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- PDB-4rmk: Crystal structure of the Olfactomedin domain of latrophilin 3 in ... -

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Basic information

Entry
Database: PDB / ID: 4rmk
TitleCrystal structure of the Olfactomedin domain of latrophilin 3 in P65 crystal form
ComponentsLatrophilin-3
KeywordsSIGNALING PROTEIN / Five-bladed beta-propeller / Trans-synaptic adhesion GPCR / FLRT3 / Central nervous system
Function / homology
Function and homology information


locomotion involved in locomotory behavior / cell-cell adhesion via plasma-membrane adhesion molecules / maintenance of postsynaptic specialization structure / positive regulation of synapse assembly / synapse assembly / response to cocaine / G protein-coupled receptor activity / synapse organization / neuron migration / Schaffer collateral - CA1 synapse ...locomotion involved in locomotory behavior / cell-cell adhesion via plasma-membrane adhesion molecules / maintenance of postsynaptic specialization structure / positive regulation of synapse assembly / synapse assembly / response to cocaine / G protein-coupled receptor activity / synapse organization / neuron migration / Schaffer collateral - CA1 synapse / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell-cell junction / carbohydrate binding / postsynaptic membrane / cell surface receptor signaling pathway / axon / glutamatergic synapse / calcium ion binding / plasma membrane
Similarity search - Function
GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / D-galactoside/L-rhamnose binding SUEL lectin domain / Galactose binding lectin domain / SUEL-type lectin domain profile. / Olfactomedin-like domain ...GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / D-galactoside/L-rhamnose binding SUEL lectin domain / Galactose binding lectin domain / SUEL-type lectin domain profile. / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2.
Similarity search - Domain/homology
Adhesion G protein-coupled receptor L3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Native-SAD / Resolution: 1.606 Å
AuthorsRanaivoson, F.M. / Liu, Q. / Martini, F. / Bergami, F. / Von daake, S. / Li, S. / Demeler, B. / Hendrickson, W.A. / Comoletti, D.
CitationJournal: Structure / Year: 2015
Title: Structural and Mechanistic Insights into the Latrophilin3-FLRT3 Complex that Mediates Glutamatergic Synapse Development.
Authors: Ranaivoson, F.M. / Liu, Q. / Martini, F. / Bergami, F. / von Daake, S. / Li, S. / Lee, D. / Demeler, B. / Hendrickson, W.A. / Comoletti, D.
History
DepositionOct 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Latrophilin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6732
Polymers36,6331
Non-polymers401
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.066, 85.066, 66.083
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Latrophilin-3 / Lectomedin-3


Mass: 36632.574 Da / Num. of mol.: 1 / Fragment: Olfactomedin Domain (199-495)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lphn3, Kiaa0768, Lec3 / Production host: Homo sapiens (human) / References: UniProt: Q80TS3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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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: 1.88 Å3/Da / Density % sol: 34.72 %
Crystal growTemperature: 293 K / Method: microbach under-oil / pH: 9
Details: 15-25 % PEG 8000, 50-300 mM MgCl2, 100 mM TAPS pH 9.0, Microbach under-oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 15, 2014
RadiationMonochromator: Single crystal bender. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.606→40 Å / Num. all: 68854 / Num. obs: 35190 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.61→1.65 Å / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MAR345data collection
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: Native-SAD / Resolution: 1.606→36.835 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 19.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1904 3923 5.7 %Random
Rwork0.1651 ---
all0.1665 69711 --
obs0.1665 68854 98.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.606→36.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 1 133 2218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072244
X-RAY DIFFRACTIONf_angle_d1.1273082
X-RAY DIFFRACTIONf_dihedral_angle_d13.319838
X-RAY DIFFRACTIONf_chiral_restr0.049331
X-RAY DIFFRACTIONf_plane_restr0.005398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6065-1.6260.31711210.27672013X-RAY DIFFRACTION87
1.626-1.64660.27641460.26082280X-RAY DIFFRACTION98
1.6466-1.66830.25171420.23392356X-RAY DIFFRACTION99
1.6683-1.69110.28391400.2222267X-RAY DIFFRACTION98
1.6911-1.71530.22531400.20682357X-RAY DIFFRACTION99
1.7153-1.74090.2251340.20632315X-RAY DIFFRACTION98
1.7409-1.76810.19481380.19442331X-RAY DIFFRACTION99
1.7681-1.79710.19851300.18222296X-RAY DIFFRACTION98
1.7971-1.82810.22591440.18282332X-RAY DIFFRACTION99
1.8281-1.86130.25731350.18992333X-RAY DIFFRACTION99
1.8613-1.89710.18361400.19642298X-RAY DIFFRACTION98
1.8971-1.93590.27171370.2162323X-RAY DIFFRACTION99
1.9359-1.97790.19311380.17982353X-RAY DIFFRACTION100
1.9779-2.02390.20271400.17232350X-RAY DIFFRACTION99
2.0239-2.07460.19261440.16062346X-RAY DIFFRACTION99
2.0746-2.13060.22161400.17032303X-RAY DIFFRACTION99
2.1306-2.19330.1861360.16662321X-RAY DIFFRACTION100
2.1933-2.26410.23721360.17882314X-RAY DIFFRACTION100
2.2641-2.3450.18891500.1832391X-RAY DIFFRACTION99
2.345-2.43890.22431460.17272315X-RAY DIFFRACTION100
2.4389-2.54990.18611400.17412313X-RAY DIFFRACTION100
2.5499-2.68430.17381480.16682342X-RAY DIFFRACTION100
2.6843-2.85240.19791440.17642365X-RAY DIFFRACTION100
2.8524-3.07250.19661400.16362341X-RAY DIFFRACTION100
3.0725-3.38150.16431390.15592343X-RAY DIFFRACTION100
3.3815-3.87040.1731420.14362344X-RAY DIFFRACTION100
3.8704-4.87450.12651420.11612341X-RAY DIFFRACTION100
4.8745-36.84430.17081510.13832348X-RAY DIFFRACTION100

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