Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 116.10 kDa 
• Atom Count: 7944 
• Residue Count: 936 
• Unique protein chains: 2

4KR0

Complex structure of MERS-CoV spike RBD bound to CD26

• DOI: 10.2210/pdb4KR0/pdb

• Classification: HYDROLASE/VIRAL PROTEIN
• Organism(s): Homo sapiens, Human betacoronavirus 2c EMC/2012
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2013-05-15 Released: 2013-07-10 
• Deposition Author(s): Lu, G., Hu, Y., Wang, Q., Qi, J., Gao, F., Li, Y., Zhang, Y., Zhang, W., Yuan, Y., Zhang, B., Shi, Y., Yan, J., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.232 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26.

Lu, G., Hu, Y., Wang, Q., Qi, J., Gao, F., Li, Y., Zhang, Y., Zhang, W., Yuan, Y., Bao, J., Zhang, B., Shi, Y., Yan, J., Gao, G.F.

(2013) Nature 500: 227-231

• PubMed: 23831647 
• DOI: 10.1038/nature12328
• Primary Citation of Related Structures:  
  4KR0, 4KQZ


• PubMed Abstract: 
  

The newly emergent Middle East respiratory syndrome coronavirus (MERS-CoV) can cause severe pulmonary disease in humans, representing the second example of a highly pathogenic coronavirus, the first being SARS-CoV. CD26 (also known as dipeptidyl peptidase 4, DPP4) was recently identified as the cellular receptor for MERS-CoV. The engagement of the MERS-CoV spike protein with CD26 mediates viral attachment to host cells and virus-cell fusion, thereby initiating infection. Here we delineate the molecular basis of this specific interaction by presenting the first crystal structures of both the free receptor binding domain (RBD) of the MERS-CoV spike protein and its complex with CD26. Furthermore, binding between the RBD and CD26 is measured using real-time surface plasmon resonance with a dissociation constant of 16.7 nM. The viral RBD is composed of a core subdomain homologous to that of the SARS-CoV spike protein, and a unique strand-dominated external receptor binding motif that recognizes blades IV and V of the CD26 β-propeller. The atomic details at the interface between the two binding entities reveal a surprising protein-protein contact mediated mainly by hydrophilic residues. Sequence alignment indicates, among betacoronaviruses, a possible structural conservation for the region homologous to the MERS-CoV RBD core, but a high variation in the external receptor binding motif region for virus-specific pathogenesis such as receptor recognition.

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Organizational Affiliation: 

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4	A	739	Homo sapiens	Mutation(s): 0  Gene Names: ADCP2, CD26, DPP4 EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens) Explore P27487  Go to UniProtKB:  P27487
NIH Common Fund Data Resources
PHAROS:  P27487 GTEx:  ENSG00000197635

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S protein	B	251	Human betacoronavirus 2c EMC/2012	Mutation(s): 0  Gene Names: S, spike
Find proteins for K0BRG7 (Human betacoronavirus 2c EMC/2012) Explore K0BRG7  Go to UniProtKB:  K0BRG7

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, F, G	2		N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.232 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.224	α = 90
b = 110.224	β = 90
c = 527.599	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-05-15 
• Released Date: 2013-07-10 
Deposition Author(s): Lu, G., Hu, Y., Wang, Q., Qi, J., Gao, F., Li, Y., Zhang, Y., Zhang, W., Yuan, Y., Zhang, B., Shi, Y., Yan, J., Gao, G.F.

Revision History 

• Version 1.0: 2013-07-10
  Type: Initial release
  
• Version 1.1: 2013-08-14
  Changes: Database references
• Version 1.2: 2019-12-18
  Changes: Database references, Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary