[English] 日本語
Yorodumi
- PDB-6qjn: Crystal Structure of the third PDZ domain of PSD-95 protein D332G... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qjn
TitleCrystal Structure of the third PDZ domain of PSD-95 protein D332G mutant: space group I4122
ComponentsDisks large homolog 4
KeywordsSIGNALING PROTEIN / pdz domain
Function / homology
Function and homology information


LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / regulation of grooming behavior / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / vocalization behavior ...LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / regulation of grooming behavior / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / vocalization behavior / neuron spine / Synaptic adhesion-like molecules / cerebellar mossy fiber / establishment or maintenance of epithelial cell apical/basal polarity / protein localization to synapse / Trafficking of AMPA receptors / dendritic spine morphogenesis / negative regulation of receptor internalization / juxtaparanode region of axon / acetylcholine receptor binding / RHO GTPases activate CIT / cellular response to potassium ion / Assembly and cell surface presentation of NMDA receptors / NMDA selective glutamate receptor signaling pathway / Neurexins and neuroligins / neuromuscular process controlling balance / Activation of Ca-permeable Kainate Receptor / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / neuron projection terminus / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor clustering / locomotory exploration behavior / Signaling by ERBB4 / AMPA glutamate receptor complex / Long-term potentiation / social behavior / D1 dopamine receptor binding / positive regulation of synaptic transmission / regulation of postsynaptic membrane neurotransmitter receptor levels / excitatory synapse / ionotropic glutamate receptor binding / dendrite cytoplasm / Ras activation upon Ca2+ influx through NMDA receptor / synaptic membrane / positive regulation of excitatory postsynaptic potential / learning / PDZ domain binding / adherens junction / neuromuscular junction / establishment of protein localization / cell-cell adhesion / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / kinase binding / 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 / dendritic spine / chemical synaptic transmission / postsynaptic membrane / neuron projection / postsynaptic density / synapse / protein kinase binding / protein-containing complex binding / glutamatergic synapse / endoplasmic reticulum / signal transduction / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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. ...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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Disks large homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsCamara-Artigas, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Conformational changes in the third PDZ domain of the neuronal postsynaptic density protein 95.
Authors: Camara-Artigas, A. / Murciano-Calles, J. / Martinez, J.C.
History
DepositionJan 24, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionApr 17, 2019ID: 5OIJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Disks large homolog 4
B: Disks large homolog 4


Theoretical massNumber of molelcules
Total (without water)22,1812
Polymers22,1812
Non-polymers00
Water1,49583
1
A: Disks large homolog 4


Theoretical massNumber of molelcules
Total (without water)11,0901
Polymers11,0901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disks large homolog 4


Theoretical massNumber of molelcules
Total (without water)11,0901
Polymers11,0901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.871, 89.871, 84.814
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21A-512-

HOH

31A-532-

HOH

41A-538-

HOH

51A-557-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 312 through 330 or resid 333 through 403))
21chain B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGGLYGLY(chain A and (resid 312 through 330 or resid 333 through 403))AA312 - 33013 - 31
12GLYGLYLYSLYS(chain A and (resid 312 through 330 or resid 333 through 403))AA333 - 40334 - 104
21ARGARGLYSLYSchain BBB312 - 40313 - 104

-
Components

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


Mass: 11090.453 Da / Num. of mol.: 2 / Fragment: PDZ domain / Mutation: D332G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLG4, PSD95 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78352
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.93 Å3/Da / Density % sol: 36.28 % / Mosaicity: 0.17 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M sodium citrate, 20% 2-Propanol, 20% PEG 4000, 5% Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.96998 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96998 Å / Relative weight: 1
ReflectionResolution: 1.8→19.85 Å / Num. obs: 16272 / % possible obs: 99.3 % / Redundancy: 4.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.039 / Rrim(I) all: 0.087 / Net I/σ(I): 11.3 / Num. measured all: 77217 / Scaling rejects: 35
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.845.10.42747979420.8960.2050.4753.499.8
9-19.854.50.0396401420.9990.020.04519.789.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K82

