[English] 日本語
Yorodumi
- PDB-5ovp: PDZ domain from rat Shank3 bound to the C terminus of CIRL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ovp
TitlePDZ domain from rat Shank3 bound to the C terminus of CIRL
Components
  • Adhesion G protein-coupled receptor L1
  • SH3 and multiple ankyrin repeat domains protein 3
KeywordsPROTEIN BINDING / PDZ domain / peptide binding / post-synaptic density / C terminus
Function / homology
Function and homology information


latrotoxin receptor activity / response to interleukin-17 / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / maintenance of postsynaptic density structure / RET signaling / postsynaptic density assembly / embryonic epithelial tube formation ...latrotoxin receptor activity / response to interleukin-17 / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / maintenance of postsynaptic density structure / RET signaling / postsynaptic density assembly / embryonic epithelial tube formation / Neurexins and neuroligins / positive regulation of synapse structural plasticity / vocal learning / negative regulation of actin filament bundle assembly / negative regulation of cell volume / positive regulation of synapse maturation / structural constituent of postsynaptic density / positive regulation of glutamate receptor signaling pathway / regulation of grooming behavior / positive regulation of long-term neuronal synaptic plasticity / NMDA glutamate receptor clustering / vocalization behavior / regulation of behavioral fear response / neuron spine / regulation of dendritic spine morphogenesis / AMPA glutamate receptor clustering / dendritic spine morphogenesis / neural precursor cell proliferation / brain morphogenesis / locomotion / positive regulation of synapse assembly / regulation of long-term synaptic potentiation / positive regulation of AMPA receptor activity / long-term synaptic depression / ciliary membrane / exploration behavior / regulation of postsynapse organization / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of long-term synaptic depression / adult behavior / positive regulation of dendritic spine development / locomotory exploration behavior / associative learning / positive regulation of excitatory postsynaptic potential / social behavior / neuromuscular process controlling balance / : / toxic substance binding / postsynaptic density, intracellular component / glial cell proliferation / cell adhesion molecule binding / synapse assembly / positive regulation of synaptic transmission, glutamatergic / learning / positive regulation of long-term synaptic potentiation / locomotory behavior / G protein-coupled receptor binding / G protein-coupled receptor activity / long-term synaptic potentiation / ionotropic glutamate receptor binding / modulation of chemical synaptic transmission / regulation of synaptic plasticity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / memory / SH3 domain binding / : / MAPK cascade / presynaptic membrane / actin binding / gene expression / growth cone / scaffold protein binding / carbohydrate binding / postsynaptic membrane / dendritic spine / postsynaptic density / learning or memory / cell surface receptor signaling pathway / neuron projection / axon / glutamatergic synapse / synapse / protein-containing complex binding / zinc ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Latrophilin-1 / 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. ...Latrophilin-1 / 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 / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / 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) / PDZ domain / Pdz3 Domain / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Ankyrin repeats (3 copies) / PDZ superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Adhesion G protein-coupled receptor L1 / SH3 and multiple ankyrin repeat domains protein 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsPonna, S.K. / Myllykoski, M. / Boeckers, T.M. / Kursula, P.
CitationJournal: J. Neurochem. / Year: 2018
Title: Structural basis for PDZ domain interactions in the post-synaptic density scaffolding protein Shank3.
Authors: Ponna, S.K. / Ruskamo, S. / Myllykoski, M. / Keller, C. / Boeckers, T.M. / Kursula, P.
History
DepositionAug 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SH3 and multiple ankyrin repeat domains protein 3
B: Adhesion G protein-coupled receptor L1


Theoretical massNumber of molelcules
Total (without water)11,0862
Polymers11,0862
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-5 kcal/mol
Surface area5630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.090, 32.090, 150.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-749-

HOH

21A-751-

HOH

-
Components

#1: Protein SH3 and multiple ankyrin repeat domains protein 3 / Shank3 / Proline-rich synapse-associated protein 2 / ProSAP2 / SPANK-2


Mass: 10400.004 Da / Num. of mol.: 1 / Fragment: PDZ domain, UNP residues 570-664
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Shank3, Prosap2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JLU4
#2: Protein/peptide Adhesion G protein-coupled receptor L1 / Calcium-independent alpha-latrotoxin receptor 1 / CIRL-1 / Latrophilin-1


Mass: 685.810 Da / Num. of mol.: 1 / Fragment: UNP residues 1510-1515 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: O88917
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.01 Å3/Da / Density % sol: 38.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 2% PEG 400, 2 M ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 14688 / % possible obs: 99.7 % / Redundancy: 10.7 % / Biso Wilson estimate: 28 Å2 / CC1/2: 1 / Rrim(I) all: 0.095 / Net I/σ(I): 15.4
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 10 % / Num. unique obs: 1055 / CC1/2: 0.557 / Rrim(I) all: 2.457 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.5→27.791 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.91
RfactorNum. reflection% reflection
Rfree0.2355 737 5.04 %
Rwork0.1934 --
obs0.1954 14613 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→27.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms783 0 0 63 846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011813
X-RAY DIFFRACTIONf_angle_d1.0381104
X-RAY DIFFRACTIONf_dihedral_angle_d21.263299
X-RAY DIFFRACTIONf_chiral_restr0.085131
X-RAY DIFFRACTIONf_plane_restr0.008143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.61580.37631440.33652728X-RAY DIFFRACTION99
1.6158-1.77840.27821490.26482733X-RAY DIFFRACTION100
1.7784-2.03560.24711460.20112739X-RAY DIFFRACTION100
2.0356-2.56440.23191470.1922781X-RAY DIFFRACTION100
2.5644-27.79550.2151510.17022895X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1456-0.6894-0.20630.542-0.15971.571-0.0885-0.08930.07240.11390.1514-0.00470.14840.17630.00080.17540.0067-0.0070.1746-0.0190.1726-8.3068-6.015514.1081
20.0338-0.1690.0072-0.0087-0.05340.00710.1952-0.0323-0.0677-0.0011-0.086-0.0698-0.30880.20080.00010.2160.03760.00430.27550.01880.2192-5.9267-6.263619.0146
30.06740.0565-0.03070.0516-0.05750.05490.16890.00950.1603-0.15430.0427-0.3616-0.1299-0.1483-0.00010.23440.015-0.01380.2057-0.00650.1642-12.292-5.2765.003
41.0680.1225-0.18880.3514-0.81951.12550.0533-0.07230.0883-0.07570.1969-0.0764-0.066-0.14970.14260.22420.0668-0.0280.1710.00710.1471-11.3504-6.8613.3467
50.4824-0.0264-0.73350.45490.00581.1226-0.31470.3004-0.2938-0.56870.3565-0.25590.30410.0896-0.00590.27440.19340.10670.1908-0.05560.27940.423-17.05869.3722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 617 through 662 )
2X-RAY DIFFRACTION2chain 'A' and (resid 663 through 674 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1510 through 1515 )
4X-RAY DIFFRACTION4chain 'A' and (resid 579 through 607 )
5X-RAY DIFFRACTION5chain 'A' and (resid 608 through 616 )

+
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://pdbjlvh1.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