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- PDB-5ftt: Octameric complex of Latrophilin 3 (Lec, Olf) , Unc5D (Ig, Ig2, T... -

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Basic information

Entry
Database: PDB / ID: 5ftt
TitleOctameric complex of Latrophilin 3 (Lec, Olf) , Unc5D (Ig, Ig2, TSP1) and FLRT2 (LRR)
Components
  • ADHESION G PROTEIN-COUPLED RECEPTOR L3
  • LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN FLRT2
  • NETRIN RECEPTOR UNC5D
KeywordsSIGNALING PROTEIN / SIGNALLING PROTEIN / LEUCINE-RICH REPEAT / LRR / UNC5 / UNC5D / FLRT2 / LPHN3 / LPHN / ADGRL / ADGRL3 / ADGR / GPCR / UNCOORDINATED-5 / NETRIN RECEPTOR / FLRT / LATROPHILIN / ADHESION / REPULSION / GUIDANCE / BETA PROPELLER / IMMUNOGLOBULIN / THROMBOSPONDIN / OLFACTOMEDIN / LECTIN / OCTAMER
Function / homology
Function and homology information


cell adhesion involved in heart morphogenesis / Downstream signaling of activated FGFR1 / netrin receptor activity / locomotion involved in locomotory behavior / cell-cell adhesion via plasma-membrane adhesion molecules / basement membrane organization / regulation of neuron migration / maintenance of postsynaptic specialization structure / fibroblast growth factor receptor binding / chemorepellent activity ...cell adhesion involved in heart morphogenesis / Downstream signaling of activated FGFR1 / netrin receptor activity / locomotion involved in locomotory behavior / cell-cell adhesion via plasma-membrane adhesion molecules / basement membrane organization / regulation of neuron migration / maintenance of postsynaptic specialization structure / fibroblast growth factor receptor binding / chemorepellent activity / positive regulation of synapse assembly / pyramidal neuron differentiation / regulation of postsynapse assembly / fibroblast growth factor receptor signaling pathway / heart morphogenesis / synapse assembly / axon guidance / response to cocaine / synapse organization / G protein-coupled receptor activity / Schaffer collateral - CA1 synapse / neuron migration / cell-cell junction / presynaptic membrane / carbohydrate binding / postsynaptic membrane / cell surface receptor signaling pathway / neuron projection / axon / focal adhesion / apoptotic process / calcium ion binding / endoplasmic reticulum membrane / glutamatergic synapse / cell surface / extracellular space / plasma membrane
Similarity search - Function
UNC5D, Death domain / Rhamnose-binding lectin domain (RBL) / UPA domain / Netrin receptor UNC5 / UPA domain / : / GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region / Leucine rich repeat C-terminal domain ...UNC5D, Death domain / Rhamnose-binding lectin domain (RBL) / UPA domain / Netrin receptor UNC5 / UPA domain / : / GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region / Leucine rich repeat C-terminal domain / 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 / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / 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 / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death 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. / Immunoglobulin I-set / Immunoglobulin I-set domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Death-like domain superfamily / Leucine-rich repeat / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Leucine-rich repeat domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Netrin receptor UNC5D / Adhesion G protein-coupled receptor L3 / Leucine-rich repeat transmembrane protein FLRT2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsJackson, V.A. / Mehmood, S. / Chavent, M. / Roversi, P. / Carrasquero, M. / del Toro, D. / Seyit-Bremer, G. / Ranaivoson, F.M. / Comoletti, D. / Sansom, M.S.P. ...Jackson, V.A. / Mehmood, S. / Chavent, M. / Roversi, P. / Carrasquero, M. / del Toro, D. / Seyit-Bremer, G. / Ranaivoson, F.M. / Comoletti, D. / Sansom, M.S.P. / Robinson, C.V. / Klein, R. / Seiradake, E.
CitationJournal: Nat.Commun. / Year: 2016
Title: Super-Complexes of Adhesion Gpcrs and Neural Guidance Receptors
Authors: Jackson, V.A. / Mehmood, S. / Chavent, M. / Roversi, P. / Carrasquero, M. / Del Toro, D. / Seyit-Bremer, G. / Ranaivoson, F.M. / Comoletti, D. / Sansom, M.S.P. / Robinson, C.V. / Klein, R. / Seiradake, E.
History
DepositionJan 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 9, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_residues
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: NETRIN RECEPTOR UNC5D
B: LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN FLRT2
C: ADHESION G PROTEIN-COUPLED RECEPTOR L3
D: ADHESION G PROTEIN-COUPLED RECEPTOR L3
E: NETRIN RECEPTOR UNC5D
F: LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN FLRT2
G: ADHESION G PROTEIN-COUPLED RECEPTOR L3
H: ADHESION G PROTEIN-COUPLED RECEPTOR L3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,35924
Polymers316,3388
Non-polymers2,02216
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34280 Å2
ΔGint128.7 kcal/mol
Surface area130560 Å2
MethodPQS
Unit cell
Length a, b, c (Å)231.961, 141.486, 151.491
Angle α, β, γ (deg.)90.00, 117.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 8 molecules AEBFCDGH

