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- PDB-8b8o: Crystal structure of Scribble PDZ1 with human papillomavirus stra... -

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Basic information

Entry
Database: PDB / ID: 8b8o
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 / establishment of T cell polarity / 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 / polarized epithelial cell differentiation ...extrinsic component of postsynaptic density membrane / establishment of T cell polarity / 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 / polarized epithelial cell differentiation / synaptic vesicle targeting / epithelial structure maintenance / neurotransmitter receptor transport, endosome to postsynaptic membrane / mammary gland duct morphogenesis / cell-cell contact zone / : / post-anal tail morphogenesis / establishment or maintenance of epithelial cell apical/basal polarity / activation of GTPase activity / protein localization to adherens junction / auditory receptor cell stereocilium organization / negative regulation of mitotic cell cycle / RND2 GTPase cycle / RND3 GTPase cycle / positive chemotaxis / regulation of postsynaptic neurotransmitter receptor internalization / receptor clustering / negative regulation of activated T cell proliferation / RHOJ GTPase cycle / RHOQ GTPase cycle / positive regulation of receptor recycling / CDC42 GTPase cycle / immunological synapse / synaptic vesicle endocytosis / signaling adaptor activity / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / cell-cell adhesion / positive regulation of type II interferon production / cell-cell junction / cell junction / cell migration / presynapse / lamellipodium / basolateral plasma membrane / host cell cytoplasm / cell population proliferation / postsynaptic density / symbiont-mediated suppression of host innate immune response / positive regulation of apoptotic process / cadherin binding / protein kinase binding / host cell nucleus / glutamatergic synapse / DNA binding / extracellular exosome / nucleoplasm / metal ion binding / 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 66
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
B: Protein scribble homolog
A: Protein scribble homolog
C: Protein E6
D: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4496
Polymers22,3254
Non-polymers1242
Water19811
1
B: Protein scribble homolog
C: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2874
Polymers11,1632
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein scribble homolog
D: Protein E6


Theoretical massNumber of molelcules
Total (without water)11,1632
Polymers11,1632
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-1 kcal/mol
Surface area5790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.091, 90.992, 36.356
Angle α, β, γ (deg.)90.000, 91.930, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1000 through 1008 or resid 1013...
d_2ens_1(chain "B" and (resid 1000 through 1008 or resid 1013...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLYGLYPROPROAB1000 - 10084 - 12
d_12PROPROPROPROAB1013 - 102817 - 32
d_13PROPROASPASPAB1034 - 109238 - 96
d_21GLYGLYPROPROBA1000 - 10084 - 12
d_22PROPROASPASPBA1013 - 109217 - 96

NCS oper: (Code: givenMatrix: (0.964038778597, 0.123768590064, -0.23518199224), (0.0639915060671, -0.967003924289, -0.246593790595), (-0.257942475199, 0.222676326812, -0.940149420553)Vector: 4. ...NCS oper: (Code: given
Matrix: (0.964038778597, 0.123768590064, -0.23518199224), (0.0639915060671, -0.967003924289, -0.246593790595), (-0.257942475199, 0.222676326812, -0.940149420553)
Vector: 4.28972382815, -53.4217806796, 16.2433308907)

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Components

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


Mass: 10082.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: At the n-terminal of chain A, 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: 1080.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) human papillomavirus 66 / References: UniProt: G8HXP2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.37 Å3/Da / Density % sol: 48.16 % / Description: Diamond plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.9 / Details: 0.1 M Na HEPES pH 7.9, 63% v/v MPD

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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: Feb 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.9→32.03 Å / Num. obs: 4654 / % possible obs: 99.57 % / Redundancy: 7 % / Biso Wilson estimate: 84.26 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1438 / Net I/σ(I): 8.41
Reflection shellResolution: 2.9→3.004 Å / Rmerge(I) obs: 1.293 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 451 / CC1/2: 0.594

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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: 2.9→32.03 Å / SU ML: 0.5153 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5046
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2889 212 4.57 %
Rwork0.2696 4428 -
obs0.2705 4640 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.69 Å2
Refinement stepCycle: LAST / Resolution: 2.9→32.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1403 0 8 11 1422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031421
X-RAY DIFFRACTIONf_angle_d0.66211913
X-RAY DIFFRACTIONf_chiral_restr0.0471229
X-RAY DIFFRACTIONf_plane_restr0.0083253
X-RAY DIFFRACTIONf_dihedral_angle_d12.8468526
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 3.10947417099 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.650.41761070.32232202X-RAY DIFFRACTION99.61
3.65-32.030.25141050.25352226X-RAY DIFFRACTION99.62
Refinement TLS params.Method: refined / Origin x: 21.3400575757 Å / Origin y: -25.5439849334 Å / Origin z: 1.20771914627 Å
111213212223313233
T0.462075946378 Å20.0279419124344 Å20.0997074400001 Å2-0.661581533304 Å20.0515015030832 Å2--0.506884329434 Å2
L1.74873954928 °20.555053445829 °2-0.146076708731 °2-4.81056056789 °23.56900298086 °2--5.39973399478 °2
S-0.166125209666 Å °0.106677100539 Å °-0.00195643131392 Å °0.290331427369 Å °0.249945318904 Å °-0.0532205452868 Å °0.219641361291 Å °-0.237213223631 Å °-0.0555669449254 Å °
Refinement TLS groupSelection details: all

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