[English] 日本語
Yorodumi
- PDB-4h11: Interaction partners of PSD-93 studied by X-ray crystallography a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4h11
TitleInteraction partners of PSD-93 studied by X-ray crystallography and fluorescent polarization spectroscopy
ComponentsDisks large homolog 2
KeywordsNEUROPEPTIDE / All beta PDZ / Protein interaction / PROTEIN BINDING
Function / homology
Function and homology information


retrograde axonal protein transport / neuronal ion channel clustering / clustering of voltage-gated potassium channels / Neurexins and neuroligins / anterograde axonal protein transport / structural constituent of postsynaptic density / receptor localization to synapse / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / cellular response to potassium ion ...retrograde axonal protein transport / neuronal ion channel clustering / clustering of voltage-gated potassium channels / Neurexins and neuroligins / anterograde axonal protein transport / structural constituent of postsynaptic density / receptor localization to synapse / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / cellular response to potassium ion / axon initial segment / juxtaparanode region of axon / RAF/MAP kinase cascade / neurotransmitter receptor localization to postsynaptic specialization membrane / receptor clustering / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / sensory perception of pain / axon cytoplasm / PDZ domain binding / postsynaptic density membrane / neuromuscular junction / cell-cell adhesion / kinase binding / synaptic vesicle membrane / cell junction / nervous system development / protein phosphatase binding / basolateral plasma membrane / chemical synaptic transmission / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / neuronal cell body / dendrite / protein-containing complex binding / protein kinase binding / glutamatergic synapse / membrane
Similarity search - Function
Disks Large homologue 2, SH3 domain / 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. ...Disks Large homologue 2, SH3 domain / 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
ACETATE ION / Disks large homolog 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsFiorentini, M. / Kastrup, J.S. / Gajhede, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Interaction partners of PSD-93 studied by X-ray crystallography and fluorescence polarization spectroscopy.
Authors: Fiorentini, M. / Bach, A. / Stromgaard, K. / Kastrup, J.S. / Gajhede, M.
History
DepositionSep 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Disks large homolog 2
B: Disks large homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3584
Polymers22,2032
Non-polymers1552
Water3,117173
1
A: Disks large homolog 2


Theoretical massNumber of molelcules
Total (without water)11,1021
Polymers11,1021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disks large homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2573
Polymers11,1021
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Disks large homolog 2
hetero molecules

A: Disks large homolog 2


Theoretical massNumber of molelcules
Total (without water)22,3584
Polymers22,2032
Non-polymers1552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area1470 Å2
ΔGint-22 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.200, 45.550, 104.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Disks large homolog 2 / Channel-associated protein of synapse-110 / Chapsyn-110 / Postsynaptic density protein PSD-93


Mass: 11101.501 Da / Num. of mol.: 2 / Fragment: PDZ1: unp residues 93-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg2, Dlgh2 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)pLYsS / References: UniProt: Q63622
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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.: 173 / 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: 1.77 Å3/Da / Density % sol: 30.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: Crystallization of PSD-93 PDZ1ext was performed using the hanging-drop vapor diffusion technique by mixing 1 microliter of a 2 mg/ml protein solution (PBS buffer) and 1 l reservoir solution ...Details: Crystallization of PSD-93 PDZ1ext was performed using the hanging-drop vapor diffusion technique by mixing 1 microliter of a 2 mg/ml protein solution (PBS buffer) and 1 l reservoir solution (0.2 M lithium sulfate, 20% PEG 1000, 0.1 M citric acid/sodium hydrogen phosphate pH 4.2. The reservoir volume was 500 microliter, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 16, 2009
RadiationMonochromator: FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→28 Å / Num. all: 19048 / Num. obs: 19048 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.67→1.73 Å / % possible all: 99.8

