5B2C | pdb_00005b2c

Crystal structure of Mumps virus hemagglutinin-neuraminidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 
    0.222 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Trisaccharide containing alpha 2,3-linked sialic acid is a receptor for mumps virus

Kubota, M.Takeuchi, K.Watanabe, S.Ohno, S.Matsuoka, R.Kohda, D.Nakakita, S.I.Hiramatsu, H.Suzuki, Y.Nakayama, T.Terada, T.Shimizu, K.Shimizu, N.Shiroishi, M.Yanagi, Y.Hashiguchi, T.

(2016) Proc Natl Acad Sci U S A 113: 11579-11584

  • DOI: https://doi.org/10.1073/pnas.1608383113
  • Primary Citation Related Structures: 
    5B2C, 5B2D

  • PubMed Abstract: 

    Mumps virus (MuV) remains an important pathogen worldwide, causing epidemic parotitis, orchitis, meningitis, and encephalitis. Here we show that MuV preferentially uses a trisaccharide containing α2,3-linked sialic acid in unbranched sugar chains as a receptor. Crystal structures of the MuV attachment protein hemagglutinin-neuraminidase (MuV-HN) alone and in complex with the α2,3-sialylated trisaccharide revealed that in addition to the interaction between the MuV-HN active site residues and sialic acid, other residues, including an aromatic residue, stabilize the third sugar of the trisaccharide. The importance of the aromatic residue and the third sugar in the MuV-HN-receptor interaction was confirmed by computational energy calculations, isothermal titration calorimetry studies, and glycan-binding assays. Furthermore, MuV-HN was found to bind more efficiently to unbranched α2,3-sialylated sugar chains compared with branched ones. Importantly, the strategically located aromatic residue is conserved among the HN proteins of sialic acid-using paramyxoviruses, and alanine substitution compromised their ability to support cell-cell fusion. These results suggest that not only the terminal sialic acid but also the adjacent sugar moiety contribute to receptor function for mumps and these paramyxoviruses. The distribution of structurally different sialylated glycans in tissues and organs may explain in part MuV's distinct tropism to glandular tissues and the central nervous system. In the crystal structure, the epitopes for neutralizing antibodies are located around the α-helices of MuV-HN that are not well conserved in amino acid sequences among different genotypes of MuV. This may explain the fact that MuV reinfection sometimes occurs.


  • Organizational Affiliation
    • Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.

Macromolecule Content 

  • Total Structure Weight: 110.5 kDa 
  • Atom Count: 7,332 
  • Modeled Residue Count: 900 
  • Deposited Residue Count: 978 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HN protein
A, B
489Mumps orthorubulavirusMutation(s): 0 
Gene Names: HN
EC: 3.2.1.18
UniProt
Find proteins for Q9WAF5 (Mumps orthorubulavirus)
Explore Q9WAF5 
Go to UniProtKB:  Q9WAF5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WAF5
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free:  0.222 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.523α = 90
b = 137.523β = 90
c = 178.269γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata processing
XDSdata processing
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-10-26
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-11-13
    Changes: Structure summary