3AIH | pdb_00003aih

Human OS-9 MRH domain complexed with alpha3,alpha6-Man5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.277 (Depositor), 0.286 (DCC) 
  • R-Value Work: 
    0.228 (Depositor) 
  • R-Value Observed: 
    0.230 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3AIH

This is version 2.1 of the entry. See complete history

Literature

Structural Basis for Oligosaccharide Recognition of Misfolded Glycoproteins by OS-9 in ER-Associated Degradation

Satoh, T.Chen, Y.Hu, D.Hanashima, S.Yamamoto, K.Yamaguchi, Y.

(2010) Mol Cell 40: 905-916

  • DOI: https://doi.org/10.1016/j.molcel.2010.11.017
  • Primary Citation Related Structures: 
    3AIH

  • PubMed Abstract: 

    Misfolded glycoproteins are translocated from endoplasmic reticulum (ER) into the cytosol for proteasome-mediated degradation. A mannose-6-phosphate receptor homology (MRH) domain is commonly identified in a variety of proteins and, in the case of OS-9 and XTP3-B, is involved in glycoprotein ER-associated degradation (ERAD). Trimming of outermost α1,2-linked mannose on C-arm of high-mannose-type glycan and binding of processed α1,6-linked mannosyl residues by the MRH domain are critical steps in guiding misfolded glycoproteins to enter ERAD. Here we report the crystal structure of a human OS-9 MRH domain (OS-9(MRH)) complexed with α3,α6-mannopentaose. The OS-9(MRH) has a flattened β-barrel structure with a characteristic P-type lectin fold and possesses distinctive double tryptophan residues in the oligosaccharide-binding site. Our crystallographic result in conjunction with nuclear magnetic resonance (NMR) spectroscopic and biochemical results provides structural insights into the mechanism whereby OS-9 specifically recognizes Manα1,6Manα1,6Man residues on the processed C-arm through the continuous double tryptophan (WW) motif.


  • Organizational Affiliation
    • Structural Glycobiology Team, RIKEN Advanced Science Institute, Saitama 351-0198, Japan.

Macromolecule Content 

  • Total Structure Weight: 29.85 kDa 
  • Atom Count: 1,983 
  • Modeled Residue Count: 221 
  • Deposited Residue Count: 248 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein OS-9
A, B
124Homo sapiensMutation(s): 0 
Gene Names: OS9
UniProt & NIH Common Fund Data Resources
Find proteins for Q13438 (Homo sapiens)
Explore Q13438 
Go to UniProtKB:  Q13438
PHAROS:  Q13438
GTEx:  ENSG00000135506 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13438
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose
C, D
3N/A
Glycosylation Resources
GlyTouCan: G91725EU
GlyCosmos: G91725EU
GlyGen: G91725EU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.277 (Depositor), 0.286 (DCC) 
  • R-Value Work:  0.228 (Depositor) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.1α = 90
b = 73.1β = 90
c = 180.3γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXSphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-12-17
    Changes: Atomic model, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-10-23
    Changes: Advisory, Data collection, Database references, Structure summary