3k82


Resolution: 1.8→19.853 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.18 / Phase error: 23.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 3071 10.23 %
Rwork0.2053 26957 -
obs0.2074 30028 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.31 Å2 / Biso mean: 41.7465 Å2 / Biso min: 13.24 Å2
Refinement stepCycle: final / Resolution: 1.8→19.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 0 83 1473
Biso mean---35.32 -
Num. residues----184
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A536X-RAY DIFFRACTION11.213TORSIONAL
12B536X-RAY DIFFRACTION11.213TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8001-1.82820.35451310.311712541385100
1.8282-1.85810.30031490.268312451394100
1.8581-1.89020.33541220.259212431365100
1.8902-1.92450.28161400.235912731413100
1.9245-1.96150.29731400.2481259139999
1.9615-2.00150.29721510.22821226137799
2.0015-2.0450.2731540.23211186134098
2.045-2.09250.26671570.22221213137097
2.0925-2.14470.24721660.22851203136999
2.1447-2.20270.23831630.216612251388100
2.2027-2.26740.22371640.22141212137698
2.2674-2.34050.2455980.20651288138699
2.3405-2.4240.25851300.21251257138799
2.424-2.52080.29071130.21241241135498
2.5208-2.63530.24891300.21261235136596
2.6353-2.77390.21111580.21691152131096
2.7739-2.94720.23561500.19971231138197
2.9472-3.17390.21751340.20391212134697
3.1739-3.49170.20871100.19351225133596
3.4917-3.99340.1791240.18341183130793
3.9934-5.01780.19251610.16421171133295
5.0178-19.85460.1921260.2011223134996
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)
15.48620.3771-0.12675.87052.25847.24610.1323-0.51940.1201-0.0146-0.1479-0.325-0.10060.5069-0.30390.13180.02190.02310.2240.00770.208436.674212.04612.7989
25.8636-1.7523-2.85932.1340.45482.31590.33240.134-1.5311-0.1739-0.22260.32370.1883-0.4930.26110.23980.0618-0.05140.24310.07370.313224.65232.2291-0.0912
33.561-0.9851-1.70815.34671.89096.4248-0.0485-0.4851-0.30210.06560.08180.09180.03550.1673-0.02410.14820.0299-0.00860.20560.0550.135729.0645.69546.5272
48.8892-3.83030.05174.5957-1.07144.17690.081-0.1673-0.00710.03860.08580.16350.0835-0.2196-0.1350.15780.01970.0040.1834-0.02260.122522.179714.04392.2117
53.1792-0.4776-1.78053.9909-0.28281.0313-0.0241-0.37640.0285-0.0588-0.15480.27710.2524-1.24850.12530.1169-0.0258-0.00190.3039-0.02620.187129.351510.9423-1.5302
68.79135.4752-1.17917.32641.52867.35740.4241-0.56640.05770.7698-0.2188-0.0895-0.56390.6125-0.20030.25510.0050.00280.3703-0.02270.133727.5479.420518.2189
73.6786-2.71850.78032.346-2.17227.20480.1823-1.2203-0.83890.0138-0.4059-1.14260.28270.65350.07950.4224-0.11820.01540.42640.14620.618711.7458-9.648421.7138
83.866-0.7303-0.6993.4079-1.07770.9668-0.03360.2668-0.65070.0766-0.25870.17070.18250.0180.2990.2471-0.0021-0.00170.1879-0.01710.284717.8983-3.106214.1301
94.69061.33010.12443.11111.90911.27130.205-1.59-1.09130.9861-0.52170.02570.89310.5881-0.75770.44790.0668-0.17520.3880.60610.596421.7263-6.444421.0618
104.78192.92620.86312.05511.31515.0606-0.3279-0.1434-1.90710.2080.5121-0.64361.69580.00810.36470.5067-0.04210.03090.30980.01180.770117.6925-13.639813.8117
113.2226-2.50340.44812.6902-2.86148.32260.5970.4219-2.0084-0.85740.6963-0.45120.8194-0.4109-0.82220.6691-0.29210.030.6341-0.26511.152114.1247-16.8118.6042
124.2032-0.4508-1.28932.21871.83184.3345-0.67611.8055-1.7096-0.4565-0.690.33970.6583-0.21180.51790.3236-0.1569-0.07260.66180.13040.623812.3422-8.930111.4209
135.4036-4.52433.09526.8545-1.07867.2770.7585-0.4939-1.4491-0.8788-0.9444-0.80390.84540.66890.14360.44180.29960.06110.80030.24390.647931.6374-9.505511.2182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 307 through 317 )A307 - 317
2X-RAY DIFFRACTION2chain 'A' and (resid 318 through 328 )A318 - 328
3X-RAY DIFFRACTION3chain 'A' and (resid 329 through 356 )A329 - 356
4X-RAY DIFFRACTION4chain 'A' and (resid 357 through 380 )A357 - 380
5X-RAY DIFFRACTION5chain 'A' and (resid 381 through 392 )A381 - 392
6X-RAY DIFFRACTION6chain 'A' and (resid 393 through 403 )A393 - 403
7X-RAY DIFFRACTION7chain 'B' and (resid 312 through 317 )B312 - 317
8X-RAY DIFFRACTION8chain 'B' and (resid 318 through 350 )B318 - 350
9X-RAY DIFFRACTION9chain 'B' and (resid 351 through 356 )B351 - 356
10X-RAY DIFFRACTION10chain 'B' and (resid 357 through 362 )B357 - 362
11X-RAY DIFFRACTION11chain 'B' and (resid 363 through 371 )B363 - 371
12X-RAY DIFFRACTION12chain 'B' and (resid 372 through 392 )B372 - 392
13X-RAY DIFFRACTION13chain 'B' and (resid 393 through 403 )B393 - 403

+
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