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- PDB-8b87: Crystal structure of Scribble PDZ1 with human papillomavirus stra... -

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Basic information

Entry
Database: PDB / ID: 8b87
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


extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation ...extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation / myelin sheath abaxonal region / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to adherens junction / cell-cell contact zone / mammary gland duct morphogenesis / post-anal tail morphogenesis / activation of GTPase activity / establishment or maintenance of epithelial cell apical/basal polarity / regulation of postsynaptic neurotransmitter receptor internalization / auditory receptor cell stereocilium organization / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of receptor recycling / positive chemotaxis / RHOJ GTPase cycle / RHOQ GTPase cycle / receptor clustering / negative regulation of activated T cell proliferation / CDC42 GTPase cycle / synaptic vesicle endocytosis / immunological synapse / negative regulation of mitotic cell cycle / signaling adaptor activity / : / Asymmetric localization of PCP proteins / neural tube closure / PDZ domain binding / adherens junction / wound healing / cell-cell adhesion / positive regulation of type II interferon production / cell-cell junction / cell migration / presynapse / cell junction / lamellipodium / 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 / cell population proliferation / host cell cytoplasm / postsynaptic density / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / cadherin binding / positive regulation of apoptotic process / DNA-templated transcription / glutamatergic synapse / host cell nucleus / regulation of DNA-templated transcription / DNA binding / extracellular exosome / nucleoplasm / metal ion binding / plasma membrane
Similarity search - Function
E6 early regulatory protein / E6 superfamily / Early Protein (E6) / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain ...E6 early regulatory protein / E6 superfamily / Early Protein (E6) / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / 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
AMMONIUM ION / DI(HYDROXYETHYL)ETHER / beta-D-talopyranose / Protein E6 / Protein scribble homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus type 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)28,77415
Polymers27,6214
Non-polymers1,15311
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.620, 31.140, 91.760
Angle α, β, γ (deg.)90.000, 107.560, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-1051-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 721 through 731 or (resid 732...
d_2ens_1(chain "B" and (resid 721 through 734 or resid 737...
d_1ens_2chain "C"
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ARGARGGLNGLNAA721 - 73426 - 39
d_12ens_1GLYGLYGLYGLYAA737 - 74742 - 52
d_13ens_1THRTHRVALVALAA749 - 76354 - 68
d_14ens_1GLUGLUGLUGLUAA765 - 81470 - 119
d_21ens_1ARGARGGLNGLNBB721 - 73426 - 39
d_22ens_1GLYGLYGLYGLYBB737 - 74742 - 52
d_23ens_1THRTHRVALVALBB749 - 76354 - 68
d_24ens_1GLUGLUGLUGLUBB765 - 81470 - 119
d_11ens_2SERSERLEULEUCC97 - 1052 - 10
d_21ens_2SERSERLEULEUDD97 - 1052 - 10

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.733203212677, -0.637654423117, 0.236241159835), (-0.649985726294, 0.555088537467, -0.519033015507), (0.199828938179, -0.534110056311, -0.821458972325)-48.4218662749, -4.47115874763, 46.0998575431
2given(-0.727876663286, -0.64741156303, 0.225950948435), (-0.651620297412, 0.550460294484, -0.521904638988), (0.213510072466, -0.527116431399, -0.82253371767)-48.109470321, -4.49357541542, 46.0626160944

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Components

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Protein / Protein/peptide / Sugars , 3 types, 5 molecules ABCD

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


Mass: 12574.082 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: 1236.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human papillomavirus type 16 / References: UniProt: A0A384KQK8
#3: Sugar ChemComp-SDY / beta-D-talopyranose / beta-D-talose / D-talose / talose / beta-D-talopyranosose / Talose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DTalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-talopyranoseCOMMON NAMEGMML 1.0
b-D-TalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
TalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 92 molecules

#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.12 Å3/Da / Density % sol: 41.95 % / Description: Rod
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium Fluoride, 0.1 M Bis-Tris propane pH 6.5, 20% w/v PEG 3350

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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: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2→35.57 Å / Num. obs: 13792 / % possible obs: 98.86 % / Redundancy: 2.9 % / Biso Wilson estimate: 33.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07899 / Net I/σ(I): 8.11
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.8362 / Num. unique obs: 1385 / CC1/2: 0.54

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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→35.57 Å / SU ML: 0.2476 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2947
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2555 723 5.24 %
Rwork0.2196 13068 -
obs0.2216 13791 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.19 Å2
Refinement stepCycle: LAST / Resolution: 2→35.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 76 82 1703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221635
X-RAY DIFFRACTIONf_angle_d0.46992167
X-RAY DIFFRACTIONf_chiral_restr0.0466241
X-RAY DIFFRACTIONf_plane_restr0.0074282
X-RAY DIFFRACTIONf_dihedral_angle_d12.3269622
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.688721807231
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS1.24382424058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.150.31391450.29022577X-RAY DIFFRACTION99.49
2.15-2.370.28931370.24362626X-RAY DIFFRACTION98.89
2.37-2.710.26581290.23692601X-RAY DIFFRACTION99.16
2.71-3.420.27121510.21782601X-RAY DIFFRACTION98.74
3.42-35.570.2311610.19982663X-RAY DIFFRACTION98.19
Refinement TLS params.Method: refined / Origin x: -24.8202922351 Å / Origin y: 0.74938457573 Å / Origin z: 21.3433728376 Å
111213212223313233
T0.274239482256 Å2-0.020332319139 Å2-0.0349186507199 Å2-0.280942719682 Å2-0.0125689581957 Å2--0.248336175533 Å2
L4.25256693201 °20.774525304672 °2-0.685033300734 °2-0.47502778635 °2-0.771158539461 °2--1.80183509871 °2
S0.140914756122 Å °-0.787356067351 Å °-0.0306838581734 Å °0.129047976491 Å °-0.128264294839 Å °0.00773779984416 Å °-0.0392848777017 Å °-0.0370806852172 Å °-0.0144396121083 Å °
Refinement TLS groupSelection details: all

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