[English] 日本語
Yorodumi
- PDB-1pdr: CRYSTAL STRUCTURE OF THE THIRD PDZ DOMAIN FROM THE HUMAN HOMOLOG ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pdr
TitleCRYSTAL STRUCTURE OF THE THIRD PDZ DOMAIN FROM THE HUMAN HOMOLOG OF DISCS LARGE PROTEIN
ComponentsHUMAN DISCS LARGE PROTEIN
KeywordsSIGNAL TRANSDUCTION / SH3 DOMAIN
Function / homology
Function and homology information


L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / membrane raft organization / establishment of centrosome localization / NrCAM interactions / GMP kinase activity / structural constituent of postsynaptic density ...L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / membrane raft organization / establishment of centrosome localization / NrCAM interactions / GMP kinase activity / structural constituent of postsynaptic density / reproductive structure development / membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of p38MAPK cascade / embryonic skeletal system morphogenesis / immunological synapse formation / receptor localization to synapse / myelin sheath abaxonal region / lateral loop / peristalsis / smooth muscle tissue development / cell projection membrane / cortical microtubule organization / bicellular tight junction assembly / astral microtubule organization / establishment or maintenance of epithelial cell apical/basal polarity / regulation of sodium ion transmembrane transport / Synaptic adhesion-like molecules / protein localization to synapse / Trafficking of AMPA receptors / positive regulation of potassium ion transport / hard palate development / regulation of ventricular cardiac muscle cell action potential / endothelial cell proliferation / amyloid precursor protein metabolic process / lens development in camera-type eye / node of Ranvier / cortical actin cytoskeleton organization / Assembly and cell surface presentation of NMDA receptors / T cell proliferation / protein-containing complex localization / regulation of myelination / branching involved in ureteric bud morphogenesis / Activation of Ca-permeable Kainate Receptor / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of actin filament polymerization / neurotransmitter receptor localization to postsynaptic specialization membrane / receptor clustering / establishment or maintenance of cell polarity / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / basement membrane / lateral plasma membrane / intercalated disc / immunological synapse / Long-term potentiation / bicellular tight junction / potassium channel regulator activity / negative regulation of T cell proliferation / regulation of postsynaptic membrane neurotransmitter receptor levels / phosphatase binding / cytoskeletal protein binding / phosphoprotein phosphatase activity / actin filament polymerization / ionotropic glutamate receptor binding / Ras activation upon Ca2+ influx through NMDA receptor / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein localization to plasma membrane / actin filament organization / positive regulation of protein localization to plasma membrane / synaptic membrane / adherens junction / phosphatidylinositol 3-kinase/protein kinase B signal transduction / neuromuscular junction / regulation of membrane potential / cell-cell adhesion / negative regulation of ERK1 and ERK2 cascade / sarcolemma / postsynaptic density membrane / negative regulation of epithelial cell proliferation / kinase binding / cytoplasmic side of plasma membrane / cell junction / cell-cell junction / regulation of cell shape / nervous system development / RAF/MAP kinase cascade / chemical synaptic transmission / molecular adaptor activity / basolateral plasma membrane / microtubule / transmembrane transporter binding / apical plasma membrane / neuron projection / cadherin binding / membrane raft / positive regulation of cell population proliferation / protein kinase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / glutamatergic synapse
Similarity search - Function
L27-1 / L27_1 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / 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 ...L27-1 / L27_1 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / 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 / : / 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
Disks large homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsCabral, J.M. / Liddington, R.
Citation
#1: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Clustering Membrane Proteins: It'S All Coming Together with the Psd-95/Sap90 Protein Family
Authors: Gomperts, S.N.
#2: Journal: Trends Biochem.Sci. / Year: 1995
Title: Dhr Domains in Syntrophins, Neuronal No Synthases and Other Intracellular Proteins
Authors: Ponting, C.P. / Phillips, C.
#3: Journal: Nature / Year: 1995
Title: Clustering of Shaker-Type K+ Channels by Interaction with a Family of Membrane-Associated Guanylate Kinases
Authors: Kim, E. / Niethammer, M. / Rothschild, A. / Jan, Y.N. / Sheng, M.
History
DepositionJul 26, 1996Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 26, 2016Group: Other
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HUMAN DISCS LARGE PROTEIN


Theoretical massNumber of molelcules
Total (without water)10,5571
Polymers10,5571
Non-polymers00
Water1448
1
A: HUMAN DISCS LARGE PROTEIN
x 6


Theoretical massNumber of molelcules
Total (without water)63,3406
Polymers63,3406
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Unit cell
Length a, b, c (Å)110.970, 110.970, 62.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

-
Components

#1: Protein HUMAN DISCS LARGE PROTEIN / HDLG / DHR3 DOMAIN


Mass: 10556.708 Da / Num. of mol.: 1 / Fragment: PDZ3 DOMAIN, DHR3 DOMAIN
Source method: isolated from a genetically manipulated source
Details: THE THIRD PDZ DOMAIN OF THE HUMAN HOMOLOGUE OF DISCS LARGE PROTEIN
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q12959
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 5.26 Å3/Da / Density % sol: 76.61 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
20.9-1.3 Msodium citrate1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 12, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 5911 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13 % / Rmerge(I) obs: 0.108
Reflection
*PLUS
Highest resolution: 2.8 Å
Reflection shell
*PLUS
Rmerge(I) obs: 0.301

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.8→10 Å / σ(F): 2
Details: SER 517 IS POSITIONED IN A VERY TIGHT LOOP AND THERE IS CLEAR DENSITY FOR ITS MAIN CHAIN ATOMS. THE PHI AND PSI ANGLES FOR THIS RESIDUE ARE OUTSIDE THE EXPECTED RANGE. THE DEPOSITORS ...Details: SER 517 IS POSITIONED IN A VERY TIGHT LOOP AND THERE IS CLEAR DENSITY FOR ITS MAIN CHAIN ATOMS. THE PHI AND PSI ANGLES FOR THIS RESIDUE ARE OUTSIDE THE EXPECTED RANGE. THE DEPOSITORS ATTEMPTED REPEATEDLY TO REGULARIZE THEM BUT THEY ALWAYS REFINED TO THE SAME VALUES.
RfactorNum. reflection
Rfree0.271 -
Rwork0.22 -
obs0.22 5793
Displacement parametersBiso mean: 16.7 Å2
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms719 0 0 8 727
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4

+
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