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- PDB-9rxl: SARS-CoV-2 nucleocapsid C-terminal domain in complex with BCY00018176 -

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Basic information

Entry
Database: PDB / ID: 9rxl
TitleSARS-CoV-2 nucleocapsid C-terminal domain in complex with BCY00018176
Components
  • BCY00018176
  • Nucleoprotein
KeywordsVIRAL PROTEIN / bicyclic peptides / antibody mimic / ELISA / LFIA / diagnostic
Function / homology
Function and homology information


response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / Maturation of nucleoprotein / poly(U) RNA binding / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / VEGFR2 mediated vascular permeability ...response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / Maturation of nucleoprotein / poly(U) RNA binding / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / VEGFR2 mediated vascular permeability / protein sequestering activity / molecular condensate scaffold activity / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / MHC class I protein complex / DDX58/IFIH1-mediated induction of interferon-alpha/beta / RNA stem-loop binding / Interleukin-1 signaling / Interferon alpha/beta signaling / viral capsid / PIP3 activates AKT signaling / viral nucleocapsid / Transcription of SARS-CoV-2 sgRNAs / Translation of Structural Proteins / Virion Assembly and Release / host cell endoplasmic reticulum-Golgi intermediate compartment / host extracellular region / Induction of Cell-Cell Fusion / host cell Golgi apparatus / Attachment and Entry / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / RNA binding / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile.
Similarity search - Domain/homology
Chem-LFI / Nucleoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsBrear, P. / Lulla, A. / Dods, R. / Bezerra, G.A. / Hyvonen, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: Acs Nano / Year: 2026
Title: Utilizing Constrained Bicyclic Peptides for In Vitro Diagnostics.
Authors: Shamsabadi, A. / Creamer, A. / Sadler, C.J. / Abdelwahed, A. / Gaynor, K.U. / Demydchuk, Y. / Ivanova-Berndt, G. / Van Rietschoten, K. / Beswick, P. / Chen, L. / Arruda Bezerra, G. / Lulla, ...Authors: Shamsabadi, A. / Creamer, A. / Sadler, C.J. / Abdelwahed, A. / Gaynor, K.U. / Demydchuk, Y. / Ivanova-Berndt, G. / Van Rietschoten, K. / Beswick, P. / Chen, L. / Arruda Bezerra, G. / Lulla, A. / Brear, P. / Hyvonen, M. / Skynner, M.J. / Stevens, M.M.
History
DepositionJul 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BCY00018176
B: BCY00018176
C: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7218
Polymers34,5534
Non-polymers1,1684
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-50 kcal/mol
Surface area13370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.043, 73.043, 116.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein/peptide BCY00018176


Mass: 1757.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 15519.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC9
#3: Chemical ChemComp-LFI / 1-[3,5-bis(3-bromanylpropanoyl)-1,3,5-triazinan-1-yl]-3-bromanyl-propan-1-one / Chemical crosslinker


Mass: 492.002 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18Br3N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Na Acet 4.6 pH,25 % w/v PEG 4K., 0.2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.46→61.94 Å / Num. obs: 55845 / % possible obs: 100 % / Redundancy: 64.8 % / CC1/2: 1 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.026 / Rrim(I) all: 0.208 / Χ2: 0.88 / Net I/σ(I): 18.6 / Num. measured all: 3616304
Reflection shellResolution: 1.46→1.54 Å / % possible obs: 100 % / Redundancy: 65.3 % / Rmerge(I) obs: 9.656 / Num. measured all: 522583 / Num. unique obs: 8002 / CC1/2: 0.421 / Rpim(I) all: 1.196 / Rrim(I) all: 9.73 / Χ2: 0.75 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→61.94 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.635 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21449 2705 4.9 %RANDOM
Rwork0.18285 ---
obs0.1844 52919 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.798 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2---0.41 Å20 Å2
3---0.82 Å2
Refinement stepCycle: 1 / Resolution: 1.46→61.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 50 340 2453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132248
X-RAY DIFFRACTIONr_bond_other_d0.0040.0162136
X-RAY DIFFRACTIONr_angle_refined_deg1.811.6873043
X-RAY DIFFRACTIONr_angle_other_deg4.0981.624920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0715278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54122.241116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53115371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1981515
X-RAY DIFFRACTIONr_chiral_restr0.0850.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022623
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02531
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2152.3921095
X-RAY DIFFRACTIONr_mcbond_other2.2112.3911094
X-RAY DIFFRACTIONr_mcangle_it3.1013.5571372
X-RAY DIFFRACTIONr_mcangle_other3.1023.5581373
X-RAY DIFFRACTIONr_scbond_it3.2222.71153
X-RAY DIFFRACTIONr_scbond_other3.222.71154
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8773.9231670
X-RAY DIFFRACTIONr_long_range_B_refined6.47429.5952610
X-RAY DIFFRACTIONr_long_range_B_other6.2628.7452528
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.46→1.496 Å
RfactorNum. reflection% reflection
Rfree0.378 214 -
Rwork0.373 3744 -
obs--97.51 %

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