8TMZ | pdb_00008tmz

Crystal structure of MERS-CoV spike stem helix peptide in complex with neutralizing antibody CHM-27

• PDB DOI: https://doi.org/10.2210/pdb8TMZ/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Macaca mulatta, Middle East respiratory syndrome-related coronavirus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-07-31 Released: 2024-07-31 
• Deposition Author(s): Yuan, M., Wilson, I.A.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.294 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: experimental

Literature

Broad Neutralizing Antibodies Against Coronaviruses.

Feng, Z., Wilson, I.A.

Not Published 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content 

• Total Structure Weight: 48.75 kDa 
• Atom Count: 3,419 
• Modeled Residue Count: 435 
• Deposited Residue Count: 460 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutralizing antibody CHM-27 Heavy Chain	A [auth H]	217	Macaca mulatta	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutralizing antibody CHM-27 Light Chain	B [auth L]	216	Macaca mulatta	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stem helix peptide of Spike glycoprotein	C [auth A]	27	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth L]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.294 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.057	α = 90
b = 71.402	β = 106
c = 74.571	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Yuan, M., Wilson, I.A.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	INV-004923

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary