3T5Q | pdb_00003t5q

3A structure of Lassa virus nucleoprotein in complex with ssRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.258 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

wwPDB Validation 3D Report Full Report

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Literature

Crystal structure of the Lassa virus nucleoprotein-RNA complex reveals a gating mechanism for RNA binding.

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.

(2011) Proc Natl Acad Sci U S A 108: 19365-19370

  • DOI: https://doi.org/10.1073/pnas.1108515108
  • Primary Citation Related Structures: 
    3T5N, 3T5Q

  • PubMed Abstract: 

    Arenaviruses cause disease in industrialized and developing nations alike. Among them, the hemorrhagic fever virus Lassa is responsible for ~300,000-500,000 infections/y in Western Africa. The arenavirus nucleoprotein (NP) forms the protein scaffold of the genomic ribonucleoprotein complexes and is critical for transcription and replication of the viral genome. Here, we present crystal structures of the RNA-binding domain of Lassa virus NP in complex with ssRNA. This structure shows, in contrast to the predicted model, that RNA binds in a deep, basic crevice located entirely within the N-terminal domain. Furthermore, the NP-ssRNA structures presented here, combined with hydrogen-deuterium exchange/MS and functional studies, suggest a gating mechanism by which NP opens to accept RNA. Directed mutagenesis and functional studies provide a unique look into how the arenavirus NPs bind to and protect the viral genome and also suggest the likely assembly by which viral ribonucleoprotein complexes are organized.


  • Organizational Affiliation
    • Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 248.38 kDa 
  • Atom Count: 14,684 
  • Modeled Residue Count: 1,850 
  • Deposited Residue Count: 2,161 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 4

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleoprotein
A,
C [auth B],
E,
G,
I,
K
353Mopeia Lassa virus reassortant 29Mutation(s): 0 
Gene Names: NP
EC: 3.1.13
UniProt
Find proteins for Q5S585 (Mopeia Lassa virus reassortant 29)
Explore Q5S585 
Go to UniProtKB:  Q5S585
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5S585
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*A)-3')B [auth C],
F
8Escherichia coli
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R(P*UP*AP*UP*CP*UP*CP*A)-3')7Escherichia coli
Sequence Annotations
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Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3')
H, L
6Escherichia coli
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*C)-3')8Escherichia coli
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
M [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.258 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.441α = 90
b = 127.441β = 90
c = 298.43γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-11
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations