4UCI

X-ray structure and activities of an essential Mononegavirales L- protein domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

X-Ray Structure and Activities of an Essential Mononegavirales L-Protein Domain.

Paesen, G.C.Collet, A.Sallamand, C.Debart, F.Vasseur, J.J.Canard, B.Decroly, E.Grimes, J.M.

(2015) Nat.Commun. 6: 8749

  • DOI: 10.1038/ncomms9749
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The L protein of mononegaviruses harbours all catalytic activities for genome replication and transcription. It contains six conserved domains (CR-I to -VI; Fig. 1a). CR-III has been linked to polymerase and polyadenylation activity, CR-V to mRNA cap ...

    The L protein of mononegaviruses harbours all catalytic activities for genome replication and transcription. It contains six conserved domains (CR-I to -VI; Fig. 1a). CR-III has been linked to polymerase and polyadenylation activity, CR-V to mRNA capping and CR-VI to cap methylation. However, how these activities are choreographed is poorly understood. Here we present the 2.2-Å X-ray structure and activities of CR-VI+, a portion of human Metapneumovirus L consisting of CR-VI and the poorly conserved region at its C terminus, the +domain. The CR-VI domain has a methyltransferase fold, which besides the typical S-adenosylmethionine-binding site ((SAM)P) also contains a novel pocket ((NS)P) that can accommodate a nucleoside. CR-VI lacks an obvious cap-binding site, and the (SAM)P-adjoining site holding the nucleotides undergoing methylation ((SUB)P) is unusually narrow because of the overhanging +domain. CR-VI+ sequentially methylates caps at their 2'O and N7 positions, and also displays nucleotide triphosphatase activity.


    Organizational Affiliation

    Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-DIRECTED RNA POLYMERASE L
A, B
415Human metapneumovirusMutation(s): 0 
Gene Names: L
Find proteins for Q91L20 (Human metapneumovirus)
Go to UniProtKB:  Q91L20
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GTP
Query on GTP

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Download CCD File 
A, B
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ADN
Query on ADN

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Download CCD File 
A, B
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
SAM
Query on SAM

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Download CCD File 
A, B
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 80.220α = 90.00
b = 83.610β = 90.00
c = 182.620γ = 90.00
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-10-21
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Other
  • Version 1.2: 2015-11-18
    Type: Database references
  • Version 1.3: 2017-06-14
    Type: Refinement description
  • Version 1.4: 2019-04-24
    Type: Data collection, Source and taxonomy