[English] 日本語
Yorodumi
- PDB-6spz: Crystal structure of PDZ1-2 from PSD-95 with peptide ligand seque... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6spz
TitleCrystal structure of PDZ1-2 from PSD-95 with peptide ligand sequence RRESEI bound to both domains
Components
  • ARG-ARG-GLU-SER-GLU-ILE
  • Disks large homolog 4
KeywordsSTRUCTURAL PROTEIN / PSD-95 fragment / clustering / protein-complex / receptor-binding / membrane associated
Function / homology
Function and homology information


Sensory perception of sour taste / Classical Kir channels / regulation of skeletal muscle contraction via regulation of action potential / relaxation of skeletal muscle / LGI-ADAM interactions / magnesium ion transport / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / P2Y1 nucleotide receptor binding / Phase 4 - resting membrane potential / beta-1 adrenergic receptor binding ...Sensory perception of sour taste / Classical Kir channels / regulation of skeletal muscle contraction via regulation of action potential / relaxation of skeletal muscle / LGI-ADAM interactions / magnesium ion transport / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / P2Y1 nucleotide receptor binding / Phase 4 - resting membrane potential / beta-1 adrenergic receptor binding / membrane repolarization during action potential / neuroligin family protein binding / regulation of grooming behavior / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / membrane repolarization during cardiac muscle cell action potential / regulation of membrane repolarization / membrane depolarization during cardiac muscle cell action potential / vocalization behavior / regulation of resting membrane potential / neuron spine / cerebellar mossy fiber / AMPA glutamate receptor clustering / Synaptic adhesion-like molecules / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / regulation of monoatomic ion transmembrane transport / Trafficking of AMPA receptors / dendritic spine morphogenesis / inward rectifier potassium channel activity / negative regulation of receptor internalization / positive regulation of potassium ion transmembrane transport / neuron projection terminus / juxtaparanode region of axon / acetylcholine receptor binding / cardiac muscle cell action potential involved in contraction / RHO GTPases activate CIT / cellular response to potassium ion / regulation of cardiac muscle cell contraction / Assembly and cell surface presentation of NMDA receptors / NMDA selective glutamate receptor signaling pathway / relaxation of cardiac muscle / Neurexins and neuroligins / Activation of Ca-permeable Kainate Receptor / neuromuscular process controlling balance / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / potassium ion import across plasma membrane / Unblocking of NMDA receptors, glutamate binding and activation / intracellular potassium ion homeostasis / regulation of heart rate by cardiac conduction / locomotory exploration behavior / AMPA glutamate receptor complex / Signaling by ERBB4 / Long-term potentiation / intercalated disc / excitatory synapse / social behavior / positive regulation of excitatory postsynaptic potential / positive regulation of synaptic transmission / D1 dopamine receptor binding / regulation of postsynaptic membrane neurotransmitter receptor levels / phosphatidylinositol-4,5-bisphosphate binding / voltage-gated potassium channel complex / ionotropic glutamate receptor binding / potassium ion transmembrane transport / T-tubule / dendrite cytoplasm / Ras activation upon Ca2+ influx through NMDA receptor / synaptic membrane / learning / adherens junction / PDZ domain binding / neuromuscular junction / establishment of protein localization / cellular response to mechanical stimulus / cell-cell adhesion / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / potassium ion transport / kinase binding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / synaptic vesicle / endocytic vesicle membrane / cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / protein-containing complex assembly / scaffold protein binding / protein phosphatase binding / protein homotetramerization / dendritic spine / chemical synaptic transmission / postsynaptic membrane / neuron projection
Similarity search - Function
Potassium channel, inwardly rectifying, Kir2.1 / Potassium channel, inwardly rectifying, Kir, N-terminal / Inward rectifier potassium channel N-terminal / 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 / Potassium channel, inwardly rectifying, transmembrane domain ...Potassium channel, inwardly rectifying, Kir2.1 / Potassium channel, inwardly rectifying, Kir, N-terminal / Inward rectifier potassium channel N-terminal / 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 / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / : / 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 / Immunoglobulin E-set / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
GLUTATHIONE / Inward rectifier potassium channel 2 / Disks large homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsRodzli, N. / Levy, C.W. / Prince, S.M.
Citation
Journal: Biophys.J. / Year: 2020
Title: The Dual PDZ Domain from Postsynaptic Density Protein 95 Forms a Scaffold with Peptide Ligand.
Authors: Rodzli, N.A. / Lockhart-Cairns, M.P. / Levy, C.W. / Chipperfield, J. / Bird, L. / Baldock, C. / Prince, S.M.
#1: Journal: Biorxiv / Year: 2019
Title: How the dual PDZ domain from Postsynaptic density protein 95 clusters ion channels and receptors.
Authors: Rodzli, N. / Lockhart-Cairns, M.P. / Levy, C.W. / Chipperfield, J. / Bird, L. / Baldock, C. / Prince, S.M.
History
DepositionSep 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Aug 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Disks large homolog 4
P: ARG-ARG-GLU-SER-GLU-ILE
Q: ARG-ARG-GLU-SER-GLU-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7584
Polymers22,4503
Non-polymers3071
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, oligomers formed at high concentration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-10 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.500, 50.500, 176.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains P Q)

