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- PDB-2oqs: Structure of the hDLG/SAP97 PDZ2 in complex with HPV-18 papilloma... -

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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


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 / GMP kinase activity / establishment of centrosome localization / myelin sheath abaxonal region / 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 / GMP kinase activity / establishment of centrosome localization / myelin sheath abaxonal region / structural constituent of postsynaptic density / membrane repolarization during ventricular cardiac muscle cell action potential / NrCAM interactions / astral microtubule organization / embryonic skeletal system morphogenesis / negative regulation of p38MAPK cascade / reproductive structure development / immunological synapse formation / peristalsis / lateral loop / receptor localization to synapse / smooth muscle tissue development / bicellular tight junction assembly / cell projection membrane / cortical microtubule organization / regulation of sodium ion transmembrane transport / Synaptic adhesion-like molecules / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / regulation of ventricular cardiac muscle cell action potential / positive regulation of potassium ion transport / Trafficking of AMPA receptors / hard palate development / protein-containing complex localization / node of Ranvier / amyloid precursor protein metabolic process / endothelial cell proliferation / Assembly and cell surface presentation of NMDA receptors / lens development in camera-type eye / cortical actin cytoskeleton organization / regulation of myelination / Activation of Ca-permeable Kainate Receptor / branching involved in ureteric bud morphogenesis / neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of G1/S transition of mitotic cell cycle / receptor clustering / establishment or maintenance of cell polarity / positive regulation of actin filament polymerization / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / phosphoprotein phosphatase activity / basement membrane / Long-term potentiation / lateral plasma membrane / intercalated disc / immunological synapse / bicellular tight junction / potassium channel regulator activity / T cell proliferation / phosphatase binding / regulation of postsynaptic membrane neurotransmitter receptor levels / cytoskeletal protein binding / negative regulation of T cell proliferation / actin filament polymerization / ionotropic glutamate receptor binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / synaptic membrane / actin filament organization / regulation of membrane potential / protein localization to plasma membrane / adherens junction / positive regulation of protein localization to plasma membrane / neuromuscular junction / phosphatidylinositol 3-kinase/protein kinase B signal transduction / sarcolemma / cell-cell adhesion / postsynaptic density membrane / negative regulation of ERK1 and ERK2 cascade / kinase binding / cytoplasmic side of plasma membrane / negative regulation of epithelial cell proliferation / cell-cell junction / cell junction / nervous system development / regulation of cell shape / RAF/MAP kinase cascade / basolateral plasma membrane / molecular adaptor activity / chemical synaptic transmission / microtubule / transmembrane transporter binding / neuron projection / apical plasma membrane / cadherin binding / membrane raft / positive regulation of cell population proliferation / endoplasmic reticulum membrane / protein kinase binding / 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)
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water00
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

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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)

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Experimental details

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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.

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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 6.5ambient 293 K
228.2 mM 6.5ambient 293 K
328.2 mM 6.5ambient 293 K
428.2 mM 6.5ambient 293 K
528.2 mM 6.5ambient 293 K
628.2 mM 6.5ambient 293 K

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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

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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

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