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- PDB-4o6h: 2.8A crystal structure of Lymphocytic Choriomeningitis Virus Nucl... -

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Basic information

Entry
Database: PDB / ID: 4o6h
Title2.8A crystal structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-terminal Domain
ComponentsNucleoprotein
KeywordsHYDROLASE / Exoribonuclease
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / host cell cytoplasm / hydrolase activity / ribonucleoprotein complex / RNA binding / metal ion binding
Similarity search - Function
Nucleocapsid protein, arenaviridae / Nucleocapsid, N-terminal, Arenaviridae / Nucleocapsid, C-terminal, Arenaviridae / Nucleocapsid, C-terminal superfamily / Arenavirus nucleocapsid N-terminal domain / Arenavirus nucleocapsid C-terminal domain
Similarity search - Domain/homology
IMIDAZOLE / : / Nucleoprotein
Similarity search - Component
Biological speciesLymphocytic choriomeningitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWest, B.R. / Hastie, K.M. / Saphire, E.O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of the LCMV nucleoprotein provides a template for understanding arenavirus replication and immunosuppression.
Authors: West, B.R. / Hastie, K.M. / Saphire, E.O.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
F: Nucleoprotein
G: Nucleoprotein
H: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,25428
Polymers211,2018
Non-polymers1,05320
Water00
1
A: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0647
Polymers52,8002
Non-polymers2635
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-12 kcal/mol
Surface area18950 Å2
MethodPISA
2
B: Nucleoprotein
hetero molecules

C: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0647
Polymers52,8002
Non-polymers2635
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area1940 Å2
ΔGint-11 kcal/mol
Surface area18850 Å2
MethodPISA
3
E: Nucleoprotein
hetero molecules

G: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0647
Polymers52,8002
Non-polymers2635
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area1780 Å2
ΔGint-12 kcal/mol
Surface area18480 Å2
MethodPISA
4
F: Nucleoprotein
H: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0647
Polymers52,8002
Non-polymers2635
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-13 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.856, 94.403, 145.124
Angle α, β, γ (deg.)90.00, 102.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 26400.145 Da / Num. of mol.: 8 / Fragment: C-Terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymphocytic choriomeningitis virus / Strain: Armstrong / Gene: N / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / References: UniProt: P09992
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K

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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: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.35M potassium phosphate, 20% PEG 3350, cryoprotected with 20% glycerol, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2012
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→47.264 Å / Num. all: 60576 / Num. obs: 58941 / % possible obs: 97.3 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 1.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q7C

3q7c


Resolution: 2.8→47.264 Å / SU ML: 0.46 / σ(F): 1.36 / Phase error: 35.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 2984 5.08 %Random
Rwork0.227 ---
all0.2287 58941 --
obs0.2287 58766 96.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→47.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12463 0 36 0 12499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312758
X-RAY DIFFRACTIONf_angle_d0.67617317
X-RAY DIFFRACTIONf_dihedral_angle_d13.6224664
X-RAY DIFFRACTIONf_chiral_restr0.0281930
X-RAY DIFFRACTIONf_plane_restr0.0032272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.84590.45361310.38852493X-RAY DIFFRACTION92
2.8459-2.8950.39631290.36022556X-RAY DIFFRACTION94
2.895-2.94760.37451410.33792573X-RAY DIFFRACTION94
2.9476-3.00430.37761290.32992590X-RAY DIFFRACTION94
3.0043-3.06560.33921270.30982585X-RAY DIFFRACTION95
3.0656-3.13220.37671450.29812596X-RAY DIFFRACTION95
3.1322-3.20510.37171580.30212580X-RAY DIFFRACTION95
3.2051-3.28520.32981440.30062625X-RAY DIFFRACTION97
3.2852-3.3740.35381330.27622641X-RAY DIFFRACTION97
3.374-3.47330.33541450.26112661X-RAY DIFFRACTION97
3.4733-3.58530.27381360.25432688X-RAY DIFFRACTION98
3.5853-3.71340.27181320.23952729X-RAY DIFFRACTION99
3.7134-3.86210.26261500.23422681X-RAY DIFFRACTION99
3.8621-4.03770.27441370.22732751X-RAY DIFFRACTION99
4.0377-4.25050.26811450.20852698X-RAY DIFFRACTION99
4.2505-4.51660.22781550.18452711X-RAY DIFFRACTION99
4.5166-4.8650.20181680.17832712X-RAY DIFFRACTION99
4.865-5.3540.21191640.19272714X-RAY DIFFRACTION100
5.354-6.12730.23181420.20782749X-RAY DIFFRACTION99
6.1273-7.71430.24061490.21522754X-RAY DIFFRACTION99
7.7143-47.27110.19141240.17822695X-RAY DIFFRACTION94

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