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- PDB-5z8y: Crystal structure of human LRRTM2 in complex with Neurexin 1beta -

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Basic information

Entry
Database: PDB / ID: 5z8y
TitleCrystal structure of human LRRTM2 in complex with Neurexin 1beta
Components
  • Leucine-rich repeat transmembrane neuronal protein 2
  • Neurexin-1-beta
KeywordsCELL ADHESION / Synapse / leucine-rich repeat / synaptic organizer
Function / homology
Function and homology information


protein-containing complex assembly involved in synapse maturation / positive regulation of presynaptic active zone assembly / gephyrin clustering involved in postsynaptic density assembly / protein complex involved in cell-cell adhesion / type 1 fibroblast growth factor receptor binding / positive regulation of neuromuscular synaptic transmission / guanylate kinase-associated protein clustering / neuronal signal transduction / neuroligin clustering involved in postsynaptic membrane assembly / postsynaptic density protein 95 clustering ...protein-containing complex assembly involved in synapse maturation / positive regulation of presynaptic active zone assembly / gephyrin clustering involved in postsynaptic density assembly / protein complex involved in cell-cell adhesion / type 1 fibroblast growth factor receptor binding / positive regulation of neuromuscular synaptic transmission / guanylate kinase-associated protein clustering / neuronal signal transduction / neuroligin clustering involved in postsynaptic membrane assembly / postsynaptic density protein 95 clustering / cerebellar granule cell differentiation / postsynaptic membrane assembly / gamma-aminobutyric acid receptor clustering / presynaptic membrane assembly / negative regulation of filopodium assembly / neuroligin family protein binding / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of postsynaptic density assembly / synaptic vesicle clustering / neuron cell-cell adhesion / neurexin family protein binding / receptor localization to synapse / protein localization to synapse / NMDA glutamate receptor clustering / vocalization behavior / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / negative regulation of receptor internalization / regulation of AMPA receptor activity / positive regulation of synapse assembly / regulation of NMDA receptor activity / Neurexins and neuroligins / positive regulation of protein kinase C activity / postsynaptic specialization membrane / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / adult behavior / positive regulation of protein kinase A signaling / social behavior / excitatory synapse / endocytic vesicle / positive regulation of excitatory postsynaptic potential / axonal growth cone / cell adhesion molecule binding / GABA-ergic synapse / synapse assembly / hippocampal mossy fiber to CA3 synapse / cellular response to calcium ion / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / learning / positive regulation of synaptic transmission, GABAergic / long-term synaptic potentiation / positive regulation of protein localization to plasma membrane / postsynaptic density membrane / synapse organization / establishment of protein localization / neuromuscular junction / Schaffer collateral - CA1 synapse / calcium-dependent protein binding / neuron projection development / transmembrane signaling receptor activity / positive regulation of peptidyl-serine phosphorylation / presynapse / presynaptic membrane / angiogenesis / nuclear membrane / vesicle / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of gene expression / signaling receptor binding / neuronal cell body / glutamatergic synapse / positive regulation of gene expression / cell surface / endoplasmic reticulum / signal transduction / extracellular space / metal ion binding / plasma membrane
Similarity search - Function
Syndecan/Neurexin domain / Syndecan domain / : / Neurexin/syndecan/glycophorin C / : / putative band 4.1 homologues' binding motif / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain ...Syndecan/Neurexin domain / Syndecan domain / : / Neurexin/syndecan/glycophorin C / : / putative band 4.1 homologues' binding motif / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Jelly Rolls - #200 / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Leucine-rich repeat transmembrane neuronal protein 2 / Neurexin-1-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsYamagata, A. / Fukai, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPS/MEXTJP16H04749 Japan
JSTJPMJCR12M5 Japan
CitationJournal: Nat Commun / Year: 2018
Title: Structural insights into modulation and selectivity of transsynaptic neurexin-LRRTM interaction.
Authors: 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.
History
DepositionFeb 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Structure summary / Category: entity / struct / Item: _entity.formula_weight / _struct.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine-rich repeat transmembrane neuronal protein 2
B: Neurexin-1-beta
C: Leucine-rich repeat transmembrane neuronal protein 2
D: Neurexin-1-beta
E: Leucine-rich repeat transmembrane neuronal protein 2
F: Neurexin-1-beta
G: Leucine-rich repeat transmembrane neuronal protein 2
H: Neurexin-1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,93530
Polymers242,7078
Non-polymers5,22822
Water724
1
A: Leucine-rich repeat transmembrane neuronal protein 2
B: Neurexin-1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0168
Polymers60,6772
Non-polymers1,3406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Leucine-rich repeat transmembrane neuronal protein 2
D: Neurexin-1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0168
Polymers60,6772
Non-polymers1,3406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Leucine-rich repeat transmembrane neuronal protein 2
F: Neurexin-1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9517
Polymers60,6772
Non-polymers1,2745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Leucine-rich repeat transmembrane neuronal protein 2
H: Neurexin-1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9517
Polymers60,6772
Non-polymers1,2745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.184, 99.858, 109.633
Angle α, β, γ (deg.)91.30, 91.20, 116.47
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Leucine-rich repeat transmembrane neuronal protein 2 / Leucine-rich repeat neuronal 2 protein


