7YLB | pdb_00007ylb

Two monobodies recognizing the conserved epitopes of SARS-CoV-2 N antigen applicable to the broad COVID-19 diagnosis

PDB DOI: https://doi.org/10.2210/pdb7YLB/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-07-26 Released: 2023-09-06
Deposition Author(s): Hu, M., Du, Y., Sun, R., Hao, Q.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.326 (Depositor), 0.283 (DCC)
R-Value Work:
0.267 (Depositor), 0.272 (DCC)
R-Value Observed:
0.270 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7YLB

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

Literature

Two monobodies recognizing the conserved epitopes of SARS-CoV-2 N antigen applicable to the broad COVID-19 diagnosis

Hu, M., Du, Y., Sun, R., Hao, Q.

To be published.

Macromolecule Content

Total Structure Weight: 150.42 kDa
Atom Count: 9,739
Modeled Residue Count: 1,221
Deposited Residue Count: 1,352
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A [auth C] B [auth D] D [auth A] E [auth B] G A [auth C], B [auth D], D [auth A], E [auth B], G, H, J, K	122	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC9 Go to UniProtKB: P0DTC9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NC2	C [auth F], F [auth E], I, L	94	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth K] SDF format, chain O [auth H] SDF format, chain N [auth B] SDF format, chain M [auth D] MOL2 format, chain P [auth K] MOL2 format, chain O [auth H] MOL2 format, chain N [auth B] MOL2 format, chain M [auth D] mmCIF format, chain P [auth K] mmCIF format, chain O [auth H] mmCIF format, chain N [auth B] mmCIF format, chain M [auth D]	M [auth D], N [auth B], O [auth H], P [auth K]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth D] Focus chain N [auth B] Focus chain O [auth H] Focus chain P [auth K] Interactions & Density Focus chain M [auth D] Focus chain N [auth B] Focus chain O [auth H] Focus chain P [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.326 (Depositor), 0.283 (DCC)
R-Value Work: 0.267 (Depositor), 0.272 (DCC)
R-Value Observed: 0.270 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.081	α = 90
b = 48.458	β = 105.16
c = 143.247	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-09-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-09-06
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.