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 
  • R-Value Observed: 0.152 

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Ligand Structure Quality Assessment 


This is version 2.2 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
  • Primary Citation of Related Structures:  
    4XL8

  • 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 HAdVs that are equipped with two different fiber proteins, one long and one short ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fiber-1A, B, C209Human adenovirus 52Mutation(s): 0 
UniProt
Find proteins for A0MK70 (Human adenovirus 52)
Explore A0MK70 
Go to UniProtKB:  A0MK70
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0MK70
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MNA
Query on MNA

Download Ideal Coordinates CCD File 
D [auth A],
I [auth C]
2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid
C12 H21 N O9
NJRVVFURCKKXOD-MIDKXNQYSA-N
 Ligand Interaction
TAM
Query on TAM

Download Ideal Coordinates CCD File 
F [auth B]TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
 Ligand Interaction
GLU
Query on GLU

Download Ideal Coordinates CCD File 
G [auth B]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
MRD
Query on MRD

Download Ideal Coordinates CCD File 
K [auth C](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
J [auth C](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ALA
Query on ALA

Download Ideal Coordinates CCD File 
H [auth B]ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-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 
  • R-Value Observed: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.77α = 90
b = 81.61β = 90
c = 92.65γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB 685

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-02-11
    Changes: Other
  • Version 1.2: 2015-03-04
    Changes: Database references
  • Version 1.3: 2015-07-22
    Changes: Database references
  • Version 2.0: 2017-09-06
    Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations
  • Version 2.1: 2019-10-16
    Changes: Data collection
  • Version 2.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary