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

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Basic information

Entry
Database: PDB / ID: 4rml
TitleCrystal structure of the Olfactomedin domain of latrophilin 3 in C2221 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 / neuron migration / synapse organization / adenylate cyclase-activating G protein-coupled receptor signaling pathway ...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 / neuron migration / synapse organization / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Schaffer collateral - CA1 synapse / 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 / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / 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 / MOLECULAR REPLACEMENT / Resolution: 1.601 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 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Latrophilin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7793
Polymers36,6331
Non-polymers1462
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.806, 96.819, 79.203
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 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.35 %
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: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 3, 2014
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.55→48.39 Å / Num. all: 84978 / Num. obs: 78279 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.063 / Net I/σ(I): 12.59
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.68 / Rsym value: 0.611 / % possible all: 61.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.601→48.39 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 19.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 3797 5.02 %random
Rwork0.1755 ---
all0.1766 77061 --
obs0.1766 75635 98.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.601→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 9 157 2229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072208
X-RAY DIFFRACTIONf_angle_d1.0683026
X-RAY DIFFRACTIONf_dihedral_angle_d12.62812
X-RAY DIFFRACTIONf_chiral_restr0.049323
X-RAY DIFFRACTIONf_plane_restr0.004387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.601-1.62120.31591120.28132082X-RAY DIFFRACTION79
1.6212-1.64260.28871270.28332434X-RAY DIFFRACTION89
1.6426-1.66510.30141320.26212482X-RAY DIFFRACTION92
1.6651-1.68890.27161370.252604X-RAY DIFFRACTION95
1.6889-1.71410.28791430.22542649X-RAY DIFFRACTION98
1.7141-1.74090.21511400.21462715X-RAY DIFFRACTION100
1.7409-1.76940.23371450.20832720X-RAY DIFFRACTION100
1.7694-1.79990.2331460.20572708X-RAY DIFFRACTION100
1.7999-1.83270.23291460.19322758X-RAY DIFFRACTION100
1.8327-1.86790.19851410.18762645X-RAY DIFFRACTION100
1.8679-1.9060.23141400.18942695X-RAY DIFFRACTION100
1.906-1.94750.23691430.18292730X-RAY DIFFRACTION100
1.9475-1.99280.1861450.18122684X-RAY DIFFRACTION100
1.9928-2.04260.22131380.17532698X-RAY DIFFRACTION100
2.0426-2.09780.21541470.16262763X-RAY DIFFRACTION100
2.0978-2.15960.18181430.17082699X-RAY DIFFRACTION100
2.1596-2.22930.20951430.1682724X-RAY DIFFRACTION100
2.2293-2.3090.21841450.17822704X-RAY DIFFRACTION100
2.309-2.40140.19981410.17572737X-RAY DIFFRACTION100
2.4014-2.51070.17391450.17742693X-RAY DIFFRACTION100
2.5107-2.6430.20691400.17742722X-RAY DIFFRACTION100
2.643-2.80860.20711410.19332676X-RAY DIFFRACTION100
2.8086-3.02550.21461480.18952721X-RAY DIFFRACTION100
3.0255-3.32990.19761470.18422716X-RAY DIFFRACTION100
3.3299-3.81150.14661380.15432701X-RAY DIFFRACTION100
3.8115-4.80140.13841420.12622740X-RAY DIFFRACTION100
4.8014-48.43160.17461420.15032638X-RAY DIFFRACTION97

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