7ZM6 | pdb_00007zm6

Nariva virus receptor binding protein

  • Classification: VIRAL PROTEIN
  • Organism(s): Narmovirus narivaense
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2022-04-19 Released: 2023-09-13 
  • Deposition Author(s): Stelfox, A.J., Rissanen, I., Rambo, R., Lee, B., Bowden, T.A.
  • Funding Organization(s): Medical Research Council (MRC, United Kingdom), Engineering and Physical Sciences Research Council, Academy of Finland, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Wellcome Trust

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 
    0.270 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 7ZM6

This is version 1.5 of the entry. See complete history

Literature

Crystal structure and solution state of the C-terminal head region of the narmovirus receptor binding protein.

Stelfox, A.J.Oguntuyo, K.Y.Rissanen, I.Harlos, K.Rambo, R.Lee, B.Bowden, T.A.

(2023) mBio 14: e0139123-e0139123

  • DOI: https://doi.org/10.1128/mbio.01391-23
  • Primary Citation Related Structures: 
    7ZM5, 7ZM6

  • PubMed Abstract: 

    Genetically diverse paramyxoviruses are united in their presentation of a receptor-binding protein (RBP), which works in concert with the fusion protein to facilitate host-cell entry. The C-terminal head region of the paramyxoviral RBP, a primary determinant of host-cell tropism and inter-species transmission potential, forms structurally distinct classes dependent upon protein and glycan receptor specificity. Here, we reveal the architecture of the C-terminal head region of the RBPs from Nariva virus (NarV) and Mossman virus (MosV), two archetypal rodent-borne paramyxoviruses within the recently established genus Narmovirus , family Paramyxoviridae . Our analysis reveals that while narmoviruses retain the general architectural features associated with paramyxoviral RBPs, namely, a six-bladed β-propeller fold, they lack the structural motifs associated with known receptor-mediated host-cell entry pathways. This investigation indicates that the RBPs of narmoviruses exhibit pathobiological features that are distinct from those of other paramyxoviruses.


  • Organizational Affiliation
    • Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford , Oxford, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 144.97 kDa 
  • Atom Count: 7,423 
  • Modeled Residue Count: 862 
  • Deposited Residue Count: 1,314 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Attachment protein
A, B
657Narmovirus narivaenseMutation(s): 0 
UniProt
Find proteins for B8XH64 (Nariva virus)
Explore B8XH64 
Go to UniProtKB:  B8XH64
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8XH64
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free:  0.270 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.382α = 90
b = 82.957β = 90.86
c = 92.988γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/L009528/1
Medical Research Council (MRC, United Kingdom)United KingdomMR/S007555/1
Engineering and Physical Sciences Research CouncilUnited KingdomEP/K503113/1
Engineering and Physical Sciences Research CouncilUnited KingdomEP/L505031/1
Engineering and Physical Sciences Research CouncilUnited KingdomEP/M50659X/1
Engineering and Physical Sciences Research CouncilUnited KingdomEP/M508111/1
Academy of FinlandFinland#309605
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI123449
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI069317
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI115226
Wellcome TrustUnited Kingdom203141/Z/16Z

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection
  • Version 1.2: 2023-10-04
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Database references
  • Version 1.4: 2024-10-09
    Changes: Structure summary
  • Version 1.5: 2026-03-04
    Changes: Refinement description