8IDI | pdb_00008idi

Crystal structure of nanobody VHH-T71 with MERS-CoV RBD

• PDB DOI: https://doi.org/10.2210/pdb8IDI/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Camelus dromedarius, Middle East respiratory syndrome-related coronavirus
• Expression System: Homo sapiens, Trichoplusia ni
• Mutation(s): No 


• Deposited: 2023-02-13 Released: 2024-02-28 
• Deposition Author(s): Wang, X., Tian, L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Models: experimental

Literature

Structural Definition of a Novel Nanobody Binding Site specifically targeting the MERS-CoV RBD Core-Domain with Neutralizing Capacity

Idoudi, F., Wang, R., Tian, L., Zhang, L., Wang, X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 82.24 kDa 
• Atom Count: 6,144 
• Modeled Residue Count: 676 
• Deposited Residue Count: 732 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH-T71	A, C	137	Camelus dromedarius	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B, D	229	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: S
UniProt
Find proteins for K9N5Q8 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)) Explore K9N5Q8  Go to UniProtKB:  K9N5Q8
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	5		N-Glycosylation

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 238.549	α = 90
b = 46.835	β = 112.52
c = 95.946	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
HKL-2000	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-28 
Deposition Author(s): Wang, X., Tian, L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-02-28
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary