4OF3 | pdb_00004of3

Crystal Structure of SYG-1 D1-D2, Glycosylated


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.253 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history

Literature

Extracellular Architecture of the SYG-1/SYG-2 Adhesion Complex Instructs Synaptogenesis.

Ozkan, E.Chia, P.H.Wang, R.R.Goriatcheva, N.Borek, D.Otwinowski, Z.Walz, T.Shen, K.Garcia, K.C.

(2014) Cell 156: 482-494

  • DOI: https://doi.org/10.1016/j.cell.2014.01.004
  • Primary Citation Related Structures: 
    4OF0, 4OF3, 4OF6, 4OF7, 4OF8, 4OFD, 4OFI, 4OFK, 4OFP, 4OFY

  • PubMed Abstract: 

    SYG-1 and SYG-2 are multipurpose cell adhesion molecules (CAMs) that have evolved across all major animal taxa to participate in diverse physiological functions, ranging from synapse formation to formation of the kidney filtration barrier. In the crystal structures of several SYG-1 and SYG-2 orthologs and their complexes, we find that SYG-1 orthologs homodimerize through a common, bispecific interface that similarly mediates an unusual orthogonal docking geometry in the heterophilic SYG-1/SYG-2 complex. C. elegans SYG-1's specification of proper synapse formation in vivo closely correlates with the heterophilic complex affinity, which appears to be tuned for optimal function. Furthermore, replacement of the interacting domains of SYG-1 and SYG-2 with those from CAM complexes that assume alternative docking geometries or the introduction of segmental flexibility compromised synaptic function. These results suggest that SYG extracellular complexes do not simply act as "molecular velcro" and that their distinct structural features are important in instructing synaptogenesis. PAPERFLICK:


  • Organizational Affiliation
    • Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.

Macromolecule Content 

  • Total Structure Weight: 62.62 kDa 
  • Atom Count: 3,714 
  • Modeled Residue Count: 460 
  • Deposited Residue Count: 548 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein SYG-1, isoform b
A, B
274Caenorhabditis elegansMutation(s): 0 
Gene Names: CELE_K02E10.8K02E10.8syg-1
UniProt
Find proteins for B1Q236 (Caenorhabditis elegans)
Explore B1Q236 
Go to UniProtKB:  B1Q236
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1Q236
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
C
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
D
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G63564LA
GlyCosmos: G63564LA
GlyGen: G63564LA
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.253 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.648α = 90
b = 92.648β = 90
c = 129.014γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-27
    Changes: Structure summary