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- PDB-3t5n: 1.8A crystal structure of Lassa virus nucleoprotein in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3t5n
Title1.8A crystal structure of Lassa virus nucleoprotein in complex with ssRNA
Components
  • Nucleoprotein
  • RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3')
Keywordsviral protein/RNA / ssRNA / single stranded RNA / viral protein-RNA complex
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 / WD40 repeat / Trp-Asp (WD) repeats profile.
Similarity search - Domain/homology
NICKEL (II) ION / RNA / Nucleoprotein
Similarity search - Component
Biological speciesMopeia Lassa reassortant 29 (virus)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.787 Å
AuthorsHastie, K.M. / Liu, T. / King, L.B. / Ngo, N. / Zandonatti, M.A. / Woods, V.L. / de la Torre, J.C. / Saphire, E.O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal structure of the Lassa virus nucleoprotein-RNA complex reveals a gating mechanism for RNA binding.
Authors: Hastie, K.M. / Liu, T. / Li, S. / King, L.B. / Ngo, N. / Zandonatti, M.A. / Woods, V.L. / de la Torre, J.C. / Saphire, E.O.
History
DepositionJul 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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_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_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
C: RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2124
Polymers41,0952
Non-polymers1172
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-24 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.159, 71.737, 56.887
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Nucleoprotein / / Nucleocapsid protein


Mass: 39281.867 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mopeia Lassa reassortant 29 (virus) / Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S585
#2: RNA chain RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3')


Mass: 1813.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: H20 / Source: (natural) Escherichia coli (E. coli)
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 1.84 Å3/Da / Density % sol: 33.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7
Details: 0.1M Hepes, pH 7.0, 18% PEG 3350, 12.5mM MgCl 2 and 7.5mM NiCl2, VAPOR DIFFUSION, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.210.9795, 1.0
ALS 5.0.22
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2010
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
211
ReflectionResolution: 1.787→37 Å / Num. obs: 39465 / % possible obs: 100 %

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Processing

Software
NameVersionClassification
BOSdata collection
Auto-Rickshawphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.787→37 Å / SU ML: 0.2 / σ(F): 1.92 / Phase error: 19.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 1491 5.08 %
Rwork0.1823 --
all0.1837 29326 -
obs0.1837 29326 99.68 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.894 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.1548 Å2-0 Å2-0 Å2
2---0.8956 Å20 Å2
3----2.2591 Å2
Refinement stepCycle: LAST / Resolution: 1.787→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2179 122 2 184 2487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072349
X-RAY DIFFRACTIONf_angle_d0.9983201
X-RAY DIFFRACTIONf_dihedral_angle_d13.728901
X-RAY DIFFRACTIONf_chiral_restr0.064386
X-RAY DIFFRACTIONf_plane_restr0.005386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7873-1.85120.31891380.30272673X-RAY DIFFRACTION97
1.8512-1.92540.23731570.2252719X-RAY DIFFRACTION100
1.9254-2.0130.2491540.17882753X-RAY DIFFRACTION100
2.013-2.11910.23481440.17682767X-RAY DIFFRACTION100
2.1191-2.25190.18091320.16962781X-RAY DIFFRACTION100
2.2519-2.42570.1821530.17262756X-RAY DIFFRACTION100
2.4257-2.66980.23671550.1812790X-RAY DIFFRACTION100
2.6698-3.05610.22991420.1982805X-RAY DIFFRACTION100
3.0561-3.850.22041630.17362819X-RAY DIFFRACTION100
3.85-45.15090.17481530.17372972X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1646-1.04880.31994.272-1.04991.65660.12250.19650.0254-0.2692-0.2083-0.1970.0330.19930.1130.09620.02010.00340.1719-0.01150.125820.556217.751819.4801
20.6988-0.68810.57970.7373-0.44371.34970.2172-0.0673-0.1684-0.6231-0.3035-0.39291.09410.92770.22240.44090.20040.13370.26460.01670.280727.41342.261617.1735
31.4525-1.16830.40783.9253-0.98311.82960.1590.2191-0.1501-0.5338-0.18040.42740.0805-0.04030.01570.15210.0294-0.05210.1444-0.04870.164410.200318.770416.8915
40.9746-0.237-0.15261.7284-0.04460.43310.00260.0448-0.07270.0698-0.0918-0.0570.08660.07070.06840.09270.0149-0.00180.15810.00940.150221.726712.524727.2169
52.7390.58821.8961.3796-1.08373.12550.48410.1499-0.0431-0.7157-0.53760.20030.5289-0.30860.14940.26950.0875-0.02330.1938-0.02310.170319.64438.675517.0992
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:107)
2X-RAY DIFFRACTION2(chain A and resid 108:170)
3X-RAY DIFFRACTION3(chain A and resid 171:296)
4X-RAY DIFFRACTION4(chain A and resid 297:339)
5X-RAY DIFFRACTION5(chain C and resid 0:4)

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