8IDM | pdb_00008idm

Crystal structure of nanobody VHH-227 with nanobody VHH-T71 and MERS-CoV RBD

• PDB DOI: https://doi.org/10.2210/pdb8IDM/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: 3.59 Å
• R-Value Free: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.254 (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: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 55.9 kDa 
• Atom Count: 3,635 
• Modeled Residue Count: 466 
• Deposited Residue Count: 500 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH-227	A [auth B]	135	Camelus dromedarius	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH-T71	B [auth A]	136	Camelus dromedarius	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C [auth D]	229	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0
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: 2

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	F [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.59 Å
• R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.44	α = 90
b = 104.44	β = 90
c = 318.223	γ = 120

Software Package:

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

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: 2024-10-30
  Changes: Structure summary