7BRC

Crystal structure of the TMK3 LRR domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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Literature

Crystal structure of the extracellular domain of the receptor-like kinase TMK3 from Arabidopsis thaliana.

Chen, H.Kong, Y.Chen, J.Li, L.Li, X.Yu, F.Ming, Z.

(2020) Acta Crystallogr F Struct Biol Commun 76: 384-390

  • DOI: 10.1107/S2053230X20010122
  • Primary Citation of Related Structures:  
    7BRC

  • PubMed Abstract: 
  • Transmembrane kinases (TMKs) are members of the plant receptor-like kinase (RLK) family. TMKs are characterized by an extracellular leucine-rich-repeat (LRR) domain, a single transmembrane region and a cytoplasmic kinase domain. TMKs have been shown to act as critical modulators of cell expansion and cell proliferation ...

    Transmembrane kinases (TMKs) are members of the plant receptor-like kinase (RLK) family. TMKs are characterized by an extracellular leucine-rich-repeat (LRR) domain, a single transmembrane region and a cytoplasmic kinase domain. TMKs have been shown to act as critical modulators of cell expansion and cell proliferation. Here, the crystal structure of the extracellular domain of TMK3 (TMK3-ECD) was determined to a resolution of 2.06 Å, with an R work of 17.69% and an R free of 20.58%. Similar to the extracellular domain of TMK1, the TMK3-ECD structure contains two solenoids with 13 LRRs and a non-LRR region (316-364) between the tenth and 11th LRRs. A comparison of TMK3-ECD with other LRR-RLKs that contain a non-LRR region indicates that the non-LRR region plays a critical role in structural integrity and may contribute to ligand interactions. The non-LRR region of TMK3-ECD is characterized by two disulfide bonds that may have critical biological implications.


    Organizational Affiliation

    State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor-like kinase TMK3A458Arabidopsis thalianaMutation(s): 0 
Gene Names: TMK3BLK2At2g01820T23K3.1
EC: 2.7.11.1
UniProt
Find proteins for Q9SIT1 (Arabidopsis thaliana)
Explore Q9SIT1 
Go to UniProtKB:  Q9SIT1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SIT1
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB, C 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.34α = 90
b = 115.61β = 92.349
c = 57.86γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31700052

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release