-
Components

#1: Protein Disks large homolog 4 / Postsynaptic density protein 95 / PSD-95 / Synapse-associated protein 90 / SAP90


Mass: 20868.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLG4, PSD95 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78352
#2: Protein/peptide ARG-ARG-GLU-SER-GLU-ILE


Mass: 790.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Syntheic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P63252*PLUS
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.41 % / Description: tetragonal bipyramid
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2 M NaCl, 0.1 M Na/K phosphate, 50% v/v PEG 200. Matrix microseeding with Apo crystal form (PDB ID: 6spv).

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.08→48.55 Å / Num. obs: 13236 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.5
Reflection shellResolution: 2.08→2.13 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 980 / CC1/2: 0.762 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073 2014/05/25refinement
xia2data reduction
XDSdata reduction
SCALAdata scaling
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rl7, 3rl8

3rl7

3rl8


Resolution: 2.08→48.549 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.386 / SU ML: 0.155 / Cross valid method: FREE R-VALUE / ESU R: 0.225 / ESU R Free: 0.185
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2399 703 -
Rwork0.2004 --
all0.203 --
obs-13216 99.97 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 47.492 Å2
Baniso -1Baniso -2Baniso -3
1-0.226 Å2-0 Å2-0 Å2
2--0.226 Å2-0 Å2
3----0.451 Å2
Refinement stepCycle: LAST / Resolution: 2.08→48.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 20 56 1602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191620
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.9942184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.465206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26724.50771
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13115289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.771512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211229
X-RAY DIFFRACTIONr_nbd_refined0.190.2661
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21047
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.245
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1850.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1530.29
X-RAY DIFFRACTIONr_mcbond_it1.7543.134827
X-RAY DIFFRACTIONr_mcangle_it3.0724.6671032
X-RAY DIFFRACTIONr_scbond_it1.9413.624793
X-RAY DIFFRACTIONr_scangle_it3.2535.2841152
X-RAY DIFFRACTIONr_lrange_it7.32826.4272252
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2.08-2.1340.284540.26792097599.89740.243
2.134-2.1930.247630.2338879501000.21
2.193-2.2560.299480.2278839311000.201
2.256-2.3250.249340.2088538871000.185
2.325-2.4010.35320.2068568881000.183
2.401-2.4850.237390.2057908291000.179
2.485-2.5790.26360.2097758111000.186
2.579-2.6840.285480.2217397871000.2
2.684-2.8030.328410.2267127531000.209
2.803-2.9390.269350.21466570199.85730.204
2.939-3.0980.261430.2146326751000.211
3.098-3.2850.288320.2146196511000.219
3.285-3.510.192270.2175856121000.229
3.51-3.790.244400.18352356499.82270.196
3.79-4.1490.202350.1834925271000.207
4.149-4.6350.178350.1424354701000.168
4.635-5.3440.212210.1693934141000.206
5.344-6.5250.318110.22734435699.71910.268
6.525-9.1450.175170.1912632801000.227
9.145-48.5490.291120.2241471591000.305
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)
12.4368-0.18850.07453.5596-0.34473.51610.0004-0.09270.08690.04440.15610.2073-0.2681-0.3032-0.15650.07350.06250.04860.0890.05430.049815.00434.6210.241
21.56480.56920.0512.9813-1.20495.76710.14280.24370.1597-0.16170.09570.1856-0.0683-0.102-0.23850.04440.01060.00770.19010.13140.10449.54111.83124.127
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA61 - 15161 - 151
21PB423 - 427423 - 427
32AA158 - 244158 - 244
42QC423 - 427423 - 427

+
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