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- PDB-6jbu: High resolution crystal structure of human FLRT3 LRR domain in co... -

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Basic information

Entry
Database: PDB / ID: 6jbu
TitleHigh resolution crystal structure of human FLRT3 LRR domain in complex with mouse CIRL3 Olfactomedin like domain
Components
  • Adhesion G protein-coupled receptor L3
  • Leucine-rich repeat transmembrane protein FLRT3
KeywordsCELL ADHESION / Membrane glycoprotein / Complex
Function / homology
Function and homology information


proepicardium cell migration involved in pericardium morphogenesis / locomotion involved in locomotory behavior / head development / synaptic membrane adhesion / growth cone membrane / cell-cell adhesion via plasma-membrane adhesion molecules / embryonic morphogenesis / fibroblast growth factor receptor binding / Signaling by ROBO receptors / maintenance of postsynaptic specialization structure ...proepicardium cell migration involved in pericardium morphogenesis / locomotion involved in locomotory behavior / head development / synaptic membrane adhesion / growth cone membrane / cell-cell adhesion via plasma-membrane adhesion molecules / embryonic morphogenesis / fibroblast growth factor receptor binding / Signaling by ROBO receptors / maintenance of postsynaptic specialization structure / Downstream signaling of activated FGFR1 / chemorepellent activity / positive regulation of synapse assembly / neuron projection extension / response to axon injury / fibroblast growth factor receptor signaling pathway / axonal growth cone / axon terminus / synapse assembly / extracellular matrix / response to cocaine / synaptic membrane / G protein-coupled receptor activity / axon guidance / synapse organization / neuron migration / Schaffer collateral - CA1 synapse / adenylate cyclase-activating G protein-coupled receptor signaling pathway / neuron projection development / cell-cell junction / cell junction / protein-macromolecule adaptor activity / heart development / carbohydrate binding / postsynaptic membrane / postsynaptic density / cell surface receptor signaling pathway / axon / focal adhesion / glutamatergic synapse / calcium ion binding / endoplasmic reticulum membrane / 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 / 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 / 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 / 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 / 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. / Leucine-rich repeat domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Adhesion G protein-coupled receptor L3 / Leucine-rich repeat transmembrane protein FLRT3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
AuthorsLiu, H. / Li, Z. / Xu, F.
CitationJournal: To Be Published
Title: High resolution crystal structure of human FLRT3 LRR domain in complex with mouse CIRL3 Olfactomedin like domain
Authors: Liu, H. / Li, Z. / Xu, F.
History
DepositionJan 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adhesion G protein-coupled receptor L3
B: Leucine-rich repeat transmembrane protein FLRT3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,21413
Polymers71,2642
Non-polymers95011
Water6,702372
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.135, 121.135, 83.413
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Adhesion G protein-coupled receptor L3 / CIRL3 / Latrophilin-3 / Lectomedin-3


Mass: 31650.949 Da / Num. of mol.: 1 / Fragment: Olfactomedin like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adgrl3, Kiaa0768, Lec3, Lphn3 / Production host: Homo sapiens (human) / References: UniProt: Q80TS3
#2: Protein Leucine-rich repeat transmembrane protein FLRT3 / Fibronectin-like domain-containing leucine-rich transmembrane protein 3


Mass: 39612.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLRT3, KIAA1469, UNQ856/PRO1865 / Production host: Homo sapiens (human) / References: UniProt: Q9NZU0

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Sugars , 1 types, 2 molecules

#6: 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.: 2
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 , 4 types, 381 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 560 mM sodium monobasic phosphate/potassium dibasic phosphate, 0.1 M Tris pH 8.5, 1.5% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.849→50 Å / Num. obs: 60397 / % possible obs: 99.7 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Rsym value: 0.071 / Χ2: 1.465 / Net I/σ(I): 28.133
Reflection shellResolution: 1.849→1.88 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.884 / Mean I/σ(I) obs: 2.737 / Num. unique obs: 2986 / CC1/2: 0.822 / Rpim(I) all: 0.357 / Rrim(I) all: 0.955 / Rsym value: 0.749 / Χ2: 1.023 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RMK, 4YEB, 5CMN

4rmk

4yeb

5cmn


Resolution: 1.849→44.403 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24
RfactorNum. reflection% reflection
Rfree0.2343 2961 4.91 %
Rwork0.2077 --
obs0.209 60353 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.849→44.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 57 372 5137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014873
X-RAY DIFFRACTIONf_angle_d1.1156631
X-RAY DIFFRACTIONf_dihedral_angle_d19.2371809
X-RAY DIFFRACTIONf_chiral_restr0.086733
X-RAY DIFFRACTIONf_plane_restr0.008856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8487-1.87910.30861320.24342671X-RAY DIFFRACTION98
1.8791-1.91150.2551630.24582716X-RAY DIFFRACTION100
1.9115-1.94620.29941430.24072716X-RAY DIFFRACTION100
1.9462-1.98360.28041410.23762730X-RAY DIFFRACTION100
1.9836-2.02410.27281330.22752680X-RAY DIFFRACTION100
2.0241-2.06810.24221330.22622748X-RAY DIFFRACTION100
2.0681-2.11630.24071350.2152696X-RAY DIFFRACTION100
2.1163-2.16920.24151170.21732773X-RAY DIFFRACTION100
2.1692-2.22780.26031640.22442699X-RAY DIFFRACTION100
2.2278-2.29340.26481650.21372693X-RAY DIFFRACTION100
2.2934-2.36740.27411340.20782746X-RAY DIFFRACTION100
2.3674-2.4520.24281030.22432771X-RAY DIFFRACTION100
2.452-2.55020.26781410.21772718X-RAY DIFFRACTION100
2.5502-2.66620.27741510.22112720X-RAY DIFFRACTION100
2.6662-2.80680.23031360.22522751X-RAY DIFFRACTION100
2.8068-2.98260.23561370.21142761X-RAY DIFFRACTION100
2.9826-3.21280.23631510.21322738X-RAY DIFFRACTION100
3.2128-3.5360.22241320.20042762X-RAY DIFFRACTION100
3.536-4.04740.21061460.19212788X-RAY DIFFRACTION100
4.0474-5.09810.20211460.16992791X-RAY DIFFRACTION100
5.0981-44.41610.22931580.22382724X-RAY DIFFRACTION94

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