6E18 | pdb_00006e18

Crystal structure of Chlamydomonas reinhardtii HAP2 ectodomain provides structural insights of functional loops in green algae.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.234 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Species-Specific Functional Regions of the Green Alga Gamete Fusion Protein HAP2 Revealed by Structural Studies.

Baquero, E.Fedry, J.Legrand, P.Krey, T.Rey, F.A.

(2019) Structure 27: 113

  • DOI: https://doi.org/10.1016/j.str.2018.09.014
  • Primary Citation Related Structures: 
    6E18

  • PubMed Abstract: 

    The cellular fusion protein HAP2, which is structurally homologous to viral class II fusion proteins, drives gamete fusion across several eukaryotic kingdoms. Gamete fusion is a highly controlled process in eukaryotes, and is allowed only between same species gametes. In spite of a conserved architecture, HAP2 displays several species-specific functional regions that were not resolved in the available X-ray structure of the green alga Chlamydomonas reinhardtii HAP2 ectodomain. Here we present an X-ray structure resolving these regions, showing a target membrane interaction surface made by three amphipathic helices in a horseshoe-shaped arrangement. HAP2 from green algae also features additional species-specific motifs inserted in regions that in viral class II proteins are critical for the fusogenic conformational change. Such insertions include a cystine ladder-like module evocative of EGF-like motifs responsible for extracellular protein-protein interactions in animals, and a mucin-like region. These features suggest potential HAP2 interaction sites involved in gamete fusion control.


  • Organizational Affiliation
    • Institut Pasteur, Unité de Virologie Structurale, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France; CNRS UMR 3569, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France.

Macromolecule Content 

  • Total Structure Weight: 63.12 kDa 
  • Atom Count: 4,137 
  • Modeled Residue Count: 529 
  • Deposited Residue Count: 581 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hapless 2581Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: HAP2GCS1
UniProt
Find proteins for A4GRC6 (Chlamydomonas reinhardtii)
Explore A4GRC6 
Go to UniProtKB:  A4GRC6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4GRC6
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
C
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G47477HI
GlyCosmos: G47477HI
GlyGen: G47477HI

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.234 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.62α = 90
b = 125.62β = 90
c = 367.88γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union340371

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.2: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-10-16
    Changes: Structure summary