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- PDB-5z8x: Crystal structure of human LRRTM2 -

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Basic information

Entry
Database: PDB / ID: 5z8x
TitleCrystal structure of human LRRTM2
ComponentsLeucine-rich repeat transmembrane neuronal protein 2
KeywordsCELL ADHESION / Synapse / leucine-rich repeat / synaptic organizer
Function / homology
Function and homology information


regulation of postsynaptic density assembly / neurexin family protein binding / negative regulation of receptor internalization / postsynaptic specialization membrane / Neurexins and neuroligins / positive regulation of synapse assembly / excitatory synapse / GABA-ergic synapse / hippocampal mossy fiber to CA3 synapse / long-term synaptic potentiation ...regulation of postsynaptic density assembly / neurexin family protein binding / negative regulation of receptor internalization / postsynaptic specialization membrane / Neurexins and neuroligins / positive regulation of synapse assembly / excitatory synapse / GABA-ergic synapse / hippocampal mossy fiber to CA3 synapse / long-term synaptic potentiation / postsynaptic density membrane / synapse organization / Schaffer collateral - CA1 synapse / glutamatergic synapse / extracellular space
Similarity search - Function
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. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Leucine-rich repeat transmembrane neuronal protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Leucine-rich repeat transmembrane neuronal protein 2
C: Leucine-rich repeat transmembrane neuronal protein 2
D: Leucine-rich repeat transmembrane neuronal protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,21212
Polymers159,4434
Non-polymers1,7708
Water00
1
A: Leucine-rich repeat transmembrane neuronal protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3033
Polymers39,8611
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leucine-rich repeat transmembrane neuronal protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3033
Polymers39,8611
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Leucine-rich repeat transmembrane neuronal protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3033
Polymers39,8611
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Leucine-rich repeat transmembrane neuronal protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3033
Polymers39,8611
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.691, 240.959, 259.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 39860.633 Da / Num. of mol.: 4 / Mutation: T59L
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: 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.: 8
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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 72.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 18% PEG 3350, 0.1 M ammonium sulfate, 0.1 M sodium malonate

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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: Apr 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 48031 / % possible obs: 96.3 % / Redundancy: 6.4 % / Rsym value: 0.102 / Net I/σ(I): 11.3
Reflection shellResolution: 3.15→3.2 Å / Redundancy: 3.2 % / CC1/2: 0.548 / Rsym value: 0.291 / % possible all: 88.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A5C

5a5c


Resolution: 3.15→49.429 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 20.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2309 2397 5.02 %
Rwork0.2028 --
obs0.2042 47760 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→49.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10644 0 112 0 10756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111028
X-RAY DIFFRACTIONf_angle_d1.14714928
X-RAY DIFFRACTIONf_dihedral_angle_d12.8363984
X-RAY DIFFRACTIONf_chiral_restr0.0591708
X-RAY DIFFRACTIONf_plane_restr0.0051872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.21430.3351230.30062443X-RAY DIFFRACTION89
3.2143-3.28420.28041170.28682475X-RAY DIFFRACTION91
3.2842-3.36060.2971400.28272534X-RAY DIFFRACTION92
3.3606-3.44460.3041470.26732578X-RAY DIFFRACTION94
3.4446-3.53770.28141490.25652560X-RAY DIFFRACTION95
3.5377-3.64170.24791430.22662623X-RAY DIFFRACTION95
3.6417-3.75930.24941370.21272667X-RAY DIFFRACTION97
3.7593-3.89360.22471470.19852637X-RAY DIFFRACTION97
3.8936-4.04940.2111350.17972696X-RAY DIFFRACTION98
4.0494-4.23360.22551470.18892706X-RAY DIFFRACTION98
4.2336-4.45670.21241140.18342760X-RAY DIFFRACTION98
4.4567-4.73570.21661440.1692717X-RAY DIFFRACTION98
4.7357-5.1010.17971530.16282719X-RAY DIFFRACTION99
5.101-5.61370.21251490.17762773X-RAY DIFFRACTION99
5.6137-6.42450.24031500.19962763X-RAY DIFFRACTION99
6.4245-8.08840.21261480.20122786X-RAY DIFFRACTION99
8.0884-49.43540.19971540.17662926X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -8.5937 Å / Origin y: 86.9882 Å / Origin z: -1.9881 Å
111213212223313233
T0.4332 Å20.0047 Å2-0.0143 Å2-0.3852 Å20.0106 Å2--0.4235 Å2
L0.3662 °2-0.0197 °2-0.0955 °2-0.1348 °2-0.0052 °2--0.1231 °2
S0.0113 Å °0.0384 Å °0.0822 Å °-0.046 Å °-0.0085 Å °0.0575 Å °0.0251 Å °-0.0824 Å °-0 Å °
Refinement TLS groupSelection details: all

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