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- PDB-4yeb: Structural characterization of a synaptic adhesion complex -

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Basic information

Entry
Database: PDB / ID: 4yeb
TitleStructural characterization of a synaptic adhesion complex
Components
  • Fibronectin leucine rich transmembrane protein 3
  • Latrophilin-3
KeywordsSIGNALING PROTEIN / Complex / Latrophilin 3 / FLRT3 / Central Nervous System
Function / homology
Function and homology information


proepicardium cell migration involved in pericardium morphogenesis / Downstream signaling of activated FGFR1 / locomotion involved in locomotory behavior / head development / growth cone membrane / synaptic membrane adhesion / cell-cell adhesion via plasma-membrane adhesion molecules / maintenance of postsynaptic specialization structure / embryonic morphogenesis / fibroblast growth factor receptor binding ...proepicardium cell migration involved in pericardium morphogenesis / Downstream signaling of activated FGFR1 / locomotion involved in locomotory behavior / head development / growth cone membrane / synaptic membrane adhesion / cell-cell adhesion via plasma-membrane adhesion molecules / maintenance of postsynaptic specialization structure / embryonic morphogenesis / fibroblast growth factor receptor binding / chemorepellent activity / positive regulation of synapse assembly / neuron projection extension / fibroblast growth factor receptor signaling pathway / response to axon injury / axonal growth cone / synapse assembly / axon terminus / axon guidance / response to cocaine / synaptic membrane / synapse organization / G protein-coupled receptor activity / Schaffer collateral - CA1 synapse / neuron migration / neuron projection development / cell-cell junction / heart development / carbohydrate binding / postsynaptic membrane / cell surface receptor signaling pathway / axon / focal adhesion / calcium ion binding / endoplasmic reticulum membrane / glutamatergic synapse / protein homodimerization activity / extracellular space / plasma membrane / cytosol
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 / D-galactoside/L-rhamnose binding SUEL lectin domain / D-galactoside/L-rhamnose binding SUEL lectin domain / SUEL-type lectin domain profile. / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) 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 / D-galactoside/L-rhamnose binding SUEL lectin domain / D-galactoside/L-rhamnose binding SUEL lectin domain / SUEL-type lectin domain profile. / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / 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 / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / 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 / Alpha-Beta Horseshoe / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Fibronectin type-III domain profile. / Fibronectin type III / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Adhesion G protein-coupled receptor L3 / Leucine-rich repeat transmembrane protein FLRT3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsRanaivoson, F.M. / Liu, Q. / Martini, F. / Bergami, F. / von Daake, S. / Li, S. / Lee, D. / 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
DepositionFeb 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 27, 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Latrophilin-3
B: Fibronectin leucine rich transmembrane protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5714
Polymers78,3102
Non-polymers2612
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.934, 121.934, 83.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Latrophilin-3 / Lectomedin-3


Mass: 36632.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lphn3, Kiaa0768, Lec3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q80TS3
#2: Protein Fibronectin leucine rich transmembrane protein 3 / Fibronectin leucine rich transmembrane protein 3 / isoform CRA_a / Protein Flrt3


Mass: 41677.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Flrt3, mCG_130708 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8BGT1
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#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.: 1
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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 6 % PEG 3350, 0.2 M NaNO3

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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: Nov 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.19→49.33 Å / Num. obs: 12230 / % possible obs: 99.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 138.31 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.4
Reflection shellResolution: 3.19→3.41 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 1.5 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4RMK and 4V2E

