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- PDB-4o6i: 2.0A crystal structure of Lymphocytic Choriomeningitis Virus Nucl... -

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Basic information

Entry
Database: PDB / ID: 4o6i
Title2.0A crystal structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-terminal Domain
ComponentsNucleoprotein
KeywordsHYDROLASE / Exoribonuclease / Ribonucleoprotein
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 / viral nucleocapsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / symbiont-mediated suppression of host NF-kappaB cascade / host cell cytoplasm / hydrolase activity / ribonucleoprotein complex ...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 / viral nucleocapsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / symbiont-mediated suppression of host NF-kappaB cascade / 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,67116
Polymers52,8002
Non-polymers87014
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-12 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.962, 89.962, 145.941
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 26400.145 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 277 K / Method: eppendorf crystallization / pH: 8
Details: 10 mM TRIS, 300 mM NaCl, protein concentration at 1.15 mg/mL, pH 8, Eppendorf Crystallization, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 / Detector: CCD / Date: Apr 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→38.955 Å / Num. all: 45091 / Num. obs: 45091 / % possible obs: 100 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9

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Processing

Software
NameClassification
JBluIce-EPICSdata 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→38.955 Å / SU ML: 0.25 / σ(F): 1.39 / Phase error: 29.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 2274 5.06 %RANDOM
Rwork0.2086 ---
all0.2095 45091 --
obs0.2095 44967 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→38.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3198 0 54 142 3394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043333
X-RAY DIFFRACTIONf_angle_d0.6394474
X-RAY DIFFRACTIONf_dihedral_angle_d12.251226
X-RAY DIFFRACTIONf_chiral_restr0.028486
X-RAY DIFFRACTIONf_plane_restr0.002588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04350.35431560.35952624X-RAY DIFFRACTION100
2.0435-2.0910.35561490.32742683X-RAY DIFFRACTION100
2.091-2.14330.34431480.31562650X-RAY DIFFRACTION100
2.1433-2.20130.32591510.28652651X-RAY DIFFRACTION100
2.2013-2.2660.32681430.28312641X-RAY DIFFRACTION100
2.266-2.33920.26721340.26752673X-RAY DIFFRACTION100
2.3392-2.42270.31771400.26762657X-RAY DIFFRACTION100
2.4227-2.51970.28561250.26722685X-RAY DIFFRACTION99
2.5197-2.63440.33461470.29272686X-RAY DIFFRACTION100
2.6344-2.77320.30051440.28312635X-RAY DIFFRACTION100
2.7732-2.94690.33341390.29062683X-RAY DIFFRACTION100
2.9469-3.17440.27621470.26472684X-RAY DIFFRACTION100
3.1744-3.49360.24571410.21872673X-RAY DIFFRACTION100
3.4936-3.99870.22171270.18922691X-RAY DIFFRACTION100
3.9987-5.03630.16741440.15492695X-RAY DIFFRACTION100
5.0363-38.96210.16391390.16462682X-RAY DIFFRACTION99

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