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- PDB-6hks: Crystal structure of the PTPN3 PDZ domain bound to the HPV16 E6 o... -

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Basic information

Entry
Database: PDB / ID: 6hks
TitleCrystal structure of the PTPN3 PDZ domain bound to the HPV16 E6 oncoprotein C-terminal peptide
Components
  • Protein E6
  • Tyrosine-protein phosphatase non-receptor type 3
KeywordsHYDROLASE / PDZ domain Protein tyrosine phosphatase Human papillomavirus E6 oncoprotein PDZ binding motif
Function / homology
Function and homology information


regulation of membrane depolarization during action potential / regulation of sodium ion transmembrane transporter activity / symbiont-mediated suppression of host transcription / negative regulation of membrane protein ectodomain proteolysis / symbiont-mediated perturbation of host apoptosis / regulation of proteolysis / activation of GTPase activity / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of mitotic cell cycle / sodium channel regulator activity ...regulation of membrane depolarization during action potential / regulation of sodium ion transmembrane transporter activity / symbiont-mediated suppression of host transcription / negative regulation of membrane protein ectodomain proteolysis / symbiont-mediated perturbation of host apoptosis / regulation of proteolysis / activation of GTPase activity / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of mitotic cell cycle / sodium channel regulator activity / cytoskeletal protein binding / protein dephosphorylation / phosphotyrosine residue binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / liver regeneration / PDZ domain binding / EGFR downregulation / cytoplasmic side of plasma membrane / Negative regulation of MAPK pathway / MAPK cascade / ATPase binding / 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 / cytoskeleton / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-3, -4 / PTPN3/4, FERM domain C-lobe / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain ...Protein-tyrosine phosphatase, non-receptor type-3, -4 / PTPN3/4, FERM domain C-lobe / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / PDZ domain / Pdz3 Domain / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Protein E6 / Tyrosine-protein phosphatase non-receptor type 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus type 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19441072073 Å
AuthorsGenera, M. / Haouz, A. / Caillet-Saguy, C.
CitationJournal: Sci Rep / Year: 2019
Title: Structural and functional characterization of the PDZ domain of the human phosphatase PTPN3 and its interaction with the human papillomavirus E6 oncoprotein.
Authors: Genera, M. / Samson, D. / Raynal, B. / Haouz, A. / Baron, B. / Simenel, C. / Guerois, R. / Wolff, N. / Caillet-Saguy, C.
History
DepositionSep 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 3
B: Tyrosine-protein phosphatase non-receptor type 3
C: Tyrosine-protein phosphatase non-receptor type 3
D: Tyrosine-protein phosphatase non-receptor type 3
E: Tyrosine-protein phosphatase non-receptor type 3
F: Tyrosine-protein phosphatase non-receptor type 3
G: Protein E6
H: Protein E6
I: Protein E6
J: Protein E6
K: Protein E6
L: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,37818
Polymers84,61712
Non-polymers7616
Water4,197233
1
A: Tyrosine-protein phosphatase non-receptor type 3
G: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2303
Polymers14,1032
Non-polymers1271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-2 kcal/mol
Surface area5980 Å2
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 3
H: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2303
Polymers14,1032
Non-polymers1271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-1 kcal/mol
Surface area5990 Å2
MethodPISA
3
C: Tyrosine-protein phosphatase non-receptor type 3
I: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2303
Polymers14,1032
Non-polymers1271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-1 kcal/mol
Surface area5700 Å2
MethodPISA
4
D: Tyrosine-protein phosphatase non-receptor type 3
J: Protein E6


Theoretical massNumber of molelcules
Total (without water)14,1032
Polymers14,1032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-2 kcal/mol
Surface area5960 Å2
MethodPISA
5
E: Tyrosine-protein phosphatase non-receptor type 3
K: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2303
Polymers14,1032
Non-polymers1271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-2 kcal/mol
Surface area6030 Å2
MethodPISA
6
F: Tyrosine-protein phosphatase non-receptor type 3
L: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3574
Polymers14,1032
Non-polymers2542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-3 kcal/mol
Surface area6040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.620, 77.430, 130.030
Angle α, β, γ (deg.)90.000, 90.140, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Tyrosine-protein phosphatase non-receptor type 3 / Protein-tyrosine phosphatase H1 / PTP-H1


