7ZAL | pdb_00007zal

FNIP family proteins from Cafeteria roenbergensis virus (CroV): leucine-rich repeats with novel structural features

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 
    0.267 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.218 (DCC) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

Literature

Crystal structures of FNIP/FGxxFN motif-containing leucine-rich repeat proteins.

Huyton, T., Jaiswal, M., Taxer, W., Fischer, M., Gorlich, D.

(2022) Sci Rep 12: 16430-16430

  • DOI: https://doi.org/10.1038/s41598-022-20758-8
  • Primary Citation Related Structures: 
    7ZAL

  • PubMed Abstract: 

    The Cafeteria roenbergensis virus (Crov), Dictyostelium, and other species encode a large family of leucine-rich repeat (LRR) proteins with FGxxFN motifs. We determined the structures of two of them and observed several unique structural features that set them aside from previously characterized LRR family members. Crov588 comprises 25 regular repeats with a LxxLxFGxxFNQxIxENVLPxx consensus, forming a unique closed circular repeat structure. Novel features include a repositioning of a conserved asparagine at the middle of the repeat, a double phenylalanine spine that generates an alternate core packing arrangement, and a histidine/tyrosine ladder on the concave surface. Crov539 is smaller, comprising 12 repeats of a similar LxxLxFGxxFNQPIExVxW/LPxx consensus and forming an unusual cap-swapped dimer structure. The phenylalanine spine of Crov539 is supplemented with a tryptophan spine, while a hydrophobic isoleucine-rich patch is found on the central concave surface. We present a detailed analysis of the structures of Crov588 and Crov539 and compare them to related repeat proteins and other LRR classes.

    • Organizational Affiliation: 
    • Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany. trevor.huyton@mpinat.mpg.de.

Macromolecule Content 

  • Total Structure Weight: 204.52 kDa 
  • Atom Count: 14,800 
  • Modeled Residue Count: 1,752 
  • Deposited Residue Count: 1,752 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Crov539292Cafeteria roenbergensis virusMutation(s): 0 
Gene Names: crov539
UniProt
Find proteins for E3T5W0 (Cafeteria roenbergensis virus (strain BV-PW1))
Explore E3T5W0 
Go to UniProtKB:  E3T5W0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE3T5W0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free:  0.267 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.218 (DCC) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.012α = 90
b = 113.453β = 90
c = 236.242γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Refinement description