4XL8

Crystal Structure of Human Adenovirus 52 Short Fiber Knob in Complex with 2-O-Methyl-5-N-Acetylneuraminic Acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Human Adenovirus 52 Uses Sialic Acid-containing Glycoproteins and the Coxsackie and Adenovirus Receptor for Binding to Target Cells.

Lenman, A.Liaci, A.M.Liu, Y.Ardahl, C.Rajan, A.Nilsson, E.Bradford, W.Kaeshammer, L.Jones, M.S.Frangsmyr, L.Feizi, T.Stehle, T.Arnberg, N.

(2015) Plos Pathog. 11: e1004657-e1004657

  • DOI: 10.1371/journal.ppat.1004657

  • PubMed Abstract: 
  • Most adenoviruses attach to host cells by means of the protruding fiber protein that binds to host cells via the coxsackievirus and adenovirus receptor (CAR) protein. Human adenovirus type 52 (HAdV-52) is one of only three gastroenteritis-causing HAd ...

    Most adenoviruses attach to host cells by means of the protruding fiber protein that binds to host cells via the coxsackievirus and adenovirus receptor (CAR) protein. Human adenovirus type 52 (HAdV-52) is one of only three gastroenteritis-causing HAdVs that are equipped with two different fiber proteins, one long and one short. Here we show, by means of virion-cell binding and infection experiments, that HAdV-52 can also attach to host cells via CAR, but most of the binding depends on sialylated glycoproteins. Glycan microarray, flow cytometry, surface plasmon resonance and ELISA analyses reveal that the terminal knob domain of the long fiber (52LFK) binds to CAR, and the knob domain of the short fiber (52SFK) binds to sialylated glycoproteins. X-ray crystallographic analysis of 52SFK in complex with 2-O-methylated sialic acid combined with functional studies of knob mutants revealed a new sialic acid binding site compared to other, known adenovirus:glycan interactions. Our findings shed light on adenovirus biology and may help to improve targeting of adenovirus-based vectors for gene therapy.


    Organizational Affiliation

    Division of Virology, Department of Clinical Microbiology, Umeå University, Umeå, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fiber-1
A, B, C
209Human adenovirus 52Mutation(s): 0 
Find proteins for A0MK70 (Human adenovirus 52)
Go to UniProtKB:  A0MK70
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MRD
Query on MRD

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Download CCD File 
C
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
GLU
Query on GLU

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Download CCD File 
B
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
ALA
Query on ALA

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Download CCD File 
B
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
 Ligand Interaction
TAM
Query on TAM

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Download CCD File 
B
TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
 Ligand Interaction
MNA
Query on MNA

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Download CCD File 
A, C
2-O-METHYL-5-N-ACETYL-ALPHA-D- NEURAMINIC ACID
C12 H21 N O9
NJRVVFURCKKXOD-MIDKXNQYSA-N
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
C
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.770α = 90.00
b = 81.610β = 90.00
c = 92.650γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB 685

Revision History 

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-02-11
    Type: Other
  • Version 1.2: 2015-03-04
    Type: Database references
  • Version 1.3: 2015-07-22
    Type: Database references
  • Version 2.0: 2017-09-06
    Type: Advisory, Atomic model, Author supporting evidence, Derived calculations