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Entry
Database: PDB / ID: 7im8
TitleGroup deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z31478538 (Nprot-x0359)
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Diamond I04-1 / PanDDA2 / XChemExplorer / crystallographic fragment screening / SARS-CoV-2 / nucleocapsid protein / N protein
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 / molecular condensate scaffold activity / protein sequestering activity / MHC class I protein complex / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / RNA stem-loop binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Interleukin-1 signaling / viral capsid / Interferon alpha/beta signaling / PIP3 activates AKT signaling / viral nucleocapsid / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / Translation of Structural Proteins / Virion Assembly and Release / Lectin pathway of complement activation / host extracellular region / Induction of Cell-Cell Fusion / Initial triggering of complement / 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 / DNA-templated transcription / 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
ISOPROPYL ALCOHOL / DI(HYDROXYETHYL)ETHER / N-Benzyl-2-methoxyacetamide / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
SARS-CoV-2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAschenbrenner, J.C. / Luptak, J. / Balcomb, B.H. / Marples, P.G. / Bellini, D. / Yu, C.W. / Douangamath, A. / Dias, A. / Powell, A. / Fearon, D. ...Aschenbrenner, J.C. / Luptak, J. / Balcomb, B.H. / Marples, P.G. / Bellini, D. / Yu, C.W. / Douangamath, A. / Dias, A. / Powell, A. / Fearon, D. / James, L. / von Delft, F.
CitationJournal: To Be Published
Title: Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD)
Authors: Luptak, J. / Aschenbrenner, J.C. / Balcomb, B.H. / Marples, P.G. / Bellini, D. / Yu, C.W. / Douangamath, A. / Dias, A. / Powell, A. / Fearon, D. / James, L. / von Delft, F.
History
DepositionAug 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4644
Polymers13,1191
Non-polymers3453
Water2,720151
1
A: Nucleoprotein
hetero molecules

A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9288
Polymers26,2372
Non-polymers6916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area6180 Å2
ΔGint-11 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.278, 88.278, 40.644
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 13118.743 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC9
#2: Chemical ChemComp-T9Q / N-Benzyl-2-methoxyacetamide / 2-methoxy-~{N}-(phenylmethyl)ethanamide


Mass: 179.216 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H13NO2 / Source: (gene. exp.) SARS-CoV-2 (virus) / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C4H10O3 / Source: (gene. exp.) SARS-CoV-2 (virus) / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O / Source: (gene. exp.) SARS-CoV-2 (virus) / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.1 M HEPES, pH 7.8, 10 % isopropanol, 23 % PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91261 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91261 Å / Relative weight: 1
ReflectionResolution: 1.649→44.139 Å / Num. obs: 9304 / % possible obs: 48.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.033 / Rrim(I) all: 0.083 / Net I/σ(I): 10.3 / Num. measured all: 58955
Reflection shellResolution: 1.649→1.791 Å / % possible obs: 11.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.83 / Num. measured all: 2347 / Num. unique obs: 466 / Rpim(I) all: 0.394 / Rrim(I) all: 0.924 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YUN

6yun


Resolution: 1.65→62.42 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.905 / SU B: 4.167 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 452 4.9 %RANDOM
Rwork0.19119 ---
obs0.19462 8853 48.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.776 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0 Å2-0 Å2
2--0.26 Å2-0 Å2
3----0.52 Å2
Refinement stepCycle: 1 / Resolution: 1.65→62.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms918 0 24 151 1093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0153320
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152266
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.6663209
X-RAY DIFFRACTIONr_angle_other_deg1.1661.6145259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9465303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89822.479121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29815420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3091516
X-RAY DIFFRACTIONr_chiral_restr0.0560.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022845
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02563
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_it1.5573.111697
X-RAY DIFFRACTIONr_mcbond_other1.6283.0971552
X-RAY DIFFRACTIONr_mcangle_it3.0684.5811469
X-RAY DIFFRACTIONr_mcangle_other3.0674.5821470
X-RAY DIFFRACTIONr_scbond_it1.2443.2921619
X-RAY DIFFRACTIONr_scbond_other1.2443.2911620
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2584.8431737
X-RAY DIFFRACTIONr_long_range_B_refined6.63436.1722951
X-RAY DIFFRACTIONr_long_range_B_other6.43935.9292866
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.59 2 -
Rwork0.351 45 -
obs--3.32 %

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