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- PDB-3mwt: Crystal structure of Lassa fever virus nucleoprotein in complex w... -

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Basic information

Entry
Database: PDB / ID: 3mwt
TitleCrystal structure of Lassa fever virus nucleoprotein in complex with Mn2+
ComponentsNucleoprotein
KeywordsNUCLEAR PROTEIN / nucleoprotein / Lassa fever virus / Structural Genomics / Scottish Structural Proteomics Facility / SSPF
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 / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell cytoplasm / 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 / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell cytoplasm / ribonucleoprotein complex / virus-mediated perturbation of host defense response / RNA binding / identical protein binding / metal ion binding
Similarity search - Function
Arenaviral nucleoprotein, C-terminal domain / 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 / Nucleotidyltransferase; domain 5 / WD40 repeat / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesLassa virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.982 Å
AuthorsQi, X. / Lan, S. / Wang, W. / Schelde, L.M. / Dong, H. / Wallat, G. / Liang, Y. / Ly, H. / Dong, C. / Scottish Structural Proteomics Facility (SSPF)
CitationJournal: Nature / Year: 2010
Title: Cap binding and immune evasion revealed by Lassa nucleoprotein structure.
Authors: Qi, X. / Lan, S. / Wang, W. / Schelde, L.M. / Dong, H. / Wallat, G.D. / Ly, H. / Liang, Y. / Dong, C.
History
DepositionMay 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 10, 2014Group: Structure summary
Revision 1.3Sep 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,2569
Polymers191,8953
Non-polymers3616
Water6,161342
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0853
Polymers63,9651
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0853
Polymers63,9651
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0853
Polymers63,9651
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)176.880, 176.880, 56.469
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 63965.145 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa virus / Strain: Mouse/Sierra Leone/Josiah/1976 / Gene: N, nucleoprotein / Plasmid: pLou3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: P13699
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG3350, 0.2 M Lithium chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.553
11K, H, -L20.447
ReflectionResolution: 1.98→153.18 Å / Num. all: 134699 / Num. obs: 134699 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.9 / Redundancy: 3.7 % / Rmerge(I) obs: 0.069 / Rsym value: 0.072 / Net I/σ(I): 2.5
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.39 / % possible all: 99

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Moppremodel building
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
Mopprephasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MWP

3mwp


Resolution: 1.982→153.18 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 16.623 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21754 6835 5 %RANDOM
Rwork0.18124 ---
obs0.18306 129740 99.52 %-
all-134882 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.41 Å2
Baniso -1Baniso -2Baniso -3
1-22.21 Å20 Å20 Å2
2--22.21 Å20 Å2
3----44.42 Å2
Refinement stepCycle: LAST / Resolution: 1.982→153.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11931 0 6 342 12279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02212097
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.97916328
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.151508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67824.733524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.415152279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5421581
X-RAY DIFFRACTIONr_chiral_restr0.1130.21904
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218830
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4091.57656
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.264212352
X-RAY DIFFRACTIONr_scbond_it3.88334572
X-RAY DIFFRACTIONr_scangle_it5.5514.54151
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.982→2.033 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 494 -
Rwork0.205 9500 -
obs--97.96 %
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)
10.4040.072-0.07310.1863-0.16990.2183-0.00810.04420.0071-0.00450.0712-0.01770.0591-0.0394-0.06310.0803-0.0107-0.02670.0884-0.02150.3081-4.548-29.386-4.074
20.2280.0578-0.1050.17250.0640.1160.034-0.0189-0.0259-0.0367-0.01610.0039-0.02920.0264-0.01790.05730.0151-0.00120.06340.00940.3215-60.965-61.63322.234
30.80270.16150.18540.2754-0.00230.1394-0.0027-0.02090.0667-0.03770.0453-0.0092-0.0113-0.0039-0.04270.01890.00930.03960.04560.02140.4012-16.963-77.774-17.802
40.07210.0477-0.02410.0402-0.01720.01390.0164-0.0059-0.02290.0203-0.014-0.0114-0.01640.0108-0.00240.05120.0074-0.00820.08440.01090.3552-31.015-51.384.931
512.5116-9.7999-26.20177.961121.080655.96220.1049-0.19250.1014-0.17490.2133-0.124-0.41190.5574-0.31820.28260.01790.37680.5488-0.01060.525219.694-26.128-14.651
60.74315.2689-5.814237.3608-41.228245.49610.0272-0.00610.0090.033-0.04480.0136-0.0320.07890.01770.2983-0.0306-0.08430.16410.35070.7517-75.645-81.1632.905
74.76727.26699.355211.089614.265918.36120.25130.0723-0.17460.49890.1211-0.29250.55780.1647-0.37240.7890.0292-0.23350.5571-0.08890.43516.428-70.2-6.991
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 561
2X-RAY DIFFRACTION2B8 - 561
3X-RAY DIFFRACTION3C8 - 561
4X-RAY DIFFRACTION4Z1 - 413
5X-RAY DIFFRACTION5D680 - 690
6X-RAY DIFFRACTION6E680 - 690
7X-RAY DIFFRACTION7F680 - 690

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