7COE

Crystal structure of Receptor binding domain of MERS-CoV and KNIH90-F1 Fab complex

PDB DOI: https://doi.org/10.2210/pdb7COE/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Middle East respiratory syndrome-related coronavirus
Expression System: Homo sapiens, Spodoptera frugiperda
Mutation(s): No

Deposited: 2020-08-04 Released: 2021-08-04
Deposition Author(s): Lee, J.Y., Song, J.Y., Lee, H.S., Hong, E., Jang, T.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.223
R-Value Work: 0.176

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The structure of a novel antibody against the spike protein inhibits Middle East respiratory syndrome coronavirus infections.

Jang, T.H., Park, W.J., Lee, H., Woo, H.M., Lee, S.Y., Kim, K.C., Kim, S.S., Hong, E., Song, J., Lee, J.Y.

(2022) Sci Rep 12: 1260-1260

PubMed: 35075213 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41598-022-05318-4
Primary Citation of Related Structures:
7COE

PubMed Abstract:
Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic virus, responsible for outbreaks of a severe respiratory illness in humans with a fatality rate of 30%. Currently, there are no vaccines or United States food and drug administration (FDA)-approved therapeutics for humans. The spike protein displayed on the surface of MERS-CoV functions in the attachment and fusion of virions to host cellular membranes and is the target of the host antibody response. Here, we provide a molecular method for neutralizing MERS-CoV through potent antibody-mediated targeting of the receptor-binding subdomain (RBD) of the spike protein. The structural characterization of the neutralizing antibody (KNIH90-F1) complexed with RBD using X-ray crystallography revealed three critical epitopes (D509, R511, and E513) in the RBD region of the spike protein. Further investigation of MERS-CoV mutants that escaped neutralization by the antibody supported the identification of these epitopes in the RBD region. The neutralizing activity of this antibody is solely provided by these specific molecular structures. This work should contribute to the development of vaccines or therapeutic antibodies for MERS-CoV.

Organizational Affiliation

New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea.

Macromolecule Content

Total Structure Weight: 148.5 kDa
Atom Count: 10,840
Modelled Residue Count: 1,286
Deposited Residue Count: 1,350
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain	A [auth H], D [auth B]	237	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain	B [auth L], E [auth C]	215	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth A], F [auth D]	223	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	K9N5Q8
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain C [auth A] Focus chain F [auth D]
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain W [auth A] SDF format, chain X [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A]	KA [auth D], LA [auth D], W [auth A], X [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain KA [auth D] Focus chain LA [auth D] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain KA [auth D] Focus chain LA [auth D] Focus chain W [auth A] Focus chain X [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain G [auth H] SDF format, chain GA [auth C] SDF format, chain H SDF format, chain HA [auth C] SDF format, chain I [auth H] SDF format, chain IA [auth D] SDF format, chain J [auth H] SDF format, chain JA [auth D] SDF format, chain K [auth H] SDF format, chain L [auth H] SDF format, chain M [auth H] SDF format, chain MA [auth D] SDF format, chain N [auth H] SDF format, chain O [auth H] SDF format, chain P [auth H] SDF format, chain Q [auth H] SDF format, chain S [auth L] SDF format, chain T [auth L] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth B] SDF format, chain R [auth L] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth H] MOL2 format, chain GA [auth C] MOL2 format, chain H MOL2 format, chain HA [auth C] MOL2 format, chain I [auth H] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth H] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] MOL2 format, chain M [auth H] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth H] MOL2 format, chain O [auth H] MOL2 format, chain P [auth H] MOL2 format, chain Q [auth H] MOL2 format, chain S [auth L] MOL2 format, chain T [auth L] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain R [auth L] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth H] mmCIF format, chain GA [auth C] mmCIF format, chain H mmCIF format, chain HA [auth C] mmCIF format, chain I [auth H] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth H] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth H] mmCIF format, chain L [auth H] mmCIF format, chain M [auth H] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth H] mmCIF format, chain O [auth H] mmCIF format, chain P [auth H] mmCIF format, chain Q [auth H] mmCIF format, chain S [auth L] mmCIF format, chain T [auth L] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain R [auth L]	AA [auth B] BA [auth B] CA [auth B] DA [auth C] EA [auth C] AA [auth B], BA [auth B], CA [auth B], DA [auth C], EA [auth C], FA [auth C], G [auth H], GA [auth C], H, HA [auth C], I [auth H], IA [auth D], J [auth H], JA [auth D], K [auth H], L [auth H], M [auth H], MA [auth D], N [auth H], O [auth H], P [auth H], Q [auth H], R [auth L], S [auth L], T [auth L], U [auth A], V [auth A], Y [auth A], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth H] Focus chain GA [auth C] Focus chain H Focus chain HA [auth C] Focus chain I [auth H] Focus chain IA [auth D] Focus chain J [auth H] Focus chain JA [auth D] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain MA [auth D] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth H] Focus chain R [auth L] Focus chain S [auth L] Focus chain T [auth L] Focus chain U [auth A] Focus chain V [auth A] Focus chain Y [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth H] Focus chain GA [auth C] Focus chain H Focus chain HA [auth C] Focus chain I [auth H] Focus chain IA [auth D] Focus chain J [auth H] Focus chain JA [auth D] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain MA [auth D] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth H] Focus chain R [auth L] Focus chain S [auth L] Focus chain T [auth L] Focus chain U [auth A] Focus chain V [auth A] Focus chain Y [auth A] Focus chain Z [auth B]