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- PDB-3mx5: Lassa fever virus nucleoprotein complexed with UTP -

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Basic information

Entry
Database: PDB / ID: 3mx5
TitleLassa fever virus nucleoprotein complexed with UTP
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
URIDINE 5'-TRIPHOSPHATE / Nucleoprotein
Similarity search - Component
Biological speciesLassa virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 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 1.2Sep 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_label_asym_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)193,5449
Polymers191,8953
Non-polymers1,6496
Water2,072115
1
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5153
Polymers63,9651
Non-polymers5502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5153
Polymers63,9651
Non-polymers5502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5153
Polymers63,9651
Non-polymers5502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)177.110, 177.110, 56.720
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-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#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.: 115 / 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: 2.68 Å3/Da / Density % sol: 54.04 %
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

Diffraction
IDMean temperature (K)Crystal-ID
1771
2771
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0310.978
SYNCHROTRONDiamond I0220.978
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJan 23, 2009
ADSC QUANTUM 3152CCDJan 23, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.513
11K, H, -L20.487
ReflectionResolution: 1.903→88.56 Å / Num. all: 79046 / Num. obs: 79030 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3.3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.075 / Rsym value: 0.076 / Net I/σ(I): 12.6
Reflection shellResolution: 1.903→1.96 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.49 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MWP

3mwp


Resolution: 1.903→76.7 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 13.225 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22403 4005 5 %RANDOM
Rwork0.18276 ---
obs0.18484 75855 51.14 %-
all-79046 --
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: 53.375 Å2
Baniso -1Baniso -2Baniso -3
1-6.74 Å20 Å20 Å2
2--6.74 Å20 Å2
3----13.47 Å2
Refinement stepCycle: LAST / Resolution: 1.903→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12071 0 90 115 12276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02212334
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.98916681
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12151530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14124.773528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.781152319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1651581
X-RAY DIFFRACTIONr_chiral_restr0.1020.21939
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218961
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_it1.4521.57662
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.12212363
X-RAY DIFFRACTIONr_scbond_it3.71534665
X-RAY DIFFRACTIONr_scangle_it4.8714.54295
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 282 -
Rwork0.23 5513 -
obs--50.14 %
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)
10.0216-0.02530.00120.13-0.05360.0627-0.01350.0107-0.00940.0120.0263-0.0114-0.0099-0.01-0.01280.5267-0.005-0.00150.5285-0.00210.518523.55318.254.713
20.0570.02410.02620.1386-0.08880.091-0.0069-0.01660.0077-0.00830.0138-0.01230.0091-0.0124-0.00690.52540.00530.00890.533-0.0010.513822.78783.419-22.54
30.02060.0181-0.01050.16030.0570.03740.0255-0.00930.0005-0.0017-0.0037-0.01490.00050.0025-0.02180.51040.00910.00150.52360.01120.532158.87653.35617.544
40.01790.0022-0.0130.0019-0.00220.011-0.002-0.00280.0053-0.01670.005-0.02270.0098-0.0263-0.00310.54020.0025-0.00210.52940.00870.523629.60154.524-3.785
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 993
2X-RAY DIFFRACTION2B2 - 993
3X-RAY DIFFRACTION3C3 - 993
4X-RAY DIFFRACTION4Z3 - 170

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