#1: Protein NETRIN RECEPTOR UNC5D / PROTEIN UNC-5 HOMOLOG D / UNC5D


Mass: 31940.809 Da / Num. of mol.: 2 / Fragment: IG1 IG2 TSP1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PHLSEC / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: F1LW30
#2: Protein LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN FLRT2 / FIBRONECTIN LEUCINE RICH TRANSMEMBRANE PROTEIN 2 / FLRT2


Mass: 38411.934 Da / Num. of mol.: 2 / Fragment: LEUCINE-RICH REPEAT DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PHLSEC / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q8BLU0
#3: Protein
ADHESION G PROTEIN-COUPLED RECEPTOR L3 / LATROPHILIN-3 / LECTOMEDIN-3 / LPHN3


Mass: 43908.012 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q80TS3

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Sugars , 1 types, 8 molecules

#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.: 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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Non-polymers , 2 types, 8 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 69.05 % / Description: NONE
Crystal growpH: 6 / Details: pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9281
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9281 Å / Relative weight: 1
ReflectionResolution: 3.38→133.83 Å / Num. obs: 59624 / % possible obs: 98.4 % / Redundancy: 8 % / Biso Wilson estimate: 83.59 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.5
Reflection shellResolution: 3.38→3.47 Å / Redundancy: 2.4 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.5 / % possible all: 92.4

