4L72

Crystal structure of MERS-CoV complexed with human DPP4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.005 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of MERS-CoV spike receptor-binding domain complexed with human receptor DPP4

Wang, N.Shi, X.Jiang, L.Zhang, S.Wang, D.Tong, P.Guo, D.Fu, L.Cui, Y.Liu, X.Arledge, K.C.Chen, Y.H.Zhang, L.Wang, X.

(2013) Cell Res. 23: 986-993

  • DOI: 10.1038/cr.2013.92

  • PubMed Abstract: 
  • The spike glycoprotein (S) of recently identified Middle East respiratory syndrome coronavirus (MERS-CoV) targets the cellular receptor, dipeptidyl peptidase 4 (DPP4). Sequence comparison and modeling analysis have revealed a putative receptor-bindin ...

    The spike glycoprotein (S) of recently identified Middle East respiratory syndrome coronavirus (MERS-CoV) targets the cellular receptor, dipeptidyl peptidase 4 (DPP4). Sequence comparison and modeling analysis have revealed a putative receptor-binding domain (RBD) on the viral spike, which mediates this interaction. We report the 3.0 Å-resolution crystal structure of MERS-CoV RBD bound to the extracellular domain of human DPP4. Our results show that MERS-CoV RBD consists of a core and a receptor-binding subdomain. The receptor-binding subdomain interacts with DPP4 β-propeller but not its intrinsic hydrolase domain. MERS-CoV RBD and related SARS-CoV RBD share a high degree of structural similarity in their core subdomains, but are notably divergent in the receptor-binding subdomain. Mutagenesis studies have identified several key residues in the receptor-binding subdomain that are critical for viral binding to DPP4 and entry into the target cell. The atomic details at the interface between MERS-CoV RBD and DPP4 provide structural understanding of the virus and receptor interaction, which can guide development of therapeutics and vaccines against MERS-CoV infection.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl peptidase 4
A
728Homo sapiensMutation(s): 0 
Gene Names: DPP4 (ADCP2, CD26)
EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens)
Go to Gene View: DPP4
Go to UniProtKB:  P27487
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MERS-CoV RBD
B
204Middle East respiratory syndrome-related coronavirusMutation(s): 0 
Find proteins for R9UQ53 (Middle East respiratory syndrome-related coronavirus)
Go to UniProtKB:  R9UQ53
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.005 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.205 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 110.609α = 90.00
b = 110.609β = 90.00
c = 527.713γ = 120.00
Software Package:
Software NamePurpose
PHASESphasing
HKL-2000data collection
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-06-13 
  • Released Date: 2013-08-21 
  • Deposition Author(s): Wang, X.Q., Wang, N.S.

Revision History 

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-09-04
    Type: Database references
  • Version 1.2: 2015-07-22
    Type: Source and taxonomy, Structure summary