[English] 日本語
Yorodumi
- PDB-5afb: Crystal structure of the Latrophilin3 Lectin and Olfactomedin Domains -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5afb
TitleCrystal structure of the Latrophilin3 Lectin and Olfactomedin Domains
ComponentsLATROPHILIN-3
KeywordsSIGNALING PROTEIN / ADHESION / REPULSION / GUIDANCE / BETA PROPELLER / OLFACTOMEDIN / LECTIN
Function / homology
Function and homology information


locomotion involved in locomotory behavior / maintenance of postsynaptic specialization structure / cell-cell adhesion via plasma-membrane adhesion molecules / positive regulation of synapse assembly / synapse assembly / response to cocaine / G protein-coupled receptor activity / synapse organization / neuron migration / Schaffer collateral - CA1 synapse ...locomotion involved in locomotory behavior / maintenance of postsynaptic specialization structure / cell-cell adhesion via plasma-membrane adhesion molecules / positive regulation of synapse assembly / synapse assembly / response to cocaine / G protein-coupled receptor activity / synapse organization / neuron migration / Schaffer collateral - CA1 synapse / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell-cell junction / carbohydrate binding / postsynaptic membrane / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / axon / glutamatergic synapse / calcium ion binding / membrane / plasma membrane
Similarity search - Function
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 / 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. ...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 / 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 / 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. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Adhesion G protein-coupled receptor L3 / Adhesion G protein-coupled receptor L3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.16 Å
AuthorsJackson, V.A. / del Toro, D. / Carrasquero, M. / Roversi, P. / Harlos, K. / Klein, R. / Seiradake, E.
CitationJournal: Structure / Year: 2015
Title: Structural Basis of Latrophilin-Flrt Interaction.
Authors: Jackson, V.A. / Del Toro, D. / Carrasquero, M. / Roversi, P. / Harlos, K. / Klein, R. / Seiradake, E.
History
DepositionJan 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Mar 9, 2016Group: Database references / Other / Structure summary
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...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 / 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_asym_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_asym_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LATROPHILIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5066
Polymers44,0371
Non-polymers4685
Water1,58588
1
A: LATROPHILIN-3
hetero molecules

A: LATROPHILIN-3
hetero molecules

A: LATROPHILIN-3
hetero molecules

A: LATROPHILIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,02224
Polymers176,1494
Non-polymers1,87420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area15480 Å2
ΔGint-124 kcal/mol
Surface area52970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.430, 96.650, 101.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2006-

HOH

21A-2077-

HOH

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein LATROPHILIN-3 /


Mass: 44037.125 Da / Num. of mol.: 1 / Fragment: LECTIN AND OLFACTOMEDIN DOMAINS, RESIDUES 97-459
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: HUMAN EMBRYONIC KIDNEY 293T / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q80TS3, UniProt: Q9HAR2*PLUS
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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

-
Non-polymers , 4 types, 92 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.84 % / Description: NONE
Crystal growpH: 6
Details: 0.1 M MES BUFFER, 4M NACL, 0.6 M NON- DETERGENT SULFO-BETAINE NDSB195, PH 6.0

-
Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.07114, 1.0716
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.071141
21.07161
ReflectionResolution: 2.16→62.09 Å / Num. obs: 39860 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.49 % / Biso Wilson estimate: 37.49 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.2
Reflection shellResolution: 2.16→2.27 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.7 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
xia2data reduction
xia2data scaling
autoSHARPphasing
RefinementMethod to determine structure: SIR
Starting model: NONE

Resolution: 2.16→22.91 Å / Cor.coef. Fo:Fc: 0.9238 / Cor.coef. Fo:Fc free: 0.9066 / SU R Cruickshank DPI: 0.248 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.248 / SU Rfree Blow DPI: 0.196 / SU Rfree Cruickshank DPI: 0.197
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 1053 5.01 %RANDOM
Rwork0.2044 ---
obs0.2064 21008 99.67 %-
Displacement parametersBiso mean: 43.1 Å2
Baniso -1Baniso -2Baniso -3
1--18.2401 Å20 Å20 Å2
2--4.1845 Å20 Å2
3---14.0557 Å2
Refine analyzeLuzzati coordinate error obs: 0.326 Å
Refinement stepCycle: LAST / Resolution: 2.16→22.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2814 0 28 88 2930
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082916HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.993970HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d973SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes77HARMONIC2
X-RAY DIFFRACTIONt_gen_planes430HARMONIC5
X-RAY DIFFRACTIONt_it2917HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion17.42
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion375SEMIHARMONIC5
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_contact3259SEMIHARMONIC4
LS refinement shellResolution: 2.16→2.27 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2693 136 4.96 %
Rwork0.2354 2605 -
all0.2372 2741 -
obs--99.67 %
Refinement TLS params.Method: refined / Origin x: 31.5692 Å / Origin y: 9.0853 Å / Origin z: 20.5878 Å
111213212223313233
T0.0785 Å20.0539 Å2-0.0255 Å2--0.1689 Å2-0.0055 Å2---0.1684 Å2
L0.5107 °20.1588 °2-0.2157 °2-0.7014 °2-0.0963 °2--1.0748 °2
S-0.0204 Å °-0.045 Å °-0.0407 Å °0.0715 Å °0.0115 Å °0.0818 Å °-0.0985 Å °-0.116 Å °0.009 Å °
Refinement TLS groupSelection details: CHAIN A

+
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