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- PDB-3mx2: Lassa fever virus Nucleoprotein complexed with dTTP -

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Basic information

Entry
Database: PDB / ID: 3mx2
TitleLassa fever virus Nucleoprotein complexed with dTTP
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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / viral nucleocapsid / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / 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
THYMIDINE-5'-TRIPHOSPHATE / Nucleoprotein
Similarity search - Component
Biological speciesLassa virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.983 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 1.1Aug 10, 2011Group: Refinement description
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)193,5389
Polymers191,8953
Non-polymers1,6436
Water8,557475
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)64,5133
Polymers63,9651
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5133
Polymers63,9651
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5133
Polymers63,9651
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)176.147, 176.147, 56.474
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
DetailsThree monomers in an asymmetry unit.

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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-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#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 / Water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.64 Å3/Da / Density % sol: 53.34 %
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 I0210.978
SYNCHROTRONDiamond I0320.978
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, L10.606
11K, H, -L20.394
ReflectionResolution: 1.98→152.548 Å / Num. all: 134689 / Num. obs: 134680 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.6 / Redundancy: 3.8 % / Rmerge(I) obs: 0.074 / Rsym value: 0.076 / Net I/σ(I): 11.9
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.53 / % possible all: 95.8

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Processing

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

3mwp


Resolution: 1.983→152.548 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 14.444 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20806 6852 5.1 %RANDOM
Rwork0.18039 ---
obs0.1818 127846 99.1 %-
all-134660 --
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: 66.686 Å2
Baniso -1Baniso -2Baniso -3
1-4.91 Å20 Å20 Å2
2--4.91 Å20 Å2
3----9.83 Å2
Refinement stepCycle: LAST / Resolution: 1.983→152.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12073 0 90 475 12638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02212333
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.98916668
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11851531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32924.745529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.871152313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3291582
X-RAY DIFFRACTIONr_chiral_restr0.1210.21943
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218973
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_it1.5831.57681
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.486212394
X-RAY DIFFRACTIONr_scbond_it4.2834704
X-RAY DIFFRACTIONr_scangle_it6.1374.54347
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.983→2.034 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 432 -
Rwork0.196 8623 -
obs--89.9 %
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)
10.2230.1281-0.15240.2268-0.04140.1350.0483-0.05310.0090.0023-0.0510.00680.02790.04750.00270.3329-0.0375-0.00290.3810.0190.1129-60.672-62.8944.687
20.20180.0586-0.07090.0803-0.08110.0843-0.02990.0118-0.00670.01940.0231-0.0218-0.0046-0.01790.00680.32310.00510.0120.274-0.00730.2224-4.095-29.212-22.431
30.15970.0933-0.00270.09880.05180.1021-0.01710.00110.0146-0.00860.0526-0.01190.0083-0.0246-0.03550.32540.00650.00990.26340.01630.2288-12.256-74.6717.429
40.07040.0210.00960.02120.01440.0250.00110.0065-0.00520.00440.0128-0.00180.004-0.0259-0.0140.28170.00450.01520.2424-0.00340.1978-19.45-53.184-2.586
500000000000000-00.2354000.235400.2354000
600000000000000-00.2354000.235400.2354000
700000000000000-00.2354000.235400.2354000
8111.6642-19.7584-76.812513.2176-7.9057100.4170.3381-1.7391-4.9603-0.2339-0.35392.42770.11442.86470.01580.1962-0.212-0.06230.6216-0.01330.4696-55.897-52.9431.86
92.96522.2373-12.71832.1172-11.075366.51440.44840.06780.3506-0.04380.57370.47050.25350.1132-1.02220.5056-0.1658-0.02571.2370.61410.3811-15.099-27.973-20.031
1012.39811.530316.458299.085767.033864.5894-0.3302-0.0306-0.7993-1.6524-0.40612.6976-1.5435-0.2790.73630.4701-0.0432-0.00690.10850.00630.2537-2.657-69.93920.481
1100000000000000-00.2354000.235400.2354000
120.01690.00160.00730.0045-0.0080.0595-0.0080.0185-0.00680.00070.0176-0.01060.0103-0.0362-0.00960.28480.00420.0130.27080.00130.1983-22.845-53.767-2.697
130.00590.00070.01330.0220.00230.0564-0.0149-0.01-0.001-0.0248-0.01140.00380.0053-0.01770.02640.279-0.01140.01670.28470.01670.2301-19.866-54.062-2.719
140.06480.0271-0.02440.09060.04630.06290.01950.00030.00790.04550.0052-0.0096-0.0049-0.0223-0.02470.2543-0.0178-0.00080.34470.04220.1505-16.166-52.053-1.196
150.1245-0.04480.0340.0209-0.00930.02110.0105-0.0143-0.00920.00040.0257-0.0076-0.0118-0.0242-0.03620.31680.02660.07540.3470.03010.238-35.381-54.9823.52
160.14790.1667-0.07770.6925-0.1320.19960.04230.0542-0.06080.0714-0.05430.0144-0.0377-0.06970.01190.24470.003-0.04660.31350.00990.196-24.686-54.967-4.335
170.24330.03560.01190.2096-0.05560.0495-0.13920.1206-0.09290.00850.0942-0.03560.0053-0.02520.0450.32230.01590.09290.2972-0.0540.2266-18.001-49.04-1.971
180.0104-0.00150.00910.00670.01760.07750.0092-0.0335-0.01030.00040.00580.0003-0.03-0.0201-0.01510.2935-0.0312-0.00760.25570.0430.2325-28.992-64.787-2.375
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
8X-RAY DIFFRACTION8A562 - 800
9X-RAY DIFFRACTION9B562 - 800
10X-RAY DIFFRACTION10C562 - 800
11X-RAY DIFFRACTION11Z1 - 326
12X-RAY DIFFRACTION12W2 - 1096
13X-RAY DIFFRACTION13D5 - 882
14X-RAY DIFFRACTION14E51 - 853
15X-RAY DIFFRACTION15F3 - 819
16X-RAY DIFFRACTION16G1 - 838
17X-RAY DIFFRACTION17H1 - 866
18X-RAY DIFFRACTION18I1 - 3

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