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 3.4→133.83 Å / Cor.coef. Fo:Fc: 0.8868 / Cor.coef. Fo:Fc free: 0.9093 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.462
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 2832 4.83 %RANDOM
Rwork0.2252 ---
obs0.2261 58669 98.49 %-
Displacement parametersBiso mean: 185.16 Å2
Baniso -1Baniso -2Baniso -3
1-23.9136 Å20 Å2-61.3933 Å2
2--8.4442 Å20 Å2
3----32.3578 Å2
Refine analyzeLuzzati coordinate error obs: 1.347 Å
Refinement stepCycle: LAST / Resolution: 3.4→133.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19490 0 120 0 19610
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00720116HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9227398HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6835SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes568HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2968HARMONIC5
X-RAY DIFFRACTIONt_it20116HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.77
X-RAY DIFFRACTIONt_other_torsion20.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2606SEMIHARMONIC5
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_contact21048SEMIHARMONIC4
LS refinement shellResolution: 3.4→3.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2526 230 5.61 %
Rwork0.2609 3873 -
all0.2604 4103 -
obs--98.49 %
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)
11.64572.06370.42021.12441.81274.3909-0.0657-0.14670.05030.47630.0499-0.0314-0.0506-0.05180.01580.0204-0.0972-0.09060.2271-0.1411-0.0877-96.9397.109265.4053
23.59723.8477-0.23455.0687-1.07193.92140.1249-0.0021-0.0778-0.01460.122-0.01180.1115-0.2533-0.2469-0.2596-0.06330.02710.2867-0.20510.0204-70.333933.304751.5285
33.1013-3.0183-0.98132.01911.59310.5067-0.01210.02490.2036-0.0502-0.11720.0129-0.3189-0.04490.1293-0.03840.06450.09140.009-0.13780.2049-49.764173.599436.2594
43.7652-1.1043-0.68580.04770.88333.2318-0.07180.11050.3816-0.1825-0.07060.1837-0.2253-0.31420.1424-0.2529-0.0452-0.05420.150.09420.1878-51.899657.878817.6113
56.0283.1581-1.2531.26110.25692.55720.02930.13790.07350.1603-0.1040.1007-0.10790.1450.0747-0.2814-0.0784-0.07390.2501-0.17660.1079-80.703935.132533.4181
6-1.41661.20750.49624.24633.93483.9603-0.0448-0.23990.03010.12780.1110.028-0.0158-0.1704-0.0662-0.0015-0.06880.17130.0405-0.19240.1335-115.674120.37859.5902
73.0995-1.58790.29214.6197-0.90631.32990.2296-0.65620.34330.4776-0.16850.23390.09180.0757-0.0611-0.1105-0.195-0.02720.25620.0433-0.3872-112.0948-10.484351.6982
83.56530.7941-2.24122.17241.2317.27430.1719-0.26390.5395-0.0892-0.26660.4541-0.30450.26580.0947-0.1607-0.11920.0258-0.28630.1088-0.1722-24.781757.21722.0052
98.07151.53321.32857.9202-1.8417-0.5353-0.01170.0412-0.0432-0.12430.0177-0.12070.03410.0877-0.006-0.1858-0.1293-0.0265-0.0188-0.08070.213-66.787-0.548537.6855
104.7780.2501-0.85254.7955-0.42893.6290.0701-0.1340.297-0.3025-0.1852-0.5010.37730.48530.1150.0332-0.00960.0818-0.07920.1554-0.3025-97.0516-7.218226.2191
114.55431.2314-1.96573.81563.88985.36730.0484-0.0689-0.26270.0159-0.0391-0.02410.1839-0.0465-0.0093-0.1101-0.19570.02020.03490.06440.0892-51.187115.829121.94
125.09062.6682-0.71324.4869-1.87933.25280.1632-0.315-0.55150.276-0.385-0.11810.5012-0.13340.22180.0621-0.19560.0353-0.14480.0683-0.2275-26.136631.303337.5235
134.1717-2.8180.99980.0951-0.89832.88030.0348-0.0972-0.00070.01840.0916-0.39280.07860.2915-0.1264-0.09840.0693-0.0214-0.10130.19380.2967-69.9214-33.042941.8906
141.66161.29380.44544.5668-0.11682.610.12360.3462-0.5548-0.1745-0.17540.44890.2448-0.10950.0518-0.022-0.11970.0367-0.304-0.09870.2954-26.116914.16160.7386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|153 A|1000 - A|1001}
2X-RAY DIFFRACTION2{ A|154 - A|249 A|1002 - A|1003}
3X-RAY DIFFRACTION3{ A|250 - A|600 }
4X-RAY DIFFRACTION4{ E|1 - E|153 E|1000 - E|1001}
5X-RAY DIFFRACTION5{ E|154 - E|249 E|1002 - E|1003}
6X-RAY DIFFRACTION6{ E|250 - E|600}
7X-RAY DIFFRACTION7{ B|1 - B|1100}
8X-RAY DIFFRACTION8{ F|1 - F|1100}
9X-RAY DIFFRACTION9{ C|10 - C|197 C|700 - C|701}
10X-RAY DIFFRACTION10{ C|198 - C|650 C|1001 - C|1002}
11X-RAY DIFFRACTION11{ G|10 - G|197 G|700 - G|700}
12X-RAY DIFFRACTION12{ G|198 - G|650 G|1001 - G|1002}
13X-RAY DIFFRACTION13{ D|1 - D|1100}
14X-RAY DIFFRACTION14{ H|1 - H|1100}

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