[English] 日本語
Yorodumi
- PDB-3jxt: Crystal structure of the third PDZ domain of SAP-102 in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jxt
TitleCrystal structure of the third PDZ domain of SAP-102 in complex with a fluorogenic peptide-based ligand
Components
  • Disks large homolog 3
  • Voltage-dependent calcium channel gamma-2 subunit
KeywordsSIGNALING PROTEIN / SAP102 / DLG3 / Stargazin / 4-DMAP / 4DB / PDZ domain / solvatochromic flurophore / fluorogenic probe / Calcium channel / Calcium transport / Ion transport / Ionic channel / Transport / Voltage-gated channel
Function / homology
Function and homology information


Presynaptic depolarization and calcium channel opening / regulation of postsynaptic neurotransmitter receptor activity / LGI-ADAM interactions / establishment of planar polarity / Trafficking of AMPA receptors / Neurexins and neuroligins / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / structural constituent of postsynaptic density / receptor localization to synapse ...Presynaptic depolarization and calcium channel opening / regulation of postsynaptic neurotransmitter receptor activity / LGI-ADAM interactions / establishment of planar polarity / Trafficking of AMPA receptors / Neurexins and neuroligins / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / structural constituent of postsynaptic density / receptor localization to synapse / cerebellar mossy fiber / neurotransmitter receptor transport, postsynaptic endosome to lysosome / Activation of Ca-permeable Kainate Receptor / regulation of AMPA receptor activity / neurotransmitter receptor internalization / establishment or maintenance of epithelial cell apical/basal polarity / membrane hyperpolarization / postsynaptic neurotransmitter receptor diffusion trapping / nervous system process / Synaptic adhesion-like molecules / protein targeting to membrane / RAF/MAP kinase cascade / voltage-gated calcium channel complex / neurotransmitter receptor localization to postsynaptic specialization membrane / neuromuscular junction development / receptor clustering / transmission of nerve impulse / channel regulator activity / regulation of postsynaptic membrane neurotransmitter receptor levels / AMPA glutamate receptor complex / membrane depolarization / positive regulation of protein tyrosine kinase activity / bicellular tight junction / Unblocking of NMDA receptors, glutamate binding and activation / postsynaptic density, intracellular component / phosphatase binding / voltage-gated calcium channel activity / somatodendritic compartment / ionotropic glutamate receptor binding / hippocampal mossy fiber to CA3 synapse / positive regulation of synaptic transmission, glutamatergic / regulation of membrane potential / dendritic shaft / PDZ domain binding / postsynaptic density membrane / neuromuscular junction / Schaffer collateral - CA1 synapse / kinase binding / cell-cell adhesion / response to calcium ion / cell-cell junction / growth cone / basolateral plasma membrane / protein phosphatase binding / chemical synaptic transmission / postsynaptic density / neuron projection / protein domain specific binding / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / synapse / protein kinase binding / cell surface / plasma membrane / cytoplasm
Similarity search - Function
Disks Large homologue 3, SH3 domain / Voltage-dependent calcium channel, gamma-2 subunit / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / PMP-22/EMP/MP20/Claudin family ...Disks Large homologue 3, SH3 domain / Voltage-dependent calcium channel, gamma-2 subunit / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / PMP-22/EMP/MP20/Claudin family / : / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / Pdz3 Domain / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Voltage-dependent calcium channel gamma-2 subunit / Disks large homolog 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSainlos, M. / Olivier, N.B. / Imperiali, B.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Caged mono- and divalent ligands for light-assisted disruption of PDZ domain-mediated interactions.
Authors: Sainlos, M. / Iskenderian-Epps, W.S. / Olivier, N.B. / Choquet, D. / Imperiali, B.
History
DepositionSep 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 10, 2013Group: Database references
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Disks large homolog 3
B: Disks large homolog 3
C: Voltage-dependent calcium channel gamma-2 subunit
D: Voltage-dependent calcium channel gamma-2 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0965
Polymers24,0374
Non-polymers591
Water6,125340
1
A: Disks large homolog 3
D: Voltage-dependent calcium channel gamma-2 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0773
Polymers12,0182
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-2.9 kcal/mol
Surface area5780 Å2
MethodPISA
2
B: Disks large homolog 3
C: Voltage-dependent calcium channel gamma-2 subunit


Theoretical massNumber of molelcules
Total (without water)12,0182
Polymers12,0182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-2.5 kcal/mol
Surface area5490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.597, 54.215, 86.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the monomeric complex composed of one PDZ domain and its ligand.

-
Components

#1: Protein Disks large homolog 3 / Synapse-associated protein 102 / SAP102 / PSD-95/SAP90-related protein 1


Mass: 11145.364 Da / Num. of mol.: 2 / Fragment: Third PDZ domain: UNP residues 393-493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg3, Dlgh3 / Plasmid: pET-NO, modified pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL / References: UniProt: Q62936
#2: Protein/peptide Voltage-dependent calcium channel gamma-2 subunit / Neuronal voltage-gated calcium channel gamma-2 subunit / Stargazin


Mass: 872.987 Da / Num. of mol.: 2
Fragment: C-terminal motif of Stargazin: UNP O88602 residues 318-323
Mutation: R318(4DB) / Source method: obtained synthetically
Details: Peptide ligand obtained by solid phase peptide synthesis
References: UniProt: O88602
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.0 M Sodium citrate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 7, 2009 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 37896 / Num. obs: 37820 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 16.346 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 28.19
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6.94 / Num. unique all: 3720 / Rsym value: 0.24 / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3JVQ

3jvq
PDB Unreleased entry


Resolution: 1.5→45.87 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21442 1886 5 %RANDOM
Rwork0.18511 ---
all0.18659 35937 --
obs0.18659 35869 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.124 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1549 0 4 340 1893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0221572
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.28922117
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4155196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.84122.20668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01215245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5691518
X-RAY DIFFRACTIONr_chiral_restr0.060.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021207
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3160.2757
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21055
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3440.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1931.5996
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.40821572
X-RAY DIFFRACTIONr_scbond_it4.6443576
X-RAY DIFFRACTIONr_scangle_it6.7954.5545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 125 -
Rwork0.246 2604 -
obs--100 %

+
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