Mass: 39723.441 Da / Num. of mol.: 4 / Mutation: H355A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRRTM2, KIAA0416, LRRN2 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: O43300
#2: Protein
Neurexin-1-beta / Neurexin I-beta


Mass: 20953.354 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRXN1 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P58400

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Sugars , 2 types, 16 molecules

#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 10 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSequence of Neurexin-1-beta was based on isoform 3b of database P58400 (NRX1B_HUMAN).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 15% PEG 3350, 0.1 M sodium/potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 49781 / % possible obs: 96.3 % / Redundancy: 3 % / Rsym value: 0.105 / Net I/σ(I): 7.2
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 2.5 % / CC1/2: 0.526 / Rsym value: 0.427 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z8X,3B3Q

5z8x

3b3q


Resolution: 3.4→49.815 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2411 2387 4.82 %
Rwork0.2088 --
obs0.2104 49545 95.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→49.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16080 0 326 4 16410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416824
X-RAY DIFFRACTIONf_angle_d0.8922764
X-RAY DIFFRACTIONf_dihedral_angle_d13.6426068
X-RAY DIFFRACTIONf_chiral_restr0.0382624
X-RAY DIFFRACTIONf_plane_restr0.0032880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4002-3.46950.35191480.28652455X-RAY DIFFRACTION85
3.4695-3.5450.27231920.28682681X-RAY DIFFRACTION94
3.545-3.62740.28641520.25772732X-RAY DIFFRACTION95
3.6274-3.71810.23751100.25152747X-RAY DIFFRACTION95
3.7181-3.81860.28081070.23922821X-RAY DIFFRACTION95
3.8186-3.93090.27781080.23152819X-RAY DIFFRACTION96
3.9309-4.05770.25621090.22122812X-RAY DIFFRACTION96
4.0577-4.20270.23491040.21142786X-RAY DIFFRACTION96
4.2027-4.37090.25061430.20732788X-RAY DIFFRACTION96
4.3709-4.56970.19651230.18792840X-RAY DIFFRACTION97
4.5697-4.81040.19981430.17172786X-RAY DIFFRACTION97
4.8104-5.11150.16711370.16982807X-RAY DIFFRACTION98
5.1115-5.50570.2491400.20542874X-RAY DIFFRACTION98
5.5057-6.05890.25671360.21442814X-RAY DIFFRACTION98
6.0589-6.93360.26331540.22282822X-RAY DIFFRACTION98
6.9336-8.7280.21441990.20272796X-RAY DIFFRACTION98
8.728-49.82050.24111820.17142778X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -21.4377 Å / Origin y: 23.7672 Å / Origin z: -3.8036 Å
111213212223313233
T0.5825 Å20.0259 Å2-0.0306 Å2-0.6028 Å20.0772 Å2--0.4975 Å2
L0.3445 °20.0683 °20.003 °2-0.4272 °2-0.0166 °2---0.1151 °2
S0.0253 Å °-0.0048 Å °-0.0049 Å °-0.0052 Å °0.0214 Å °-0.0232 Å °0.0129 Å °0.0226 Å °-0.0043 Å °
Refinement TLS groupSelection details: all

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