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- PDB-2i0i: X-ray crystal structure of Sap97 PDZ3 bound to the C-terminal pep... -

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Basic information

Entry
Database: PDB / ID: 2i0i
TitleX-ray crystal structure of Sap97 PDZ3 bound to the C-terminal peptide of HPV18 E6
Components
  • Disks large homolog 1
  • peptide E6
KeywordsPEPTIDE BINDING PROTEIN / Sap97 PDZ3 / HPV18 E6 / tumor suppressor / cervical carcinoma
Function / homology
Function and homology information


tissue morphogenesis / 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 ...tissue morphogenesis / 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 / cortical microtubule organization / embryonic skeletal system morphogenesis / astral microtubule organization / structural constituent of postsynaptic density / lateral loop / reproductive structure development / immunological synapse formation / myelin sheath abaxonal region / peristalsis / cell projection membrane / smooth muscle tissue development / paranode region of axon / bicellular tight junction assembly / positive regulation of potassium ion transport / Trafficking of AMPA receptors / Activation of Ca-permeable Kainate Receptor / node of Ranvier / regulation of ventricular cardiac muscle cell action potential / protein-containing complex localization / establishment or maintenance of epithelial cell apical/basal polarity / amyloid precursor protein metabolic process / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / neurotransmitter receptor localization to postsynaptic specialization membrane / endothelial cell proliferation / lens development in camera-type eye / regulation of myelination / ureteric bud development / cortical actin cytoskeleton organization / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of actin filament polymerization / receptor clustering / kinesin binding / microvillus / immunological synapse / basement membrane / lateral plasma membrane / potassium channel regulator activity / bicellular tight junction / Unblocking of NMDA receptors, glutamate binding and activation / postsynaptic density, intracellular component / phosphatase binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / T cell proliferation / negative regulation of T cell proliferation / cellular response to brain-derived neurotrophic factor stimulus / T-tubule / T cell activation / actin filament polymerization / phosphatidylinositol 3-kinase/protein kinase B signal transduction / basal plasma membrane / synaptic membrane / protein localization to plasma membrane / PDZ domain binding / regulation of membrane potential / positive regulation of protein localization to plasma membrane / actin filament organization / postsynaptic density membrane / ionotropic glutamate receptor binding / neuromuscular junction / protein localization / cytoplasmic side of plasma membrane / negative regulation of ERK1 and ERK2 cascade / cerebral cortex development / synaptic vesicle membrane / cell-cell adhesion / negative regulation of epithelial cell proliferation / regulation of protein localization / cell-cell junction / cell junction / presynaptic membrane / regulation of cell shape / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / chemical synaptic transmission / basolateral plasma membrane / symbiont-mediated perturbation of host ubiquitin-like protein modification / postsynaptic membrane / microtubule / transmembrane transporter binding / cell population proliferation / host cell cytoplasm / molecular adaptor activity / postsynaptic density / cell adhesion / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / neuron projection / membrane raft / apical plasma membrane / virus-mediated perturbation of host defense response
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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChen, X.S. / Zhang, Y. / Dasgupta, J. / Banks, L. / Thomas, M.
Citation
Journal: J.Virol. / Year: 2007
Title: Structures of a Human Papillomavirus (HPV) E6 Polypeptide Bound to MAGUK Proteins: Mechanisms of Targeting Tumor Suppressors by a High-Risk HPV Oncoprotein.
Authors: Zhang, Y. / Dasgupta, J. / Ma, R.Z. / Banks, L. / Thomas, M. / Chen, X.S.
#1: Journal: Oncogene / Year: 2001
Title: HPV E6 and MAGUK protein interactions: determination of the molecular basis for specific protein recognition and degradation.
Authors: Thomas, M. / Glaunsinger, B. / Pim, D. / Javier, R. / Banks, L.
History
DepositionAug 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disks large homolog 1
D: peptide E6
B: Disks large homolog 1
E: peptide E6
C: Disks large homolog 1
F: peptide E6


Theoretical massNumber of molelcules
Total (without water)29,1726
Polymers29,1726
Non-polymers00
Water1,36976
1
A: Disks large homolog 1
D: peptide E6


Theoretical massNumber of molelcules
Total (without water)9,7242
Polymers9,7242
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disks large homolog 1
E: peptide E6


Theoretical massNumber of molelcules
Total (without water)9,7242
Polymers9,7242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-3 kcal/mol
Surface area5010 Å2
MethodPISA
3
C: Disks large homolog 1
F: peptide E6


Theoretical massNumber of molelcules
Total (without water)9,7242
Polymers9,7242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-3 kcal/mol
Surface area5000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.167, 61.919, 57.142
Angle α, β, γ (deg.)90.00, 123.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 8776.911 Da / Num. of mol.: 3 / Fragment: PDZ3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q62696
#2: Protein/peptide peptide E6


Mass: 947.074 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: The sequence of this peptide can be found in human papillomavirus type 18 (virus).
References: UniProt: P06463
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: PEG4000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 7, 2006
RadiationMonochromator: copper K alpha / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 6843 / Num. obs: 6381 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 52.9 Å2

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.97 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 1594112.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 360 5.6 %RANDOM
Rwork0.223 ---
obs0.223 6381 93.2 %-
all-6843 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.2021 Å2 / ksol: 0.301438 e/Å3
Displacement parametersBiso mean: 50.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å23.62 Å2
2--6.72 Å20 Å2
3----7.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 0 76 1981
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.441.5
X-RAY DIFFRACTIONc_mcangle_it4.172
X-RAY DIFFRACTIONc_scbond_it4.112
X-RAY DIFFRACTIONc_scangle_it5.662.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.452 50 5.2 %
Rwork0.357 903 -
obs--84.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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