4rmk

4v2e


Resolution: 3.19→14.43 Å / Cor.coef. Fo:Fc: 0.9387 / Cor.coef. Fo:Fc free: 0.8891 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.653
RfactorNum. reflection% reflectionSelection details
Rfree0.3357 1201 10 %RANDOM
Rwork0.257 ---
obs0.2651 12008 98.8 %-
Displacement parametersBiso mean: 154.44 Å2
Baniso -1Baniso -2Baniso -3
1--3.1804 Å20 Å20 Å2
2---3.1804 Å20 Å2
3---6.3609 Å2
Refine analyzeLuzzati coordinate error obs: 1.343 Å
Refinement stepCycle: LAST / Resolution: 3.19→14.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4722 0 15 0 4737
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094851HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.116606HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1668SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes132HARMONIC2
X-RAY DIFFRACTIONt_gen_planes693HARMONIC5
X-RAY DIFFRACTIONt_it4851HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.34
X-RAY DIFFRACTIONt_other_torsion22.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion627SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5562SEMIHARMONIC4
LS refinement shellResolution: 3.19→3.49 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3354 280 10 %
Rwork0.2876 2519 -
all0.292 2799 -
obs--98.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.86521.3586-1.0225.191-1.02343.7692-0.0257-0.85050.93270.29220.08450.0987-0.67510.5782-0.05880.9113-0.2215-0.00280.2934-0.1667-0.588350.8398-22.5245-20.2187
2-5.01893.0064-1.89096.64113.92780.82480.06170.00070.33160.0566-0.16580.0792-0.244-0.3670.1040.555-0.0032-0.1572-0.29640.29080.34827.2998-7.0666-28.6277
33.1054-2.19535.57074.36683.49240-0.03960.31080.3463-0.35780.0035-0.0397-0.2957-0.22320.03610.5770.0003-0.2041-0.05820.22960.331123.4772-12.1115-34.4111
4-0.2802-0.24030.201910.92222.11248.2837-0.03850.04380.26580.0442-0.10210.3348-0.0685-0.53140.14050.3626-0.1899-0.20590.03140.2384-0.235824.5466-18.0623-36.332
52.0221-2.2180.66967.24053.29322.018-0.06220.3790.491-0.075-0.01610.0276-0.267-0.3450.07830.2801-0.209-0.03070.46330.1398-0.287822.8031-22.5822-40.6012
611.6934-0.23082.99499.74483.90429.61620.01540.48270.1014-0.3135-0.17630.3484-0.2888-0.09390.16080.4666-0.2334-0.01890.47850.1184-0.547123.5284-28.5894-43.6573
74.20942.58082.21535.83323.17025.3499-0.23580.49080.13550.0809-0.29590.40130.0162-0.00690.53170.3875-0.1640.05810.59510.0566-0.590826.8332-33.5035-42.4372
85.99010.155-1.444517.52144.40612.7918-0.0090.4527-0.1068-0.2113-0.10620.7739-0.21140.11930.11520.1778-0.34230.06990.5724-0.0685-0.659928.7191-39.5782-43.7969
94.092-3.39511.29259.4618.40514.90170.06670.425-0.5481-0.1806-0.18270.3414-0.14340.20760.1160.2959-0.35910.07860.5512-0.1283-0.604931.7829-45.7826-44.7201
109.8268-6.73061.420214.21555.82988.8895-0.07960.29140.30350.2453-0.284-0.21490.06890.16930.36370.2941-0.47590.15040.362-0.0732-0.732336.6933-46.9345-42.9617
117.1754-1.1295.233914.78263.484312.0669-0.08630.41550.11780.0501-0.1171-0.420.28560.12790.20340.3327-0.30480.23660.5108-0.2617-0.665440.4892-52.9935-41.4495
125.0277-3.42015.73232.7822-1.36074.4324-0.22730.05220.49830.5371-0.0591-0.32270.24270.41890.28640.2908-0.14880.08770.3717-0.38-0.445244.8481-55.8245-38.6402
132.7285-2.14864.68796.6719-4.91014.3502-0.10770.00670.17620.21230.0394-0.10910.1401-0.05680.06820.5340.188-0.22820.4789-0.4789-0.370550.8278-63.8073-31.2275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|30 - B|58 }
3X-RAY DIFFRACTION3{ B|59 - B|83 }
4X-RAY DIFFRACTION4{ B|84 - B|104 }
5X-RAY DIFFRACTION5{ B|105 - B|128 }
6X-RAY DIFFRACTION6{ B|129 - B|154 }
7X-RAY DIFFRACTION7{ B|155 - B|175 }
8X-RAY DIFFRACTION8{ B|176 - B|199 }
9X-RAY DIFFRACTION9{ B|200 - B|225 }
10X-RAY DIFFRACTION10{ B|226 - B|247 B|351 }
11X-RAY DIFFRACTION11{ B|248 - B|271 }
12X-RAY DIFFRACTION12{ B|272 - B|293 }
13X-RAY DIFFRACTION13{ B|294 - B|350 }

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