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- EMDB-19276: Cryo-EM of tetrameric collagenase-cleaved Xenopus ZP2-N2N3 (cleav... -

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Basic information

Entry
Database: EMDB / ID: EMD-19276
TitleCryo-EM of tetrameric collagenase-cleaved Xenopus ZP2-N2N3 (cleaved xZP2-N2N3) (C1)
Map dataSharpened cryo-EM map of tetrameric collagenase-cleaved Xenopus ZP2-N2N3 (cleaved xZP2-N2N3) (C1)
Sample
  • Complex: Tetrameric collagenase-cleaved Xenopus ZP2-N2N3 (cleaved xZP2-N2N3)
    • Protein or peptide: Zona pellucida sperm-binding protein 2 (ZP2) / gp69/64
KeywordsCell adhesion / fertilization / egg-sperm interaction / gamete recognition / sperm receptor / extracellular matrix / egg coat / zona pellucida / glycoprotein / N-glycan / structural protein / ZP-N domain / block to polyspermy / post-fertilization cleavage / ovastacin
Function / homology
Function and homology information


egg coat / single fertilization / plasma membrane
Similarity search - Function
: / : / Zona pellucida, ZP-C domain / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain
Similarity search - Domain/homology
Vitelline envelope 69/64 kDa glycoprotein
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsWiseman B / Nishio S / Jovine L
Funding support Sweden, 3 items
OrganizationGrant numberCountry
Swedish Research Council2016-03999 Sweden
Swedish Research Council2020-04936 Sweden
Knut and Alice Wallenberg Foundation2018.0042 Sweden
CitationJournal: Int J Dev Biol / Year: 2008
Title: Anuran and pig egg zona pellucida glycoproteins in fertilization and early development.
Authors: Jerry L Hedrick /
Abstract: The envelope surrounding the eggs of all animals has many biological functions in fertilization and development. This review focuses on the anuran egg envelope in terms of its biochemistry, ...The envelope surrounding the eggs of all animals has many biological functions in fertilization and development. This review focuses on the anuran egg envelope in terms of its biochemistry, biophysics, structural biology and function in sperm-egg interactions and early development (embryo hatching). Egg envelopes from Xenopus laevis are among the most studied of the anurans, and are the central theme of this review. Comparisons of Xenopus laevis envelopes with those of other anurans and with pig egg envelopes are also included. This article presents historical as well as contemporary comparative perspectives on molecular and cellular mechanisms of sperm-egg envelope binding, block to polyspermy, envelope hardening, and hatching.
History
DepositionDec 25, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19276.png

Downloads & links

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Map

FileDownload / File: emd_19276.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened cryo-EM map of tetrameric collagenase-cleaved Xenopus ZP2-N2N3 (cleaved xZP2-N2N3) (C1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 200 pix.
= 189.18 Å		0.95 Å/pix.
x 200 pix.
= 189.18 Å		0.95 Å/pix.
x 200 pix.
= 189.18 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9459 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.47857627 - 0.6358875
Average (Standard dev.)0.00010262039 (±0.021288138)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 189.18001 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unprocessed cryo-EM map of tetrameric collagenase-cleaved Xenopus ZP2-N2N3...

Fileemd_19276_additional_1.map
AnnotationUnprocessed cryo-EM map of tetrameric collagenase-cleaved Xenopus ZP2-N2N3 (cleaved xZP2-N2N3) (C1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half map 1 of tetrameric collagenase-cleaved Xenopus...

Fileemd_19276_half_map_1.map
AnnotationCryo-EM half map 1 of tetrameric collagenase-cleaved Xenopus ZP2-N2N3 (cleaved xZP2-N2N3) (C1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half map 2 of tetrameric collagenase-cleaved Xenopus...

Fileemd_19276_half_map_2.map
AnnotationCryo-EM half map 2 of tetrameric collagenase-cleaved Xenopus ZP2-N2N3 (cleaved xZP2-N2N3) (C1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetrameric collagenase-cleaved Xenopus ZP2-N2N3 (cleaved xZP2-N2N3)

EntireName: Tetrameric collagenase-cleaved Xenopus ZP2-N2N3 (cleaved xZP2-N2N3)
Components
  • Complex: Tetrameric collagenase-cleaved Xenopus ZP2-N2N3 (cleaved xZP2-N2N3)
    • Protein or peptide: Zona pellucida sperm-binding protein 2 (ZP2) / gp69/64

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Supramolecule #1: Tetrameric collagenase-cleaved Xenopus ZP2-N2N3 (cleaved xZP2-N2N3)

SupramoleculeName: Tetrameric collagenase-cleaved Xenopus ZP2-N2N3 (cleaved xZP2-N2N3)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus laevis (African clawed frog) / Location in cell: Egg vitelline envelope

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Macromolecule #1: Zona pellucida sperm-binding protein 2 (ZP2) / gp69/64

MacromoleculeName: Zona pellucida sperm-binding protein 2 (ZP2) / gp69/64
type: protein_or_peptide / ID: 1
Details: The protein consists of two polypeptide fragments, generated by collagenase cleavage between P160 and V161, that remain covalently linked via a disulfide bond between C139 and C244
Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DEPGSSVVTC TKDSMTVRIP RTLSGFDDEI PVAAPSFWDL EVKFTGQTSL LGMSEARQRG YQFSSDPYYL TVQASYSAFG LNVFNLENQR LYVADLRLVS QFGSPRISID TPMICARDSP SCNSTHATVL IPFFGGVLTG INVNSVNIQL SSYSLQQHGI TLDSRNGYRL ...String:
DEPGSSVVTC TKDSMTVRIP RTLSGFDDEI PVAAPSFWDL EVKFTGQTSL LGMSEARQRG YQFSSDPYYL TVQASYSAFG LNVFNLENQR LYVADLRLVS QFGSPRISID TPMICARDSP SCNSTHATVL IPFFGGVLTG INVNSVNIQL SSYSLQQHGI TLDSRNGYRL YIKRSTLKGD RNDVLVLTFI YYGKTVPMLI SLVCSGGSNL EHHHHHHHH

UniProtKB: Vitelline envelope 69/64 kDa glycoprotein

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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: 7.8
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Details: 20 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Incubate 30 seconds, blot for 3 seconds, force 0 before plunging.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 1347 / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 15000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.4000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 867589
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 94899
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.2)
Final 3D classificationNumber classes: 2 / Avg.num./class: 86500 / Software - Name: cryoSPARC (ver. 3.2)
FSC plot (resolution estimation)

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