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- PDB-3t5q: 3A structure of Lassa virus nucleoprotein in complex with ssRNA -

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Basic information

Entry
Database: PDB / ID: 3t5q
Title3A structure of Lassa virus nucleoprotein in complex with ssRNA
Components
  • Nucleoprotein
  • RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3')
  • RNA (5'-R(P*UP*AP*UP*CP*UP*CP*A)-3')
  • RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*A)-3')
  • RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*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
Arenavirus nucleocapsid protein, head domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1200 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular ...Arenavirus nucleocapsid protein, head domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1200 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / DNA polymerase; domain 1 / Trp-Asp (WD) repeats profile. / WD40 repeat / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / RNA / Nucleoprotein
Similarity search - Component
Biological speciesMopeia Lassa reassortant 29 (virus)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 / 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 / _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*UP*AP*UP*CP*UP*CP*A)-3')
B: Nucleoprotein
D: RNA (5'-R(P*UP*AP*UP*CP*UP*CP*A)-3')
E: Nucleoprotein
F: RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*A)-3')
G: Nucleoprotein
H: RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3')
I: Nucleoprotein
J: RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*C)-3')
K: Nucleoprotein
L: RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,37813
Polymers248,28312
Non-polymers951
Water1629
1
A: Nucleoprotein
C: RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7423
Polymers41,6472
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-21 kcal/mol
Surface area15100 Å2
MethodPISA
2
B: Nucleoprotein
D: RNA (5'-R(P*UP*AP*UP*CP*UP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)41,3412
Polymers41,3412
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-12 kcal/mol
Surface area14600 Å2
MethodPISA
3
E: Nucleoprotein
F: RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)41,6472
Polymers41,6472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-18 kcal/mol
Surface area14590 Å2
MethodPISA
4
G: Nucleoprotein
H: RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)41,0122
Polymers41,0122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-15 kcal/mol
Surface area15010 Å2
MethodPISA
5
I: Nucleoprotein
J: RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)41,6232
Polymers41,6232
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-19 kcal/mol
Surface area14720 Å2
MethodPISA
6
K: Nucleoprotein
L: RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)41,0122
Polymers41,0122
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-13 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.441, 127.441, 298.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 9:57 or resseq 59:64 or resseq...
211chain B and (resseq 9:57 or resseq 59:64 or resseq...
311chain E and (resseq 9:57 or resseq 59:64 or resseq...
411chain G and (resseq 9:57 or resseq 59:64 or resseq...
511chain I and (resseq 9:57 or resseq 59:64 or resseq...
611chain K and (resseq 9:57 or resseq 59:64 or resseq...

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Components

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Protein , 1 types, 6 molecules ABEGIK

#1: Protein
Nucleoprotein / / Nucleocapsid protein


Mass: 39198.848 Da / Num. of mol.: 6 / 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

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RNA chain , 4 types, 6 molecules CFDHLJ

#2: RNA chain RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*A)-3')


Mass: 2448.481 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ssRNA / Source: (natural) Escherichia coli (E. coli)
#3: RNA chain RNA (5'-R(P*UP*AP*UP*CP*UP*CP*A)-3')


Mass: 2142.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ssRNA / Source: (natural) Escherichia coli (E. coli)
#4: RNA chain RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3')


Mass: 1813.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ssRNA / Source: (natural) Escherichia coli (E. coli)
#5: RNA chain RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*C)-3')


Mass: 2424.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ssRNA / Source: (natural) Escherichia coli (E. coli)

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Non-polymers , 2 types, 10 molecules

#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE SSRNA OBSERVED IN THE STRUCTURE WAS DERIVED FROM THE E.COLI HOST (RATHER THAN OF SYNTHETIC ...THE SSRNA OBSERVED IN THE STRUCTURE WAS DERIVED FROM THE E.COLI HOST (RATHER THAN OF SYNTHETIC ORIGIN) AND IS THEREFORE OF RANDOM SEQUENCE. THE AUTHORS ARBITRARILY CHOSE U AND C TO MODEL THE RNA, UNLESS IT WAS CLEAR THE NUCLEOBASE WAS A PURINE, IN WHICH CASE THE RESIDUE WAS MODELED AS AN ADENOSINE. FOR CHAINS C, F AND J, EIGHT BASES WERE APPARENT (RESIDUES 1-8), ALTHOUGH DENSITY FOR POSITION 8 IN CHAIN J WAS NOT CLEAR ENOUGH TO MODEL AS AN ADENOSINE, AND WAS THUS INSTEAD MODELED AS CYTIDINE. SEVEN BASES (2-8) WERE VISIBLE IN CHAIN D, WHILE ONLY SIX BASES (2-7) WERE VISIBLE IN CHAINS H AND L.

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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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8.4
Details: 0.1M Tris, pH 8.4, 0.2M Na/K phosphate, and 20% PEG 3350, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2010
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal; asymetric cut 12.2 degs.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→48 Å / Num. obs: 54709 / % possible obs: 100 %

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→39.769 Å / SU ML: 0.46 / σ(F): 0 / Phase error: 27.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2577 2769 5.07 %
Rwork0.2258 --
obs0.2275 54599 99.85 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.204 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8903 Å2-0 Å20 Å2
2---0.8903 Å2-0 Å2
3---1.7807 Å2
Refinement stepCycle: LAST / Resolution: 3→39.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13792 878 5 9 14684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114917
X-RAY DIFFRACTIONf_angle_d1.17420340
X-RAY DIFFRACTIONf_dihedral_angle_d15.0035680
X-RAY DIFFRACTIONf_chiral_restr0.082478
X-RAY DIFFRACTIONf_plane_restr0.0042445
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2112X-RAY DIFFRACTIONPOSITIONAL
12B2112X-RAY DIFFRACTIONPOSITIONAL0.061
13E2088X-RAY DIFFRACTIONPOSITIONAL0.082
14G2058X-RAY DIFFRACTIONPOSITIONAL0.071
15I2064X-RAY DIFFRACTIONPOSITIONAL0.063
16K2047X-RAY DIFFRACTIONPOSITIONAL0.064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10720.34982780.30825230X-RAY DIFFRACTION100
3.1072-3.23150.35482650.30045157X-RAY DIFFRACTION100
3.2315-3.37850.3432890.2935158X-RAY DIFFRACTION100
3.3785-3.55660.31852710.26535190X-RAY DIFFRACTION100
3.5566-3.77920.29242650.25685196X-RAY DIFFRACTION100
3.7792-4.07080.28922770.24395171X-RAY DIFFRACTION100
4.0708-4.47990.25992870.22095162X-RAY DIFFRACTION100
4.4799-5.1270.22862780.19645206X-RAY DIFFRACTION100
5.127-6.4550.23872820.21365175X-RAY DIFFRACTION100
6.455-39.77240.20092770.18875185X-RAY DIFFRACTION99

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