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- PDB-8b82: Crystal structure of Scribble PDZ1 with human papillomavirus stra... -

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Basic information

Entry
Database: PDB / ID: 8b82
TitleCrystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide
Components
  • Protein E6
  • Protein scribble homolog
KeywordsPROTEIN BINDING / Scribble / human papillomavirus / E6 / PDZ domain / cell polarity
Function / homology
Function and homology information


establishment of T cell polarity / apoptotic process involved in morphogenesis / cochlear nucleus development / establishment of apical/basal cell polarity / astrocyte cell migration / Scrib-APC-beta-catenin complex / symbiont-mediated perturbation of host apoptosis / polarized epithelial cell differentiation / synaptic vesicle targeting / epithelial structure maintenance ...establishment of T cell polarity / apoptotic process involved in morphogenesis / cochlear nucleus development / establishment of apical/basal cell polarity / astrocyte cell migration / Scrib-APC-beta-catenin complex / symbiont-mediated perturbation of host apoptosis / polarized epithelial cell differentiation / synaptic vesicle targeting / epithelial structure maintenance / neurotransmitter receptor transport, endosome to postsynaptic membrane / myelin sheath abaxonal region / protein localization to adherens junction / cell-cell contact zone / mammary gland duct morphogenesis / establishment or maintenance of epithelial cell apical/basal polarity / post-anal tail morphogenesis / activation of GTPase activity / auditory receptor cell stereocilium organization / RND2 GTPase cycle / RND3 GTPase cycle / extrinsic component of postsynaptic density membrane / positive regulation of receptor recycling / regulation of postsynaptic neurotransmitter receptor internalization / positive chemotaxis / receptor clustering / RHOJ GTPase cycle / negative regulation of activated T cell proliferation / RHOQ GTPase cycle / CDC42 GTPase cycle / synaptic vesicle endocytosis / negative regulation of mitotic cell cycle / immunological synapse / signaling adaptor activity / PDZ domain binding / adherens junction / Asymmetric localization of PCP proteins / neural tube closure / wound healing / cell-cell adhesion / positive regulation of type II interferon production / cell junction / cell-cell junction / cell migration / lamellipodium / presynapse / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / basolateral plasma membrane / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / cell population proliferation / postsynaptic density / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / cadherin binding / positive regulation of apoptotic process / negative regulation of DNA-templated transcription / DNA-templated transcription / protein kinase binding / host cell nucleus / glutamatergic synapse / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
E6 early regulatory protein / E6 superfamily / Early Protein (E6) / : / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...E6 early regulatory protein / E6 superfamily / Early Protein (E6) / : / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Protein E6 / Protein scribble homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus type 18
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsStewart, B.Z. / Kvansakul, M.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1103871 Australia
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: To Be Published
Title: Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide
Authors: Stewart, B.Z. / Caria, S. / Humbert, P.O. / Kvansakul, M.
History
DepositionOct 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein scribble homolog
B: Protein scribble homolog
C: Protein E6
D: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4218
Polymers27,2794
Non-polymers1424
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-37 kcal/mol
Surface area14160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.410, 55.253, 114.284
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Protein scribble homolog / Scribble / hScrib / Protein LAP4


Mass: 12293.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCRIB, CRIB1, KIAA0147, LAP4, SCRB1, VARTUL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Codon+ / References: UniProt: Q14160
#2: Protein/peptide Protein E6


Mass: 1345.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human papillomavirus type 18 / References: UniProt: P06463
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.47 % / Description: Rod
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 15% PEG 4000, 0.05 M Ammonium Sulfate / PH range: 8 / Temp details: 293.15

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.8→49.74 Å / Num. obs: 5671 / % possible obs: 99.23 % / Redundancy: 12.7 % / Biso Wilson estimate: 47.35 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1381 / Net I/σ(I): 12.18
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.5239 / Num. unique obs: 560 / CC1/2: 0.964

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MTV

6mtv


Resolution: 2.8→49.74 Å / SU ML: 0.3488 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.121
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2778 289 5.1 %
Rwork0.2418 5382 -
obs0.2438 5671 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.31 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1777 0 4 66 1847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00241792
X-RAY DIFFRACTIONf_angle_d0.47072408
X-RAY DIFFRACTIONf_chiral_restr0.0445267
X-RAY DIFFRACTIONf_plane_restr0.0054328
X-RAY DIFFRACTIONf_dihedral_angle_d14.4485689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.530.31121340.26362651X-RAY DIFFRACTION98.93
3.53-49.740.26461550.2322731X-RAY DIFFRACTION97.63
Refinement TLS params.Method: refined / Origin x: -13.3072185206 Å / Origin y: 17.2103366331 Å / Origin z: -15.7530182633 Å
111213212223313233
T0.416777417764 Å2-0.0367406946966 Å2-0.100639603926 Å2-0.714108084261 Å20.0625207183262 Å2--0.0255657679302 Å2
L0.223445986636 °2-0.0499772467896 °2-0.145681709328 °2-1.40765933368 °2-0.0574491026893 °2--0.178030133337 °2
S-0.0116244979935 Å °0.108199871182 Å °0.0254448388445 Å °0.31351672605 Å °-0.0473456872117 Å °-0.0893062608182 Å °-0.0818640622125 Å °-0.112570364175 Å °-0.0351176506005 Å °
Refinement TLS groupSelection details: all

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