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 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GTPClick on this verticalbar to view detailsBest fitted SAMClick on this verticalbar to view detailsBest fitted ADNClick on this verticalbar to view details

This is version 1.5 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: https://doi.org/10.1038/ncomms9749
  • Primary Citation of Related Structures:  
    4UCI, 4UCJ, 4UCK, 4UCL, 4UCY, 4UCZ, 4UD0

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-DIRECTED RNA POLYMERASE L
A, B
415human metapneumovirusMutation(s): 0 
EC: 2.7.7.48 (UniProt), 2.1.1.375 (UniProt), 2.7.7.88 (UniProt)
UniProt
Find proteins for Q91L20 (human metapneumovirus)
Explore Q91L20 
Go to UniProtKB:  Q91L20
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91L20
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
SAM
Query on SAM

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
ADN
Query on ADN

Download Ideal Coordinates CCD File 
I [auth A],
Q [auth B]
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
M [auth B]
N [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free:  0.201 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.22α = 90
b = 83.61β = 90
c = 182.62γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GTPClick on this verticalbar to view detailsBest fitted SAMClick on this verticalbar to view detailsBest fitted ADNClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-10-21
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other
  • Version 1.2: 2015-11-18
    Changes: Database references
  • Version 1.3: 2017-06-14
    Changes: Refinement description
  • Version 1.4: 2019-04-24
    Changes: Data collection, Source and taxonomy
  • Version 1.5: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary