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Basic information

Entry
Database: PDB / ID: 7iml
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 Z1220452176 (Nprot-x0423)
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
Chem-HWH / ISOPROPYL ALCOHOL / DI(HYDROXYETHYL)ETHER / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
SARS-CoV-2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)13,5835
Polymers13,1191
Non-polymers4654
Water2,954164
1
A: Nucleoprotein
hetero molecules

A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,16710
Polymers26,2372
Non-polymers9298
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area6640 Å2
ΔGint-8 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.276, 88.276, 40.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-402-

PEG

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 168 molecules

#2: Chemical ChemComp-HWH / ~{N}-[2-(5-fluoranyl-1~{H}-indol-3-yl)ethyl]ethanamide


Mass: 220.243 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C12H13FN2O / 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H6OS / Source: (gene. exp.) SARS-CoV-2 (virus) / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.03 Å3/Da / Density % sol: 59.47 %
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: 1.55→44.138 Å / Num. obs: 11096 / % possible obs: 48.2 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.028 / Rrim(I) all: 0.07 / Net I/σ(I): 12.5 / Num. measured all: 69052
Reflection shellResolution: 1.55→1.694 Å / % possible obs: 10.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.809 / Num. measured all: 2328 / Num. unique obs: 556 / Rpim(I) all: 0.413 / Rrim(I) all: 0.917 / Net I/σ(I) obs: 1.3

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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: 1.55→44.18 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / SU B: 2.412 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25145 556 5 %RANDOM
Rwork0.19174 ---
obs0.19478 10540 48.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.209 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0 Å2
2--0.06 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.55→44.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms918 0 31 164 1113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131534
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151333
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.6641926
X-RAY DIFFRACTIONr_angle_other_deg1.2471.6113088
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.065182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.74222.60373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.35915247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.426159
X-RAY DIFFRACTIONr_chiral_restr0.0610.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021739
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02343
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_it1.8892.823764
X-RAY DIFFRACTIONr_mcbond_other1.8932.823761
X-RAY DIFFRACTIONr_mcangle_it3.0664.294889
X-RAY DIFFRACTIONr_mcangle_other3.0514.281887
X-RAY DIFFRACTIONr_scbond_it2.0243.119768
X-RAY DIFFRACTIONr_scbond_other2.0223.12769
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1334.6461036
X-RAY DIFFRACTIONr_long_range_B_refined7.28234.4891755
X-RAY DIFFRACTIONr_long_range_B_other7.2834.4931756
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 5 -
Rwork0.336 48 -
obs--3.1 %

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