5Z8Y

Crystal structure of human LRRTM2 in complex with Neurexin 1beta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report



Literature

Structural insights into modulation and selectivity of transsynaptic neurexin-LRRTM interaction.

Yamagata, A.Goto-Ito, S.Sato, Y.Shiroshima, T.Maeda, A.Watanabe, M.Saitoh, T.Maenaka, K.Terada, T.Yoshida, T.Uemura, T.Fukai, S.

(2018) Nat Commun 9: 3964-3964

  • DOI: 10.1038/s41467-018-06333-8
  • Primary Citation of Related Structures:  
    5Z8X, 5Z8Y

  • PubMed Abstract: 
  • Leucine-rich repeat transmembrane neuronal proteins (LRRTMs) function as postsynaptic organizers that induce excitatory synapses. Neurexins (Nrxns) and heparan sulfate proteoglycans have been identified as presynaptic ligands for LRRTMs. Specifically, LR ...

    Leucine-rich repeat transmembrane neuronal proteins (LRRTMs) function as postsynaptic organizers that induce excitatory synapses. Neurexins (Nrxns) and heparan sulfate proteoglycans have been identified as presynaptic ligands for LRRTMs. Specifically, LRRTM1 and LRRTM2 bind to the Nrxn splice variant lacking an insert at the splice site 4 (S4). Here, we report the crystal structure of the Nrxn1β-LRRTM2 complex at 3.4 Å resolution. The Nrxn1β-LRRTM2 interface involves Ca 2+ -mediated interactions and overlaps with the Nrxn-neuroligin interface. Together with structure-based mutational analyses at the molecular and cellular levels, the present structural analysis unveils the mechanism of selective binding between Nrxn and LRRTM1/2 and its modulation by the S4 insertion of Nrxn.


    Organizational Affiliation

    Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan. fukai@iam.u-tokyo.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Leucine-rich repeat transmembrane neuronal protein 2 ACEG346Homo sapiensMutation(s): 1 
Gene Names: LRRTM2KIAA0416LRRN2
Find proteins for O43300 (Homo sapiens)
Explore O43300 
Go to UniProtKB:  O43300
NIH Common Fund Data Resources
PHAROS:  O43300
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Neurexin-1-beta BDFH193Homo sapiensMutation(s): 0 
Gene Names: NRXN1
Find proteins for P58400 (Homo sapiens)
Explore P58400 
Go to UniProtKB:  P58400
NIH Common Fund Data Resources
PHAROS:  P58400
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
I, J, K, L
3 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.184α = 91.3
b = 99.858β = 91.2
c = 109.633γ = 116.47
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPS/MEXTJapanJP16H04749
JSTJapanJPMJCR12M5

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary