5Z8X | pdb_00005z8x

Crystal structure of human LRRTM2

• PDB DOI: https://doi.org/10.2210/pdb5Z8X/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2018-02-01 Released: 2018-10-10 
• Deposition Author(s): Yamagata, A., Fukai, S.
• Funding Organization(s): JSPS/MEXT, JST

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

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

• PubMed: 30262834 
• DOI: https://doi.org/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, 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.

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Organizational Affiliation: 
• Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.
Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan.
CREST, JST, Saitama, 332-0012, Japan.
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan.
Department of Anatomy, Hokkaido University Faculty of Medicine, Sapporo, 060-8638, Japan.
Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Hokkaido University of Science, Sapporo, 006-8585, Japan.
Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan.
Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan.
Interfaculty Initiative in Information Studies, The University of Tokyo, Tokyo, 113-0033, Japan.
Department of Molecular Neuroscience, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan.
PRESTO, JST, Saitama, 332-0012, Japan.
CREST, JST, Saitama, 332-0012, Japan. [e-mail].
Division of Gene Research, Research Center for Supports to Advanced Science, Shinshu University, Nagano, 390-8621, Japan. [e-mail].
Department of Biological Sciences for Intractable Neurological Diseases, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Nagano, 390-8621, Japan. [e-mail].
Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan. [e-mail].
Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan. [e-mail].
CREST, JST, Saitama, 332-0012, Japan. [e-mail].
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 161.21 kDa 
• Atom Count: 10,756 
• Modeled Residue Count: 1,312 
• Deposited Residue Count: 1,384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat transmembrane neuronal protein 2	A, B, C, D	346	Homo sapiens	Mutation(s): 1  Gene Names: LRRTM2, KIAA0416, LRRN2
UniProt & NIH Common Fund Data Resources
Find proteins for O43300 (Homo sapiens) Explore O43300  Go to UniProtKB:  O43300
PHAROS:  O43300 GTEx:  ENSG00000146006
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: O43300-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.691	α = 90
b = 240.959	β = 90
c = 259.434	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-10 
Deposition Author(s): Yamagata, A., Fukai, S.

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Funding Organization	Location	Grant Number
JSPS/MEXT	Japan	JP16H04749
JST	Japan	JPMJCR12M5

Revision History  

• Version 1.0: 2018-10-10
  Type: Initial release
  
• Version 1.1: 2018-10-31
  Changes: Data collection, Structure summary
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-11-13
  Changes: Structure summary