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- PDB-3q7c: Exonuclease domain of Lassa virus nucleoprotein bound to manganese -

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Basic information

Entry
Database: PDB / ID: 3q7c
TitleExonuclease domain of Lassa virus nucleoprotein bound to manganese
ComponentsNucleoprotein
KeywordsHYDROLASE / DEDDh exonuclease / 3' exonuclease / arenavirus nucleoprotein
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
: / PHOSPHATE ION / Nucleoprotein
Similarity search - Component
Biological speciesLassa virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHastie, K.M. / Kimberlin, C.R. / Zandonatti, M.A. / MacRae, I.J. / Saphire, E.O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure of the Lassa virus nucleoprotein reveals a dsRNA-specific 3' to 5' exonuclease activity essential for immune suppression.
Authors: Hastie, K.M. / Kimberlin, C.R. / Zandonatti, M.A. / Macrae, I.J. / Saphire, E.O.
History
DepositionJan 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 7, 2011Group: Structure summary
Revision 1.3Feb 21, 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.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_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_conn.ptnr2_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4854
Polymers27,2701
Non-polymers2153
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.870, 67.940, 78.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nucleoprotein / / Nucleocapsid protein / Protein N


Mass: 27270.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa virus / Strain: Mouse/Sierra Leone/Josiah/1976 / Production host: Escherichia coli (E. coli) / References: UniProt: P13699
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.4M potassium phosphate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2010
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.5→34 Å / Num. all: 38172 / Num. obs: 38157 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.5→1.5527 Å / Redundancy: 3.57 % / Rmerge(I) obs: 0.067 / Mean I/σ(I) obs: 10.1 / Num. unique all: 38172 / % possible all: 97

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.refine: 1.6_289)model building
PHENIX(phenix.refine: 1.6_289)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIX1.6_289phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→33.809 Å / SU ML: 0.19 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 1909 5 %random
Rwork0.1897 ---
obs0.191 38157 97.01 %-
all-38172 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.729 Å2 / ksol: 0.384 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0494 Å20 Å2-0 Å2
2--1.7792 Å20 Å2
3----0.7298 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1634 0 7 306 1947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061674
X-RAY DIFFRACTIONf_angle_d1.0832265
X-RAY DIFFRACTIONf_dihedral_angle_d15.132624
X-RAY DIFFRACTIONf_chiral_restr0.071258
X-RAY DIFFRACTIONf_plane_restr0.004290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.55270.2321910.20663415X-RAY DIFFRACTION93
1.5527-1.61480.22771930.19233671X-RAY DIFFRACTION99
1.6148-1.68830.20462010.17983649X-RAY DIFFRACTION100
1.6883-1.77740.2291870.18013683X-RAY DIFFRACTION100
1.7774-1.88870.20311860.17063728X-RAY DIFFRACTION100
1.8887-2.03450.19091910.1733680X-RAY DIFFRACTION100
2.0345-2.23920.18761820.16363718X-RAY DIFFRACTION100
2.2392-2.56310.19922070.17213727X-RAY DIFFRACTION100
2.5631-3.22890.21151950.18173775X-RAY DIFFRACTION99
3.2289-33.81720.22171760.19663202X-RAY DIFFRACTION81
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)
10.52220.0252-0.03410.16020.2320.3374-0.0211-0.00850.05950.0417-0.05920.08720.0301-0.01210.06180.0833-0-0.00250.1021-0.03290.1147-19.450413.4574-4.2504
20.50680.1417-0.07040.5040.47610.8885-0.0085-0.0386-0.01770.04570.0367-0.00320.03030.0399-0.02770.06780.0022-0.00290.0679-0.00650.0872-9.33736.2846-7.6494
30.984-0.2772-0.08950.37770.38810.7288-0.02260.0215-0.17510.0059-0.07190.0720.1691-0.06940.07640.1433-0.01550.00530.1032-0.02120.1406-18.8132-0.9321-10.7178
40.2945-0.1778-0.22470.14540.22470.4948-0.0060.0566-0.15270.123-0.01420.00110.26720.17340.04130.19290.06260.01770.1523-0.05080.17670.2747-10.452-19.1323
50.3999-0.1929-0.14520.18720.17770.72360.0380.1703-0.0391-0.0241-0.09290.066-0.02-0.0640.02310.11170.0012-0.01010.1116-0.03110.118-17.52034.2645-17.8801
60.40610.1540.52970.65020.52750.9041-0.19060.210.09010.17140.13520.050.04770.29690.0540.1568-0.01310.00490.15950.03810.13133.650222.9443-8.5623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 360:393)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 394:455)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 456:508)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 509:523)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 524:559)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 560:569)

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