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- PDB-2i04: X-ray crystal structure of MAGI-1 PDZ1 bound to the C-terminal pe... -

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Basic information

Entry
Database: PDB / ID: 2i04
TitleX-ray crystal structure of MAGI-1 PDZ1 bound to the C-terminal peptide of HPV18 E6
Components
  • Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
  • peptide E6
KeywordsPEPTIDE BINDING PROTEIN / PDZ / E6 binding / tumor suppressor
Function / homology
Function and homology information


positive regulation of cell-cell adhesion / alpha-actinin binding / bicellular tight junction / cell projection / PDZ domain binding / adherens junction / cell-cell junction / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm ...positive regulation of cell-cell adhesion / alpha-actinin binding / bicellular tight junction / cell projection / PDZ domain binding / adherens junction / cell-cell junction / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / negative regulation of DNA-templated transcription / DNA-templated transcription / host cell nucleus / nucleolus / signal transduction / DNA binding / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Unstructured region on MAGI / Unstructured region on MAGI / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / 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 ...Unstructured region on MAGI / Unstructured region on MAGI / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / 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. / WW domain / WW/rsp5/WWP domain signature. / PDZ domain / Pdz3 Domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Protein E6 / Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
C: peptide E6
B: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
D: peptide E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2396
Polymers20,0474
Non-polymers1922
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-42 kcal/mol
Surface area8720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.961, 27.611, 59.525
Angle α, β, γ (deg.)90.00, 105.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1 / BAI1-associated protein 1 / BAP-1 / Membrane-associated guanylate kinase inverted 1 / MAGI-1


Mass: 9076.373 Da / Num. of mol.: 2 / Fragment: PDZ1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: Q6RHR9
#2: Protein/peptide peptide E6


Mass: 947.074 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The sequence of this peptide can be found in human papillomavirus type 18 (virus)
References: UniProt: P06463
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 1.93 Å3/Da / Density % sol: 36.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.6
Details: PEG2000, 0.1 M Na Acetate , pH 4.6, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 10, 2006
RadiationMonochromator: 1.54 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 8651 / Num. obs: 9305 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 10.8 Å2
Reflection shellHighest resolution: 2.15 Å / % possible all: 94.5

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→28.69 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 906461.48 / 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
Rfree0.269 478 5.6 %RANDOM
Rwork0.215 ---
all0.215 8651 --
obs0.215 8603 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.0265 Å2 / ksol: 0.330239 e/Å3
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.61 Å20 Å2-2.06 Å2
2--0.64 Å20 Å2
3---1.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.15→28.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 10 224 1608
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.04
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_deg2.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.4
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.421.5
X-RAY DIFFRACTIONc_mcangle_it4.442
X-RAY DIFFRACTIONc_scbond_it5.572
X-RAY DIFFRACTIONc_scangle_it7.272.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 70 5 %
Rwork0.245 1330 -
obs--98.5 %
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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