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- PDB-2m3m: Solution structure of a complex consisting of hDlg/SAP-97 residue... -

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Basic information

Entry
Database: PDB / ID: 2m3m
TitleSolution structure of a complex consisting of hDlg/SAP-97 residues 318-406 and HPV51 oncoprotein E6 residues 141-151
Components
  • Disks large homolog 1
  • Protein E6
KeywordsONCOPROTEIN/CELL ADHESION / Papillomavirus E6 Proteins / HPV / Oncoprotein E6 / E6 / Viral / Oncogene Proteins / PDZ Domain / hDlgPDZ2 / hDlg / hDlg1 / SAP-97 / Dlg / ONCOPROTEIN - CELL ADHESION protein complex / ONCOPROTEIN-CELL ADHESION complex
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 / symbiont-mediated perturbation of host apoptosis / GMP kinase activity / establishment of centrosome localization / myelin sheath abaxonal region ...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 / symbiont-mediated perturbation of host apoptosis / 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 / regulation of proteolysis / 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 / PDZ domain binding / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / basolateral plasma membrane / molecular adaptor activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / chemical synaptic transmission / microtubule / transmembrane transporter binding / host cell cytoplasm / neuron projection / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / apical plasma membrane
Similarity search - Function
L27-1 / L27_1 / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / 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 ...L27-1 / L27_1 / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / 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
Protein E6 / Disks large homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsMischo, A. / Ohlenschlager, O. / Gorlach, M.
CitationJournal: Plos One / Year: 2013
Title: Structural insights into a wildtype domain of the oncoprotein E6 and its interaction with a PDZ domain.
Authors: Mischo, A. / Ohlenschlager, O. / Hortschansky, P. / Ramachandran, R. / Gorlach, M.
History
DepositionJan 22, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 2.0Dec 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_nmr_software ...entity_poly / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 2.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disks large homolog 1
B: Protein E6


Theoretical massNumber of molelcules
Total (without water)11,8022
Polymers11,8022
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1289 Å2
ΔGint-2 kcal/mol
Surface area5362.2 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Disks large homolog 1 / Synapse-associated protein 97 / SAP-97 / SAP97 / hDlg


Mass: 10400.886 Da / Num. of mol.: 1 / Fragment: hDlgPDZ2, UNP residues 318-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLG1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) / References: UniProt: Q12959
#2: Protein/peptide Protein E6


Mass: 1401.508 Da / Num. of mol.: 1 / Fragment: E6CT11, UNP residues 141-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus / Strain: TYPE 51 / Gene: E6 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) / References: UniProt: P26554
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1413D HN(CA)CB
1513D 1H-15N NOESY
1623D 1H-13C NOESY aliphatic
1723D 1H-13C NOESY aromatic
1823D (H)CCH-COSY
1913D HNCO
11013D HNHA
11142D 1H-15N HSQC
11232D 1H-13C HSQC aliphatic
11332D 1H-13C HSQC aromatic
11443D HN(CA)CB
11543D 1H-15N NOESY
11633D 1H-13C NOESY aliphatic
11733D 1H-13C NOESY aromatic
11833D (H)CCH-COSY
11943D HNCO
12043D HNHA
NMR detailsText: In addition to the experiments listed below, filtered/edited experiments were performed to distinguish intra- and inter-molecular NOEs

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 13C; U-100% 15N] hDlgPDZ2, 2.0 mM E6CT11, 20 mM sodium phosphate, 4 mM TCEP, 0.05 w/v sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 13C; U-100% 15N] hDlgPDZ2, 2.0 mM E6CT11, 20 mM sodium phosphate, 4 mM TCEP, 0.05 w/v sodium azide, 100% D2O100% D2O
33.12 mM hDlgPDZ2, 1.25 mM [U-100% 13C; U-100% 15N] E6CT11, 20 mM sodium phosphate, 4 mM TCEP, 0.05 w/v sodium azide, 100% D2O100% D2O
43.12 mM hDlgPDZ2, 1.25 mM [U-100% 13C; U-100% 15N] E6CT11, 20 mM sodium phosphate, 4 mM TCEP, 0.05 w/v sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMhDlgPDZ2-1[U-100% 13C; U-100% 15N]1
2.0 mME6CT11-21
20 mMsodium phosphate-31
4 mMTCEP-41
0.05 w/vsodium azide-51
0.8 mMhDlgPDZ2-6[U-100% 13C; U-100% 15N]2
2.0 mME6CT11-72
20 mMsodium phosphate-82
4 mMTCEP-92
0.05 w/vsodium azide-102
3.12 mMhDlgPDZ2-113
1.25 mME6CT11-12[U-100% 13C; U-100% 15N]3
20 mMsodium phosphate-133
4 mMTCEP-143
0.05 w/vsodium azide-153
3.12 mMhDlgPDZ2-164
1.25 mME6CT11-17[U-100% 13C; U-100% 15N]4
20 mMsodium phosphate-184
4 mMTCEP-194
0.05 w/vsodium azide-204
Sample conditionsIonic strength: 20 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceIIIBrukerAVANCE III7501
Bruker AvanceIIIBrukerAVANCE III6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CARAKeller and Wuthrichdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpinBruker Biospincollection & processing
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: DGSA-distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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