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- PDB-8b9t: Crystal structure of Scribble PDZ1 with human papillomavirus stra... -

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Basic information

Entry
Database: PDB / ID: 8b9t
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 / extrinsic component of postsynaptic density membrane / symbiont-mediated perturbation of host apoptosis / cochlear nucleus development / apoptotic process involved in morphogenesis / astrocyte cell migration / myelin sheath abaxonal region / Scrib-APC-beta-catenin complex / establishment of apical/basal cell polarity / synaptic vesicle targeting ...establishment of T cell polarity / extrinsic component of postsynaptic density membrane / symbiont-mediated perturbation of host apoptosis / cochlear nucleus development / apoptotic process involved in morphogenesis / astrocyte cell migration / myelin sheath abaxonal region / Scrib-APC-beta-catenin complex / establishment of apical/basal cell polarity / synaptic vesicle targeting / polarized epithelial cell differentiation / epithelial structure maintenance / neurotransmitter receptor transport, endosome to postsynaptic membrane / mammary gland duct morphogenesis / cell-cell contact zone / protein localization to adherens junction / 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 / positive chemotaxis / regulation of postsynaptic neurotransmitter receptor internalization / receptor clustering / RHOJ GTPase cycle / negative regulation of activated T cell proliferation / positive regulation of receptor recycling / RHOQ GTPase cycle / CDC42 GTPase cycle / negative regulation of mitotic cell cycle / immunological synapse / synaptic vesicle endocytosis / signaling adaptor activity / Asymmetric localization of PCP proteins / adherens junction / PDZ domain binding / neural tube closure / wound healing / cell-cell adhesion / positive regulation of type II interferon production / cell junction / cell migration / cell-cell junction / 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 / positive regulation of apoptotic process / cadherin binding / DNA-templated transcription / regulation of 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
ISOPROPYL ALCOHOL / Protein E6 / Protein scribble homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus type 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 7, 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 E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3558
Polymers11,3192
Non-polymers1,0366
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint2 kcal/mol
Surface area6330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.611, 70.611, 140.782
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 10082.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: At the n-terminal of chain B, the sequence GPLGS is part of the expression tag
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: 1236.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human papillomavirus type 16 / References: UniProt: A0A384KQK8

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Non-polymers , 4 types, 32 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 5.17 Å3/Da / Density % sol: 76.19 % / Description: hexagonal dipyramid
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2.5 M NaCl, 0.1 m Na HEPES pH 8.0 / PH range: 7.0-8.0

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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: Aug 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.5→37.23 Å / Num. obs: 7707 / % possible obs: 99.44 % / Redundancy: 6.2 % / Biso Wilson estimate: 65.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1008 / Net I/σ(I): 23.29
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 1.363 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 732 / CC1/2: 0.939 / % possible all: 97.98

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XA6

6xa6


Resolution: 2.5→37.23 Å / SU ML: 0.3352 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.2697
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2812 373 4.86 %
Rwork0.2743 7300 -
obs0.2747 7673 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.32 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms737 0 65 26 828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151806
X-RAY DIFFRACTIONf_angle_d1.61191083
X-RAY DIFFRACTIONf_chiral_restr0.0593117
X-RAY DIFFRACTIONf_plane_restr0.0173134
X-RAY DIFFRACTIONf_dihedral_angle_d23.7104330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.860.3621180.33662336X-RAY DIFFRACTION99.07
2.86-3.60.34781140.31162408X-RAY DIFFRACTION99.64
3.61-37.230.25031410.25222556X-RAY DIFFRACTION99.7
Refinement TLS params.Method: refined / Origin x: 29.4120609011 Å / Origin y: -11.862134485 Å / Origin z: 3.9200487087 Å
111213212223313233
T0.370633589743 Å2-0.0230008489842 Å2-0.0459339538896 Å2-0.243090872266 Å20.116739297913 Å2--0.396290370831 Å2
L5.19851624918 °2-0.0513628975848 °20.385851115115 °2-6.90302535132 °2-0.410119329159 °2--6.48648665375 °2
S0.159849086949 Å °-0.135769646057 Å °0.0022399187161 Å °0.165721444994 Å °-0.00414854366821 Å °0.145683902922 Å °-0.363039294302 Å °-0.035232096052 Å °-0.155078348403 Å °
Refinement TLS groupSelection details: all

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