[English] 日本語
Yorodumi
- PDB-2oqs: Structure of the hDLG/SAP97 PDZ2 in complex with HPV-18 papilloma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2oqs
TitleStructure of the hDLG/SAP97 PDZ2 in complex with HPV-18 papillomavirus E6 peptide
Components
  • C-terminal HPV-18 E6 peptide
  • Disks large homolog 1
KeywordsPEPTIDE BINDING PROTEIN / HPV E6 / hDLG PDZ domain / protein-peptide complex / PEPTIDE-BINDING PROTEIN
Function / homology
Function and homology information


regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / establishment of centrosome localization / negative regulation of p38MAPK cascade ...regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / establishment of centrosome localization / negative regulation of p38MAPK cascade / guanylate kinase activity / cortical microtubule organization / regulation of sodium ion transmembrane transport / NrCAM interactions / embryonic skeletal system morphogenesis / astral microtubule organization / structural constituent of postsynaptic density / lateral loop / reproductive structure development / myelin sheath abaxonal region / immunological synapse formation / peristalsis / Synaptic adhesion-like molecules / cell projection membrane / smooth muscle tissue development / bicellular tight junction assembly / positive regulation of potassium ion transport / node of Ranvier / regulation of ventricular cardiac muscle cell action potential / protein-containing complex localization / establishment or maintenance of epithelial cell apical/basal polarity / Trafficking of AMPA receptors / Assembly and cell surface presentation of NMDA receptors / amyloid precursor protein metabolic process / endothelial cell proliferation / neurotransmitter receptor localization to postsynaptic specialization membrane / lens development in camera-type eye / regulation of myelination / Activation of Ca-permeable Kainate Receptor / cortical actin cytoskeleton organization / branching involved in ureteric bud morphogenesis / establishment or maintenance of cell polarity / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of actin filament polymerization / receptor clustering / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / phosphoprotein phosphatase activity / Long-term potentiation / immunological synapse / basement membrane / intercalated disc / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / bicellular tight junction / potassium channel regulator activity / phosphatase binding / T cell proliferation / negative regulation of T cell proliferation / actin filament polymerization / regulation of membrane potential / Ras activation upon Ca2+ influx through NMDA receptor / cytoskeletal protein binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / synaptic membrane / actin filament organization / protein localization to plasma membrane / postsynaptic density membrane / positive regulation of protein localization to plasma membrane / adherens junction / sarcolemma / neuromuscular junction / negative regulation of ERK1 and ERK2 cascade / cytoplasmic side of plasma membrane / cell-cell adhesion / kinase binding / negative regulation of epithelial cell proliferation / cell-cell junction / cell junction / regulation of cell shape / chemical synaptic transmission / RAF/MAP kinase cascade / basolateral plasma membrane / microtubule / transmembrane transporter binding / molecular adaptor activity / neuron projection / cadherin binding / membrane raft / apical plasma membrane / glutamatergic synapse / positive regulation of cell population proliferation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / extracellular exosome / nucleus / plasma membrane
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)
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, Y. / Baleja, J.D. / Henry, G.D. / Hegde, R.S.
CitationJournal: Biochemistry / Year: 2007
Title: Solution structure of the hDlg/SAP97 PDZ2 domain and its mechanism of interaction with HPV-18 papillomavirus E6 protein.
Authors: Liu, Y. / Henry, G.D. / Hegde, R.S. / Baleja, J.D.
History
DepositionFeb 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_keywords.text / _struct_ref_seq_dif.details
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Disks large homolog 1
B: C-terminal HPV-18 E6 peptide


Theoretical massNumber of molelcules
Total (without water)11,1912
Polymers11,1912
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 30all calculated structures submitted
RepresentativeModel #1lowest energy

-
Components

#1: Protein Disks large homolog 1 / Synapse-associated protein 97 / SAP-97 / hDlg


Mass: 10400.886 Da / Num. of mol.: 1 / Fragment: second PDZ domain, residues 318-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLG1 / Plasmid: pET30a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12959
#2: Protein/peptide C-terminal HPV-18 E6 peptide


Mass: 789.880 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Homo sapiens (human)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
3233D 15N-separated NOESY
333(H)CCH-TOCSY
343HN(CA)CB
353CBCA(CO)NH
363HBHA(CO)NH
474CT-13C/1H-HSQC
585HSQC-DSSE (IPAP) for HN RDC
696HSQC-DSSE (IPAP) for HN RDC
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

-
Sample preparation

Details
Solution-IDContentsSolvent system
12mM hDLG/SAP97 PDZ2 domain, 3mM HPV-18 E6 peptide, 4 mM TCEP, 20 uM DSS, 20mM phosphate buffer, pH 6.5, 99.5% D2O99.5% D2O
22mM hDLG/SAP97 PDZ2 domain U-15N, 3mM HPV-18 E6 peptide, 4 mM TCEP, 20 uM DSS, 20mM phosphate buffer, pH 6.5, 90% H2O, 10% D2O90% H2O/10% D2O
32 mM hDLG/SAP97 PDZ2 domain U-15N, 13C, 3 mM HPV-18 E6 peptide, 4 mM TCEP, 20 uM DSS, 20 mM phosphate buffer, pH 6.5, 90% H2O, 10% D2O90% H2O/10% D2O
42 mM hDLG/SAP97 PDZ2 domain, U-15N, U-10%13C, 3 mM HPV-18 E6 peptide, 4 mM TCEP, 20 uM DSS, 20mM phosphate buffer, pH 6.590% H2O/10% D2O
52 mM hDLG/SAP97 PDZ2 domain, U-15N, 3 mM HPV-18 E6 peptide, 5% C8E5, C8E5/n-octanol 0.87, 4 mM TCEP, 20 uM DSS, 20mM phosphate buffer, pH 6.5, 90% H2O, 10% D2O90% H2O/10% D2O
62 mM hDLG/SAP97 PDZ2 domain, U-15N, 3 mM HPV-18 E6 peptide, 10 mg/ml pf1 phage, 4 mM TCEP, 20 uM DSS, 20mM phosphate buffer, pH 6.5,90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
128.2 mM 6.5 ambient 293 K
228.2 mM 6.5 ambient 293 K
328.2 mM 6.5 ambient 293 K
428.2 mM 6.5 ambient 293 K
528.2 mM 6.5 ambient 293 K
628.2 mM 6.5 ambient 293 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE DRX / Manufacturer: Bruker / Model: AVANCE DRX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
Sparky3.112T. D. Goddard and D. G. Knellerdata analysis
CNS1.1Brungerrefinement
CNS1.1Brungerstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 1426 restraints, 1126 are NOE-derived distance constraints, 163 dihedral angle restraints, 50 distance restraints from hydrogen bonds and 87 NH residual dipolar couplings.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 30 / Conformers submitted total number: 30

+
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