6Z6B

Structure of full-length La Crosse virus L protein (polymerase)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.96 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.264 

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Literature

Pre-initiation and elongation structures of full-length La Crosse virus polymerase reveal functionally important conformational changes.

Arragain, B.Effantin, G.Gerlach, P.Reguera, J.Schoehn, G.Cusack, S.Malet, H.

(2020) Nat Commun 11: 3590-3590

  • DOI: 10.1038/s41467-020-17349-4
  • Primary Citation of Related Structures:  
    6Z6B, 6Z6G, 6Z8K

  • PubMed Abstract: 
  • Bunyavirales is an order of segmented negative-strand RNA viruses comprising several life-threatening pathogens against which no effective treatment is currently available. Replication and transcription of the RNA genome constitute essential processes performed by the virally encoded multi-domain RNA-dependent RNA polymerase ...

    Bunyavirales is an order of segmented negative-strand RNA viruses comprising several life-threatening pathogens against which no effective treatment is currently available. Replication and transcription of the RNA genome constitute essential processes performed by the virally encoded multi-domain RNA-dependent RNA polymerase. Here, we describe the complete high-resolution cryo-EM structure of La Crosse virus polymerase. It reveals the presence of key protruding C-terminal domains, notably the cap-binding domain, which undergoes large movements related to its role in transcription initiation, and a zinc-binding domain that displays a fold not previously observed. We capture the polymerase structure at pre-initiation and elongation states, uncovering the coordinated movement of the priming loop, mid-thumb ring linker and lid domain required for the establishment of a ten-base-pair template-product RNA duplex before strand separation into respective exit tunnels. These structural details and the observed dynamics of key functional elements will be instrumental for structure-based development of polymerase inhibitors.


    Organizational Affiliation

    Université Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), F-38000, Grenoble, France. helene.malet@ibs.fr.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymerase LD [auth EEE],
F [auth PPP]
2285La Crosse virusMutation(s): 0 
Gene Names: L
EC: 2.7.7.48 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for A5HC98 (Bunyavirus La Crosse)
Explore A5HC98 
Go to UniProtKB:  A5HC98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5HC98
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*AP*GP*UP*AP*GP*UP*GP*UP*GP*C)-3')A [auth BBB],
G [auth UUU]
10La Crosse orthobunyavirus
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*UP*UP*AP*GP*UP*AP*GP*UP*AP*CP*AP*CP*UP*AP*CP*U)-3')B [auth CCC],
E [auth HHH]
16La Crosse orthobunyavirus
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*CP*UP*AP*CP*UP*AP*A)-3')C [auth DDD],
H [auth XXX]
8La Crosse orthobunyavirus
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
I [auth EEE],
J [auth PPP]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.96 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.264 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 371.187α = 90
b = 145.32β = 116.333
c = 234.193γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release