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- PDB-2gib: Crystal structure of the SARS coronavirus nucleocapsid protein di... -

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Basic information

Entry
Database: PDB / ID: 2gib
TitleCrystal structure of the SARS coronavirus nucleocapsid protein dimerization domain
ComponentsNucleocapsid protein
KeywordsVIRAL PROTEIN / SARS / nucleocapsid / dimer
Function / homology
Function and homology information


SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / negative regulation of interferon-beta production / Maturation of nucleoprotein / SARS-CoV-1 modulates host translation machinery / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry ...SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / negative regulation of interferon-beta production / Maturation of nucleoprotein / SARS-CoV-1 modulates host translation machinery / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry / SARS-CoV-1 activates/modulates innate immune responses / viral capsid / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / host cell Golgi apparatus / molecular adaptor activity / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / host cell nucleus / DNA binding / RNA binding / identical protein binding / plasma membrane
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
Biological speciesSARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsYu, I.M. / Oldham, M.L. / Zhang, J. / Chen, J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal structure of the severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein dimerization domain reveals evolutionary linkage between corona- and arteriviridae.
Authors: Yu, I.M. / Oldham, M.L. / Zhang, J. / Chen, J.
History
DepositionMar 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleocapsid protein
B: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2063
Polymers23,1102
Non-polymers961
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-27 kcal/mol
Surface area10880 Å2
MethodPISA
2
A: Nucleocapsid protein
B: Nucleocapsid protein
hetero molecules

A: Nucleocapsid protein
B: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4126
Polymers46,2204
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area9630 Å2
ΔGint-93 kcal/mol
Surface area20860 Å2
MethodPISA
3
A: Nucleocapsid protein
B: Nucleocapsid protein
hetero molecules

A: Nucleocapsid protein
B: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4126
Polymers46,2204
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9860 Å2
ΔGint-68 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.163, 50.490, 41.479
Angle α, β, γ (deg.)90.00, 108.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-371-

SO4

21A-229-

HOH

DetailsThe biologic assembly is a dimer as found in the asymmetric unit

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Components

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


Mass: 11554.877 Da / Num. of mol.: 2 / Fragment: dimerization domain (residues 270-370)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Gene: N / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P59595
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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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: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 277.5 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30-33% Pentaerythritol ethoxylate 15/4 EO/OH, 50 mM Ammonium sulfate, 50 mM Bis-Tris , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929, 0.97940, 0.94285
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2005
RadiationMonochromator: Rosenbaum-Rock monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.97941
30.942851
ReflectionResolution: 1.75→30.93 Å / Num. all: 23293 / Num. obs: 23088 / % possible obs: 99.12 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.75→1.795 Å / % possible all: 96.12

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→30.93 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.535 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23451 1166 4.8 %RANDOM
Rwork0.18726 ---
all0.18951 23293 --
obs0.18951 23088 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.965 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å2-0.47 Å2
2---0.76 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 5 212 1727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221560
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.9312121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0365191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3624.74478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43815233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.965156
X-RAY DIFFRACTIONr_chiral_restr0.1260.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021241
X-RAY DIFFRACTIONr_nbd_refined0.230.2720
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21067
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.2169
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5380.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4190.230
X-RAY DIFFRACTIONr_mcbond_it1.6271.5987
X-RAY DIFFRACTIONr_mcangle_it2.17721539
X-RAY DIFFRACTIONr_scbond_it3.1243662
X-RAY DIFFRACTIONr_scangle_it3.9124.5582
X-RAY DIFFRACTIONr_rigid_bond_restr2.14231649
X-RAY DIFFRACTIONr_sphericity_free7.7653212
X-RAY DIFFRACTIONr_sphericity_bonded3.05231516
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 75 -
Rwork0.163 1649 -
obs-1649 96.21 %

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