8IDO | pdb_00008ido

Crystal structure of nanobody VHH-T148 with MERS-CoV RBD

PDB DOI: https://doi.org/10.2210/pdb8IDO/pdb

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

Deposited: 2023-02-14 Released: 2024-02-28
Deposition Author(s): Wang, X., Tian, L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.262 (Depositor), 0.258 (DCC)
R-Value Work:
0.220 (Depositor)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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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: 81.94 kDa
Atom Count: 5,405
Modeled Residue Count: 651
Deposited Residue Count: 728
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth B], B [auth A]	229	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0 Gene Names: S
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 B [auth A]
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH-T148	C, D	135	Camelus dromedarius	Mutation(s): 0

Oligosaccharides

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	5		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.262 (Depositor), 0.258 (DCC)
R-Value Work: 0.220 (Depositor)
R-Value Observed: 0.222 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.896	α = 90
b = 47.19	β = 90
c = 124.213	γ = 90

Software Package:

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

Structure Validation

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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: 2024-11-20
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.