8S79

Lotus japonicus NFR5 intracellular domain in complex with Nanobody 200


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 
    0.231 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A conserved juxtamembrane motif in plant NFR5 receptors is essential for root nodule symbiosis.

Hansen, S.B.Luu, T.B.Gysel, K.Lironi, D.Kronauer, C.Rubsam, H.Jensen, I.B.Tsitsikli, M.Birkefeldt, T.G.Trgovcevic, A.Stougaard, J.Radutoiu, S.Andersen, K.R.

(2024) Proc Natl Acad Sci U S A 121: e2405671121-e2405671121

  • DOI: https://doi.org/10.1073/pnas.2405671121
  • Primary Citation of Related Structures:  
    8S79

  • PubMed Abstract: 

    Establishment of root nodule symbiosis is initiated by the perception of bacterial Nod factor ligands by the plant LysM receptor kinases NFR1 and NFR5. Receptor signaling initiating the symbiotic pathway depends on the kinase activity of NFR1, while the signaling mechanism of the catalytically inactive NFR5 pseudokinase is unknown. Here, we present the crystal structure of the signaling-competent Lotus japonicus NFR5 intracellular domain, comprising the juxtamembrane region and pseudokinase domain. The juxtamembrane region is structurally well defined and forms two α-helices, αA and αA', which contain an exposed hydrophobic motif. We demonstrate that this "juxtamembrane motif" promotes NFR5-NFR5 and NFR1-NFR5 interactions and is essential for symbiotic signaling. Conservation analysis reveals that the juxtamembrane motif is present throughout NFR5-type receptors and is required for symbiosis signaling from barley RLK10, suggesting a conserved and broader function for this motif in plant-microbe symbioses.


  • Organizational Affiliation

    Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nod-factor receptor 5
A, B
288Lotus japonicusMutation(s): 0 
Gene Names: nfr5
UniProt
Find proteins for Q70KR1 (Lotus japonicus)
Explore Q70KR1 
Go to UniProtKB:  Q70KR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70KR1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 200
C, D
123Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
Q [auth B],
U [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
BME
Query on BME

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free:  0.231 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.755α = 90
b = 126.755β = 90
c = 137.875γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish Council for Independent ResearchDenmark9040-00175B
Danish Council for Independent ResearchDenmark3103-00137B
Bill & Melinda Gates FoundationUnited StatesINV-57461
Bill & Melinda Gates FoundationUnited StatesINV-55767

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references