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→28 Å / SU ML: 0.15 / σ(F): 0 / Phase error: 21.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.213 974 5.16 %Random
Rwork0.1716 ---
obs0.1738 18859 99.03 %-
all-18859 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 9 173 1726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111604
X-RAY DIFFRACTIONf_angle_d1.2532174
X-RAY DIFFRACTIONf_dihedral_angle_d13.13612
X-RAY DIFFRACTIONf_chiral_restr0.079247
X-RAY DIFFRACTIONf_plane_restr0.006293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.7580.2771410.20822518X-RAY DIFFRACTION100
1.758-1.86820.22881440.19622502X-RAY DIFFRACTION100
1.8682-2.01240.23451480.18352527X-RAY DIFFRACTION100
2.0124-2.21480.22351160.15862573X-RAY DIFFRACTION100
2.2148-2.53510.20821380.16982592X-RAY DIFFRACTION100
2.5351-3.19330.21261600.16352568X-RAY DIFFRACTION100
3.1933-28.00550.18861270.16762605X-RAY DIFFRACTION94
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)
10.48280.15620.40810.26570.05450.35540.0263-0.0490.1889-0.0245-0.07590.0943-0.2389-0.263-0.10540.20560.07760.02430.08980.05040.1431-1.713818.694634.8609
20.2484-0.07510.19240.0509-0.0330.1346-0.1144-0.0132-0.2337-0.0605-0.0221-0.04270.11010.0638-0.03020.1236-0.00730.04550.0986-0.00320.13034.73975.039237.1947
30.03770.0376-0.04370.07310.05910.17230.07510.16390.0064-0.0584-0.01860.0712-0.0804-0.34240.00370.1175-0.01570.03240.1748-0.02310.1573-8.61558.12438.8832
40.04690.01990.02320.0576-0.00990.0124-0.03230.06940.1248-0.0889-0.0394-0.1163-0.23880.0818-0.04180.127-0.0162-0.00090.0726-0.00680.10077.739514.581341.9795
50.0020.0013-0.00320.00360.00560.00740.069-0.2173-0.0226-0.00750.0137-0.04770.07460.01530.00280.11090.04630.00010.13730.02750.12479.07555.469845.138
60.35360.1680.12090.0920.09110.1293-0.0847-0.22990.189-0.1825-0.06950.01610.0756-0.0811-0.06220.13850.00190.01760.12540.00020.07720.231913.868843.8513
70.18720.11330.07410.06830.04460.02690.2251-0.1909-0.27540.0510.0786-0.26620.0340.07340.12160.2748-0.07270.02150.30830.13390.3146-4.269220.435117.8923
81.27830.22090.65460.07340.06720.401-0.0427-0.15570.2105-0.4472-0.1432-0.1493-0.0911-0.0762-0.09810.28030.03330.07010.1060.03070.1822-18.1048-4.782335.3927
90.07190.0290.05180.00330.02990.20350.0141-0.39880.06330.0789-0.04250.03780.0837-0.02710.00430.17360.02810.03690.1484-0.00010.1743-16.9352-19.243545.7718
100.6137-0.01850.2069-0.0007-0.00490.0782-0.23220.20760.1795-0.13090.2039-0.13750.23810.1734-0.03050.2040.00360.04170.15420.00090.1052-2.2461-15.895331.1911
110.1449-0.15770.06620.1217-0.0980.2227-0.0939-0.12250.0462-0.1490.07130.0179-0.0255-0.2450.03950.0680.0120.00960.0709-0.00950.0837-19.2395-14.858137.8534
120.04490.0378-0.01290.03850.01680.0215-0.0498-0.35140.1443-0.0346-0.0033-0.02880.04310.1776-00.12460.0309-0.00260.1567-0.0250.1772-5.8769-12.545544.0306
130.02320.09140.0240.38630.10710.03080.125-0.32710.2853-0.16530.00330.08280.0046-0.08370.00470.13180.00120.03220.2298-0.0040.1491-15.8041-9.245344.4513
140.006-0.01170.00180.0143-0.0070.014-0.1228-0.0563-0.06440.0418-0.0114-0.10320.07310.0102-0.00020.3234-0.11060.00810.24430.00710.1892-21.1233-2.899918.1454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 91 through 102 )
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 148 )
4X-RAY DIFFRACTION4chain 'A' and (resid 149 through 162 )
5X-RAY DIFFRACTION5chain 'A' and (resid 163 through 171 )
6X-RAY DIFFRACTION6chain 'A' and (resid 172 through 184 )
7X-RAY DIFFRACTION7chain 'A' and (resid 185 through 192 )
8X-RAY DIFFRACTION8chain 'B' and (resid 92 through 102 )
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 114 )
10X-RAY DIFFRACTION10chain 'B' and (resid 115 through 126 )
11X-RAY DIFFRACTION11chain 'B' and (resid 127 through 153 )
12X-RAY DIFFRACTION12chain 'B' and (resid 154 through 171 )
13X-RAY DIFFRACTION13chain 'B' and (resid 172 through 184 )
14X-RAY DIFFRACTION14chain 'B' and (resid 185 through 192 )

+
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