3GWJ

Crystal structure of Antheraea pernyi arylphorin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

The presence of monoglucosylated N196-glycan is important for the structural stability of storage protein, arylphorin

Ryu, K.S., Lee, J.O., Kwon, T.H., Choi, H.H., Park, H.S., Hwang, S.K., Lee, Z.W., Lee, K.B., Han, Y.H., Choi, Y.S., Jeon, Y.H., Cheong, C., Kim, S.

(2009) Biochem.J. 421: 87-96

  • DOI: 10.1042/BJ20082170

  • PubMed Abstract: 

    • Although N-glycosylation has been known to increase the stability of glycoproteins, it is difficult to assess the structural importance of glycans in the stabilization of glycoproteins. APA (Antheraea pernyi arylphorin) is an insect hexamerin that ha ...

    Although N-glycosylation has been known to increase the stability of glycoproteins, it is difficult to assess the structural importance of glycans in the stabilization of glycoproteins. APA (Antheraea pernyi arylphorin) is an insect hexamerin that has two N-glycosylations at Asn196 and Asn344 respectively. The glycosylation of Asn344 is critical for the folding process; however, glycosylation of Asn196 is not. Interestingly, the N196-glycan (glycosylation of Asn196) remains in an immature form (Glc1Man9GlcNAc2). The mutation of Asn196 to glutamine does not change the ecdysone-binding activity relative to that of the wild-type. In the present study, we determined the crystal structure of APA, and all sugar moieties of the N196-glycan were clearly observed in the electron-density map. Although the sugar moieties of the glycan generally have high structural flexibility, most sugar moieties of the N196-glycan were well organized in the deep cleft of the subunit interface and mediated many inter- and intrasubunit hydrogen bonds. Analytical ultracentrifugation and GdmCl (guanidinium chloride) unfolding experiments revealed that the presence of the N196-glycan was important for stabilizing the hexameric state and overall stability of APA respectively. Our results could provide a structural basis for studying not only other glycoproteins that carry an immature N-glycan, but also the structural role of N-glycans that are located in the deep cleft of a protein.

    Organizational Affiliation: 

    Magnetic Resonance Team, Korea Basic Science Institute, Gwahangno 113, Daejeon 305-333, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Arylphorin
A, B, C, D, E, F
674Antheraea pernyiMutation(s): 0 
Find proteins for Q7Z1F8 (Antheraea pernyi)
Go to UniProtKB:  Q7Z1F8
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT
Download SDF File 
Download CCD File 
A, B, C, D, E, F
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN
Download SDF File 
Download CCD File 
A, B, C, D, E, F
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA
Download SDF File 
Download CCD File 
A, B, C, D, E, F
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
GLC
Query on GLC
Download SDF File 
Download CCD File 
A, B, C, D, E, F
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, B, C, D, E, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 121.196α = 90.00
b = 119.470β = 90.00
c = 319.878γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
CNSphasing
HKL-2000data scaling
CNSrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance