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- PDB-2jxa: Mouse Latrophilin-1 GPCR Gal_lectin domain in complex with Rhamnose -

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Basic information

Entry
Database: PDB / ID: 2jxa
TitleMouse Latrophilin-1 GPCR Gal_lectin domain in complex with Rhamnose
ComponentsLatrophilin 1
KeywordsCELL ADHESION / SIGNALING PROTEIN / Lectin / beta-sandwich / disulphide / glycosylated / L-Rhamnose / complex / G-protein coupled receptor / Membrane / Receptor / Transducer / Transmembrane
Function / homology
Function and homology information


latrotoxin receptor activity / positive regulation of synapse assembly / cell adhesion molecule binding / G protein-coupled receptor activity / presynaptic membrane / growth cone / carbohydrate binding / cell surface receptor signaling pathway / neuron projection / axon ...latrotoxin receptor activity / positive regulation of synapse assembly / cell adhesion molecule binding / G protein-coupled receptor activity / presynaptic membrane / growth cone / carbohydrate binding / cell surface receptor signaling pathway / neuron projection / axon / synapse / plasma membrane
Similarity search - Function
Latrophilin-1 / Rhamnose-binding lectin domain (RBL) / 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 ...Latrophilin-1 / Rhamnose-binding lectin domain (RBL) / 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 / AGRL2-4 GAIN subdomain A / 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. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-L-rhamnopyranose / : / Adhesion G protein-coupled receptor L1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsVakonakis, I. / Campbell, I.D.
CitationJournal: To be Published
Title: Solution structure and sugar-binding mechanism of mouse Latrophilin-1 RBL: a novel 7TM receptor-attached lectin-like domain.
Authors: Vakonakis, I. / Langenhan, T. / Promel, S. / Russ, A. / Campbell, I.D.
History
DepositionNov 9, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nmr_software / struct_conn / 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_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 30, 2024Group: 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Latrophilin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3833
Polymers11,9981
Non-polymers3852
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Latrophilin 1


Mass: 11997.645 Da / Num. of mol.: 1 / Fragment: Gal_lectin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: gene construct integrated in the organism's genome
Gene: Lphn1 / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: Q5U4D5, UniProt: Q80TR1*PLUS
#2: 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
#3: Sugar ChemComp-RAM / alpha-L-rhamnopyranose / alpha-L-rhamnose / 6-deoxy-alpha-L-mannopyranose / L-rhamnose / rhamnose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LRhapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-rhamnopyranoseCOMMON NAMEGMML 1.0
a-L-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D HNHA
1413D 1H-15N NOESY
1513D HNHB
1624D 13C/13C NOESY
1722D 13C methyl-carbonyl
1822D 13C methyl-nitrogen
1922D 13C methyl-ca
110315N IPAP-HSQC
11153D 1H-15N NOESY
11242D 13C-purged/13C-filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2 mM [U-100% 15N] protein, 20 mM sodium phosphate, 0.1 mM DSS, 0.02 % sodium azide; 95% H2O/5% D2O95% H2O/5% D2O
21-2 mM [U-100% 13C; U-100% 15N] protein, 20 mM sodium phosphate, 0.1 mM DSS, 0.02 % sodium azide; 100% D2O100% D2O
31-2 mM [U-100% 15N] protein, 20 mM sodium phosphate, 0.1 mM DSS, 0.02 % sodium azide, 4 % PEG C12E5, 0.96 molecular ratio hexanol; 95% H2O/5% D2O95% H2O/5% D2O
41-2 mM [U-100% 13C; U-100% 15N] protein, 20 mM sodium phosphate, 0.1 mM DSS, 0.02 % sodium azide, 10 mM L-Rhamnose; 100% D2O100% D2O
51-2 mM [U-100% 15N] protein, 20 mM sodium phosphate, 0.1 mM DSS, 0.02 % sodium azide, 10 mM L-Rhamnose; 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein[U-100% 15N]1
5 %D2O1
20 mMsodium phosphate1
0.1 mMDSS1
0.02 %sodium azide1
1 mMprotein[U-100% 13C; U-100% 15N]2
100 %D2O2
20 mMsodium phosphate2
0.1 mMDSS2
0.02 %sodium azide2
1 mMprotein[U-100% 15N]3
5 %D2O3
20 mMsodium phosphate3
0.1 mMDSS3
0.02 %sodium azide3
4 %PEG C12E53
0.96 %hexanol3
1 mMprotein[U-100% 13C; U-100% 15N]4
100 %D2O4
20 mMsodium phosphate4
0.1 mMDSS4
0.02 %sodium azide4
10 mML-Rhamnose4
1 mMprotein[U-100% 15N]5
5 %D2O5
20 mMsodium phosphate5
0.1 mMDSS5
0.02 %sodium azide5
10 mML-Rhamnose5
Sample conditionsIonic strength: 30 / pH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
Field strength (MHz)Spectrometer-ID
7501
6002
5003
9504

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Processing

NMR software
NameVersionDeveloperClassification
OmegaBeta 6.0.3b2GE/Brukercollection
NMRPipe2.4 Rev 2006.095.11.35Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPP4.3.7Garrettdata analysis
PIPP4.3.7Garrettpeak picking
X-PLOR NIH2.17.0Schwieters, Kuszewski, Tjandra, Cloregeometry optimization
X-PLOR NIH2.17.0Schwieters, Kuszewski, Tjandra, Clorerefinement
X-PLOR NIH2.17.0Schwieters, Kuszewski, Tjandra, Clorestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Simulated annealing in the presence of Rhamnose starting from average apo-protein coordinates
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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