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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.294 (Depositor), 0.294 (DCC)
R-Value Work:
0.244 (Depositor), 0.245 (DCC)
R-Value Observed:
0.247 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Broad Neutralizing Antibodies Against Coronaviruses.

Feng, Z., Wilson, I.A.

Not Published

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

Find similar proteins by:

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

Find similar proteins by:

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K9N5Q8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth L] MOL2 format, chain D [auth L] mmCIF format, chain D [auth L]	D [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth L] Interactions & Density Focus chain D [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.294 (Depositor), 0.294 (DCC)
R-Value Work: 0.244 (Depositor), 0.245 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-31

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.