8IFN | pdb_00008ifn

MERS-CoV spike trimer in complex with nanobody VHH-T148

PDB DOI: https://doi.org/10.2210/pdb8IFN/pdb
EM Map EMD-35422: EMDB EMDataResource

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

Deposited: 2023-02-19 Released: 2024-02-28
Deposition Author(s): Wang, X., Tian, L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.81 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8IFN

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

Literature

Structures and neutralizing mechanisms of camel nanobodies targeting the receptor-binding domain of MERS-CoV spike glycoprotein

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

To be published.

Macromolecule Content

Total Structure Weight: 491.85 kDa
Atom Count: 30,441
Modeled Residue Count: 3,924
Deposited Residue Count: 4,446
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth B], C, E	1,347	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
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth B] Focus chain C Focus chain E
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH-T148	B [auth A], D, F	135	Camelus dromedarius	Mutation(s): 0

Oligosaccharides

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I	4		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Interactions & Density Focus chain G Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.81 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-02-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-02-28
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, 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.