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- PDB-5ftu: Tetrameric complex of Latrophilin 3, Unc5D and FLRT2 -

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Basic information

Entry
Database: PDB / ID: 5ftu
TitleTetrameric complex of Latrophilin 3, Unc5D and FLRT2
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 / APOPTOSIS / UNCOORDINATED-5 / NETRIN RECEPTOR / FLRT / LATROPHILIN / ADHESION / REPULSION / GUIDANCE / BETA PROPELLOR / IMMUNOGLOBULIN / THROMBOSPONDIN / OLFACTOMEDIN / LECTIN / TETRAMER
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 / regulation of neuron migration / basement membrane organization / maintenance of postsynaptic specialization structure / cell-cell adhesion via plasma-membrane adhesion molecules / fibroblast growth factor receptor binding / pyramidal neuron differentiation ...cell adhesion involved in heart morphogenesis / Downstream signaling of activated FGFR1 / netrin receptor activity / locomotion involved in locomotory behavior / regulation of neuron migration / basement membrane organization / maintenance of postsynaptic specialization structure / cell-cell adhesion via plasma-membrane adhesion molecules / fibroblast growth factor receptor binding / pyramidal neuron differentiation / chemorepellent activity / positive regulation of synapse assembly / fibroblast growth factor receptor signaling pathway / heart morphogenesis / synapse assembly / response to cocaine / G protein-coupled receptor activity / axon guidance / synapse organization / neuron migration / Schaffer collateral - CA1 synapse / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell-cell junction / postsynaptic membrane / carbohydrate binding / cell surface receptor signaling pathway / neuron projection / axon / focal adhesion / glutamatergic synapse / synapse / apoptotic process / calcium ion binding / endoplasmic reticulum membrane / cell surface / extracellular space / plasma membrane
Similarity search - Function
UNC5D, Death domain / 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 / GAIN domain, N-terminal ...UNC5D, Death domain / 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 / 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 / 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 / GPS 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 / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Death 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. / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Death-like domain superfamily / Leucine-rich repeat / Fibronectin type III domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Leucine-rich repeat domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
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: 6.01 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 1.1May 11, 2016Group: Other
Revision 1.2Jul 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / 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
I: NETRIN RECEPTOR UNC5D
J: LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN FLRT2
K: ADHESION G PROTEIN-COUPLED RECEPTOR L3
L: ADHESION G PROTEIN-COUPLED RECEPTOR L3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)428,82533
Polymers426,45512
Non-polymers2,36921
Water0
1
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,94211
Polymers142,1524
Non-polymers7907
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
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)142,94211
Polymers142,1524
Non-polymers7907
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
I: NETRIN RECEPTOR UNC5D
J: LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN FLRT2
K: ADHESION G PROTEIN-COUPLED RECEPTOR L3
L: ADHESION G PROTEIN-COUPLED RECEPTOR L3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,94211
Polymers142,1524
Non-polymers7907
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)292.360, 292.360, 291.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.001, -1, -0.001), (-0.005, -0.001, 1), (-1, 0.001, -0.005)219.568, -181.61, 402.891
2given(0.001, -1), (-1, 0.007, -0.001), (0.007, 1)401.036, 218.484, 181.537
3given(0.002, -1, 0.001), (-0.001, 0.001, 1), (-1, 0.002, 0.001)218.953, -182.022, 401.162

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Components

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Protein , 3 types, 12 molecules AEIBFJCDGHKL

#1: Protein NETRIN RECEPTOR UNC5D


Mass: 15923.799 Da / Num. of mol.: 3 / Fragment: IMMUNOGLOBULIN-1
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.: 3 / 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


Mass: 43908.012 Da / Num. of mol.: 6 / Fragment: LECTIN AND OLFACTOMEDIN DOMAINS
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: Q80TS3

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Sugars , 1 types, 9 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
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, 12 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.33 Å3/Da / Density % sol: 71.62 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 6→92.45 Å / Num. obs: 16120 / % possible obs: 99.8 % / Redundancy: 75.7 % / Biso Wilson estimate: 459.95 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 0.89
Reflection shellResolution: 6→6.15 Å / Redundancy: 74.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.89 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FTT, 5AFB, 4V2C

5ftt

5afb

4v2c


Resolution: 6.01→206.73 Å / Cor.coef. Fo:Fc: 0.7473 / Cor.coef. Fo:Fc free: 0.6878 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 2.098
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 719 4.55 %RANDOM
Rwork0.2757 ---
obs0.2758 15788 97.86 %-
Displacement parametersBiso mean: 187.68 Å2
Baniso -1Baniso -2Baniso -3
1--2.598 Å20 Å20 Å2
2---2.598 Å20 Å2
3---5.1959 Å2
Refine analyzeLuzzati coordinate error obs: 1.64 Å
Refinement stepCycle: LAST / Resolution: 6.01→206.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25542 0 138 0 25680
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00726295HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8635769HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8931SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes747HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3840HARMONIC5
X-RAY DIFFRACTIONt_it26295HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.42
X-RAY DIFFRACTIONt_other_torsion20.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3390SEMIHARMONIC5
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_contact26716SEMIHARMONIC4
LS refinement shellResolution: 6.01→6.42 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2295 122 4.82 %
Rwork0.2233 2411 -
all0.2237 2533 -
obs--97.86 %

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