Mass: 12709.242 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN3, PTPH1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B / References: UniProt: P26045, protein-tyrosine-phosphatase
#2: Protein/peptide
Protein E6


Mass: 1393.554 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 16 / Gene: E6 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B / References: UniProt: P03126
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 3.47 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG 3350 0.2 mM KI pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.978549599648 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978549599648 Å / Relative weight: 1
ReflectionResolution: 2.19→46.62 Å / Num. obs: 47024 / % possible obs: 99.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 47.643622563 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.14 / Net I/σ(I): 8.17
Reflection shellResolution: 2.19→2.23 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.11 / CC1/2: 0.726 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EZ0

5ez0


Resolution: 2.19441072073→43.3432039427 Å / SU ML: 0.386490308239 / Cross valid method: FREE R-VALUE / σ(F): 1.36457088824 / Phase error: 32.2236856577
RfactorNum. reflection% reflection
Rfree0.246797249095 2345 5.00330708997 %
Rwork0.194138416618 --
obs0.196735201568 46869 98.7173006445 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.9100392383 Å2
Refinement stepCycle: LAST / Resolution: 2.19441072073→43.3432039427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4746 0 6 233 4985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007549219614874813
X-RAY DIFFRACTIONf_angle_d0.9375071099576483
X-RAY DIFFRACTIONf_chiral_restr0.0571069356299740
X-RAY DIFFRACTIONf_plane_restr0.00531482508244863
X-RAY DIFFRACTIONf_dihedral_angle_d7.168715169573207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1944-2.23920.4362319896051210.4131138167062305X-RAY DIFFRACTION88.2823871907
2.2392-2.28790.3682258408041380.3752597386272622X-RAY DIFFRACTION99.7470184315
2.2879-2.34110.3859783254511380.3503899337522626X-RAY DIFFRACTION98.2580874511
2.3411-2.39960.3930931980031370.3116540438822585X-RAY DIFFRACTION99.6704503845
2.3996-2.46450.3219491508721380.3062882963822638X-RAY DIFFRACTION98.7548914977
2.4645-2.5370.3680301134041370.2813645469832606X-RAY DIFFRACTION99.7817388141
2.537-2.61890.2783803941081400.235399825662644X-RAY DIFFRACTION98.7584249734
2.6189-2.71250.2733238173421380.2295394463432612X-RAY DIFFRACTION99.8185117967
2.7125-2.82110.2881201221551390.225761992052643X-RAY DIFFRACTION99.1093694336
2.8211-2.94950.2573881513171380.2191569386232613X-RAY DIFFRACTION99.2066354129
2.9495-3.10490.3047541044511410.2185005626322680X-RAY DIFFRACTION99.6819787986
3.1049-3.29940.2966251745291380.2025488047572610X-RAY DIFFRACTION99.5652173913
3.2994-3.5540.2555511866921400.1876107421262648X-RAY DIFFRACTION99.6782266714
3.554-3.91150.2151180476151400.159281838132670X-RAY DIFFRACTION99.7161107168
3.9115-4.4770.1983003117851390.1429533817922647X-RAY DIFFRACTION99.8566308244
4.477-5.63850.1690850692981410.1367524234612673X-RAY DIFFRACTION99.7165131113
5.6385-43.35160.2021378464731420.166695060392702X-RAY DIFFRACTION98.5446985447
Refinement TLS params.Method: refined / Origin x: -0.439637573517 Å / Origin y: 41.323561443 Å / Origin z: 32.3646606666 Å
111213212223313233
T0.347321006402 Å20.00495558438158 Å20.007804100398 Å2-0.319123002595 Å2-0.00615151381584 Å2--0.441373160619 Å2
L0.572930671347 °20.0463971242377 °20.173975497222 °2-0.0564162221765 °20.0452452188037 °2--0.376760985189 °2
S0.00905199564195 Å °-0.0130681133317 Å °0.0145353863225 Å °-0.00171004685407 Å °0.0201275320829 Å °-0.0143708510004 Å °-0.0105256241143 Å °0.0185141793415 Å °-0.027999439771 Å °
Refinement TLS groupSelection details: all

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