[English] 日本語
Yorodumi
- PDB-2jxa: Mouse Latrophilin-1 GPCR Gal_lectin domain in complex with Rhamnose -

+
Open data


ID or keywords:

Loading...

-
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 / toxic substance binding / cell adhesion molecule binding / G protein-coupled receptor activity / growth cone / carbohydrate binding / presynaptic membrane / cell surface receptor signaling pathway / neuron projection ...latrotoxin receptor activity / positive regulation of synapse assembly / toxic substance binding / cell adhesion molecule binding / G protein-coupled receptor activity / growth cone / carbohydrate binding / presynaptic membrane / cell surface receptor signaling pathway / neuron projection / G protein-coupled receptor signaling pathway / axon / synapse / glutamatergic 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 / GPCR proteolysis site, GPS, motif / GAIN domain superfamily / : / GPS motif / G-protein-coupled receptor proteolytic site domain / GAIN-B domain profile. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
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

-
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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more