVR YGSDFALNYL NGPGDSSTKV EFVAKA

UniProtKB: Uncharacterized protein

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Macromolecule #2: PcOvo3s

MacromoleculeName: PcOvo3s / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pomacea canaliculata (invertebrata)
Molecular weightTheoretical: 22.252473 KDa
SequenceString: MYALAIALLA FSTFVSNAFA NKEYLLLDIR DATTSEIISA LRDVEIELKV KAKGIARHLI VVKQNDANLQ KLGEIDIPGR SCSTPVEDL DNLMEDIGIS WPRNELTNVN VTLFERTLDL KDKTMEQFWS EAKAYGQLVK PVLSSFTYRA FKANGAYPPK V YFFVNLPR ...String:
MYALAIALLA FSTFVSNAFA NKEYLLLDIR DATTSEIISA LRDVEIELKV KAKGIARHLI VVKQNDANLQ KLGEIDIPGR SCSTPVEDL DNLMEDIGIS WPRNELTNVN VTLFERTLDL KDKTMEQFWS EAKAYGQLVK PVLSSFTYRA FKANGAYPPK V YFFVNLPR ENLNDASSKG IDIFGGPGKA RTTVQYVTKL S

UniProtKB: Uncharacterized protein

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Macromolecule #3: Perivitellin ovorubin-1

MacromoleculeName: Perivitellin ovorubin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pomacea canaliculata (invertebrata)
Molecular weightTheoretical: 22.408697 KDa
SequenceString: MFVATSLLLA IATLVVRASP HNYLIMDIEP PKSVSERDIL NLLSPLQVKH SFRVTGSTRL LIVIRLDAQS YEKLDEITVP GKVEVIPAV NMADTMERCG VSWPRVELTD DNVTLFESES TLTDVTKEQL KAMLIGYGEH MSGLLQAHRF EYYQAAGATP H RHFVFVNS ...String:
MFVATSLLLA IATLVVRASP HNYLIMDIEP PKSVSERDIL NLLSPLQVKH SFRVTGSTRL LIVIRLDAQS YEKLDEITVP GKVEVIPAV NMADTMERCG VSWPRVELTD DNVTLFESES TLTDVTKEQL KAMLIGYGEH MSGLLQAHRF EYYQAAGATP H RHFVFVNS VPDEIEVFGR EGVDIWGGPG EFVVKPQYVT RI

UniProtKB: Perivitellin ovorubin-1

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Macromolecule #4: Perivitellin protein

MacromoleculeName: Perivitellin protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pomacea canaliculata (invertebrata)
Molecular weightTheoretical: 22.467189 KDa
SequenceString: MTAILALLLA MSILLPSGAV EDVQDLVFAE WDKGSSHEHA CSALRNSSVI EKGLTVKEVG TSKFAAVLSE PILARLKFHG LVEAVPVVE VGTVMKRLNV SIPPAQDISD NNLTLIKMSP KLKGQTLQQI DAELRYLGEY MNTVLQKCSH RVYISKGTFP P KIYVFLNM ...String:
MTAILALLLA MSILLPSGAV EDVQDLVFAE WDKGSSHEHA CSALRNSSVI EKGLTVKEVG TSKFAAVLSE PILARLKFHG LVEAVPVVE VGTVMKRLNV SIPPAQDISD NNLTLIKMSP KLKGQTLQQI DAELRYLGEY MNTVLQKCSH RVYISKGTFP P KIYVFLNM PLDQIRQFYP SLDIFGGPSS TKNEISYVQI LILRN

UniProtKB: Perivitellin protein

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Macromolecule #5: Perivitellin ovorubin-2

MacromoleculeName: Perivitellin ovorubin-2 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pomacea canaliculata (invertebrata)
Molecular weightTheoretical: 23.827533 KDa
SequenceString: MAEHRIPVLL LLVVVAASSL AQQIPLQKHY IIYEVRNIEK TPEEVKEEMK DTDILYSFKA LGAPSYHIVV EVNPRNMRKL EEVELKGKI RMVPVVNMVD VAETLGVSWP RSGARLLDVN LTLIERTLNQ EGLTSQESEA HLKGFMEELK DRLQQYNYQA F FTIGASPP ...String:
MAEHRIPVLL LLVVVAASSL AQQIPLQKHY IIYEVRNIEK TPEEVKEEMK DTDILYSFKA LGAPSYHIVV EVNPRNMRKL EEVELKGKI RMVPVVNMVD VAETLGVSWP RSGARLLDVN LTLIERTLNQ EGLTSQESEA HLKGFMEELK DRLQQYNYQA F FTIGASPP KMYIYINIPY EEVDKFACIG INQFGGPAAV NTTVSFISSF PK

UniProtKB: Perivitellin ovorubin-2

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Macromolecule #8: (Z)-docos-13-enoic acid

MacromoleculeName: (Z)-docos-13-enoic acid / type: ligand / ID: 8 / Number of copies: 4 / Formula: 08O
Molecular weightTheoretical: 338.568 Da
Chemical component information

ChemComp-08O:
(Z)-docos-13-enoic acid

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 319 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration9.9 mg/mL
BufferpH: 7.5 / Component - Concentration: 50.0 mM / Component - Name: Tris
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.5 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
SoftwareName: EPU (ver. 3.3)
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 6418 / 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: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 215000
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: 1621962
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Automatic model building by Phenix using the map for chains B, C, E, G, I, and J. Manual model building by visual map interpretation for chains A, D, F, and H as these proteins were not ...Details: Automatic model building by Phenix using the map for chains B, C, E, G, I, and J. Manual model building by visual map interpretation for chains A, D, F, and H as these proteins were not previously known to be parts of the complex.
Final reconstructionNumber classes used: 5 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 336633
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

6-f1

chain_id: C, source_name: Other, initial_model_type: otherAutomatic model building by Phenix using the map

6-f1

chain_id: I, source_name: Other, initial_model_type: otherAutomatic model building by Phenix using the map

0-f1

chain_id: E, source_name: Other, initial_model_type: otherAutomatic model building by Phenix using the map

0-f1

chain_id: G, source_name: Other, initial_model_type: otherAutomatic model building by Phenix using the map

5-f1

chain_id: B, source_name: Other, initial_model_type: otherAutomatic model building by Phenix using the map

5-f1

chain_id: J, source_name: Other, initial_model_type: otherAutomatic model building by Phenix using the map

6-f1

chain_id: D, source_name: Other, initial_model_type: otherManual model building by visual map interpretation

6-f1

chain_id: H, source_name: Other, initial_model_type: otherManual model building by visual map interpretation

5-f1

chain_id: A, source_name: Other, initial_model_type: otherManual model building by visual map interpretation

5-f1

chain_id: F, source_name: Other, initial_model_type: otherManual model building by visual map interpretation
SoftwareName: Coot (ver. 0.9.8.93)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 51.4
Output model

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

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