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- PDB-2ge8: Structure of the C-terminal dimerization domain of infectious bro... -

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Basic information

Entry
Database: PDB / ID: 2ge8
TitleStructure of the C-terminal dimerization domain of infectious bronchitis virus nucleocapsid protein
ComponentsNucleocapsid protein
KeywordsVIRUS/VIRAL PROTEIN/RNA BINDING PROTEIN / Nucleocapsid protein / N protein / Coronavirus / IBV N protein / Dimerization domain / VIRUS-VIRAL PROTEIN-RNA BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


viral nucleocapsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / ribonucleoprotein complex / RNA binding / identical protein binding
Similarity search - Function
Nucleocapsid protein, gammacoronavirus / 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 speciesInfectious bronchitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJayaram, H. / Fan, H. / Bowman, B.R. / Ooi, A. / Jayaram, J. / Collisson, E.W. / Lescar, J. / Prasad, B.V.
CitationJournal: J.Virol. / Year: 2006
Title: X-ray structures of the N- and C-terminal domains of a coronavirus nucleocapsid protein: implications for nucleocapsid formation.
Authors: Jayaram, H. / Fan, H. / Bowman, B.R. / Ooi, A. / Jayaram, J. / Collisson, E.W. / Lescar, J. / Prasad, B.V.
History
DepositionMar 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
F: Nucleocapsid protein
G: Nucleocapsid protein
C: Nucleocapsid protein
D: Nucleocapsid protein
I: Nucleocapsid protein
J: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)102,7978
Polymers102,7978
Non-polymers00
Water00
1
A: Nucleocapsid protein
B: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)25,6992
Polymers25,6992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-37 kcal/mol
Surface area11040 Å2
MethodPISA
2
F: Nucleocapsid protein
G: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)25,6992
Polymers25,6992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-33 kcal/mol
Surface area10330 Å2
MethodPISA
3
C: Nucleocapsid protein
D: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)25,6992
Polymers25,6992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-34 kcal/mol
Surface area10930 Å2
MethodPISA
4
I: Nucleocapsid protein
J: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)25,6992
Polymers25,6992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-37 kcal/mol
Surface area10620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.990, 128.534, 71.435
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsDimer in solution and 4 dimers in assymetric unit. Hypothesized dimer-dimer interaction to form linaer arrays seen in assymetric unit with 8 molecules

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Components

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


Mass: 12849.602 Da / Num. of mol.: 8 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious bronchitis virus / Genus: Coronavirus / Strain: Gray / Gene: N / Plasmid: pET 41 Ek-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P32923

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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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 30% PEG 4000, 100 mM Tris-HCl pH 8.6, 800 mM LiCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 178 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 19, 2003
Details: Bent conical Si-mirror (Rh coated). Bent Ge(111) monochromator
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→129.473 Å / Num. all: 69504 / Num. obs: 66258 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 4.8
Reflection shellResolution: 2→2.11 Å / % possible obs: 97.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.013 / Mean I/σ(I) obs: 0.5 / Num. measured all: 35383 / Num. unique obs: 9713 / Rsym value: 0.01276

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
ADSCdata collection
CCP4(SCALA)data scaling
PHASERphasing
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GE7 4 copies

2ge7


Resolution: 2.2→47.78 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.884 / SU B: 7.789 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.309 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.291 2615 5.1 %RANDOM
Rwork0.237 ---
all0.24 69504 --
obs0.24 51179 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.178 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6881 0 0 0 6881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0227034
X-RAY DIFFRACTIONr_angle_refined_deg1.9191.9779483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3735866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14423.582335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.133151224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0021562
X-RAY DIFFRACTIONr_chiral_restr0.1420.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025456
X-RAY DIFFRACTIONr_nbd_refined0.2510.23205
X-RAY DIFFRACTIONr_nbtor_refined0.3220.24657
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2400
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2850.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4730.28
X-RAY DIFFRACTIONr_mcbond_it1.0661.54465
X-RAY DIFFRACTIONr_mcangle_it1.71927071
X-RAY DIFFRACTIONr_scbond_it2.90632815
X-RAY DIFFRACTIONr_scangle_it4.5314.52412
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 166 -
Rwork0.279 3128 -
obs-3294 100 %

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