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- PDB-7pc7: The PDZ domain of SNTG1 complexed with the acetylated PDZ-binding... -

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Basic information

Entry
Database: PDB / ID: 7pc7
TitleThe PDZ domain of SNTG1 complexed with the acetylated PDZ-binding motif of PTEN
Components
  • Gamma-1-syntrophin,Annexin A2
  • Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
KeywordsPEPTIDE BINDING PROTEIN / PDZ / complex / crystallization chaperone
Function / homology
Function and homology information


PTEN Loss of Function in Cancer / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity / central nervous system myelin maintenance ...PTEN Loss of Function in Cancer / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity / central nervous system myelin maintenance / negative regulation of wound healing, spreading of epidermal cells / phosphatidylinositol-3-phosphate phosphatase activity / syntrophin complex / central nervous system neuron axonogenesis / positive regulation of low-density lipoprotein particle receptor binding / postsynaptic density assembly / PCSK9-AnxA2 complex / AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / neuron-neuron synaptic transmission / positive regulation of vacuole organization / dystrophin-associated glycoprotein complex / positive regulation of low-density lipoprotein particle clearance / presynaptic membrane assembly / phospholipase A2 inhibitor activity / synapse maturation / Regulation of PTEN mRNA translation / Negative regulation of the PI3K/AKT network / cellular response to electrical stimulus / positive regulation of vesicle fusion / negative regulation of cell cycle G1/S phase transition / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / negative regulation of axonogenesis / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / myelin sheath adaxonal region / Transcriptional Regulation by MECP2 / negative regulation of organ growth / negative regulation of excitatory postsynaptic potential / forebrain morphogenesis / negative regulation of focal adhesion assembly / cadherin binding involved in cell-cell adhesion / phosphatidylinositol dephosphorylation / cell communication / anaphase-promoting complex binding / Schmidt-Lanterman incisure / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / cornified envelope / vesicle budding from membrane / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of receptor internalization / dentate gyrus development / plasma membrane protein complex / positive regulation of ubiquitin protein ligase activity / ubiquitin ligase activator activity / spindle assembly involved in female meiosis / maternal behavior / positive regulation of ubiquitin-dependent protein catabolic process / phosphatidylinositol biosynthetic process / osteoclast development / negative regulation of cell size / calcium-dependent phospholipid binding / dendritic spine morphogenesis / Dissolution of Fibrin Clot / S100 protein binding / collagen fibril organization / vesicle membrane / positive regulation of low-density lipoprotein receptor activity / negative regulation of epithelial to mesenchymal transition / epithelial cell apoptotic process / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of G1/S transition of mitotic cell cycle / protein serine/threonine phosphatase activity / molecular function inhibitor activity / myosin phosphatase activity / protein-serine/threonine phosphatase / positive regulation of receptor recycling / adult behavior / ubiquitin-specific protease binding / regulation of neuron projection development / negative regulation of peptidyl-serine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / phosphatidylserine binding / locomotor rhythm / negative regulation of cellular senescence / positive regulation of exocytosis / Synthesis of PIPs at the plasma membrane / negative regulation of vascular associated smooth muscle cell proliferation / phosphoprotein phosphatase activity / social behavior / positive regulation of excitatory postsynaptic potential / regulation of neurogenesis / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Smooth Muscle Contraction / multicellular organismal response to stress / canonical Wnt signaling pathway / prepulse inhibition
Similarity search - Function
Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / PTEN, phosphatase domain / Syntrophin / Syntrophin C-terminal PH domain / : / Inositol hexakisphosphate / Annexin A2 / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein ...Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / PTEN, phosphatase domain / Syntrophin / Syntrophin C-terminal PH domain / : / Inositol hexakisphosphate / Annexin A2 / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Polymorphic toxin system, DSP-PTPase phosphatase / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / C2 domain superfamily / PH domain profile. / PDZ domain / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Annexin A2 / Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN / Gamma-1-syntrophin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCousido-Siah, A. / Trave, G. / Gogl, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: A scalable strategy to solve structures of PDZ domains and their complexes.
Authors: Cousido-Siah, A. / Carneiro, L. / Kostmann, C. / Ecsedi, P. / Nyitray, L. / Trave, G. / Gogl, G.
History
DepositionAug 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-1-syntrophin,Annexin A2
B: Gamma-1-syntrophin,Annexin A2
E: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
F: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,87320
Polymers96,0234
Non-polymers84916
Water7,296405
1
A: Gamma-1-syntrophin,Annexin A2
E: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,43610
Polymers48,0122
Non-polymers4258
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-59 kcal/mol
Surface area19430 Å2
MethodPISA
2
B: Gamma-1-syntrophin,Annexin A2
F: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
hetero molecules


  • defined by author&software
  • 48.4 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)48,43610
Polymers48,0122
Non-polymers4258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-67 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.310, 61.740, 285.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Gamma-1-syntrophin,Annexin A2 / G1SYN / Syntrophin-4 / SYN4 / Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy ...G1SYN / Syntrophin-4 / SYN4 / Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy chain / Chromobindin-8 / Lipocortin II / Placental anticoagulant protein IV / PAP-IV / Protein I / p36


Mass: 46770.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNTG1, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NSN8, UniProt: P07355
#2: Protein/peptide Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN / Mutated in multiple advanced cancers 1 / Phosphatase and tensin homolog


Mass: 1241.326 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: N-terminal biotin-ttds (trioxatridecan-succinamic acid) label
Source: (synth.) Homo sapiens (human)
References: UniProt: P60484, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase, phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris 8.5, 22 % v/v PEG Smear Broad

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→46.687 Å / Num. obs: 63552 / % possible obs: 100 % / Redundancy: 13.36 % / CC1/2: 0.999 / Rrim(I) all: 0.14 / Net I/σ(I): 14.38
Reflection shellResolution: 2.1→2.15 Å / Mean I/σ(I) obs: 1.71 / Num. unique obs: 4649 / CC1/2: 0.57 / Rrim(I) all: 1.766

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N7D, 2PDZ

5n7d

2pdz


Resolution: 2.1→46.687 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 3176 5.01 %
Rwork0.1852 60277 -
obs0.1869 63453 99.98 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.45 Å2 / Biso mean: 56.4524 Å2 / Biso min: 19.41 Å2
Refinement stepCycle: final / Resolution: 2.1→46.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6494 0 36 405 6935
Biso mean--56.09 50.56 -
Num. residues----816
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1-2.13130.33361360.2832576
2.1313-2.16460.33671360.25042586
2.1646-2.20010.26761350.24182574
2.2001-2.23810.27191360.24382581
2.2381-2.27880.24981370.26062593
2.2788-2.32260.25871360.22152581
2.3226-2.370.24711360.21272581
2.37-2.42150.24751360.20292582
2.4215-2.47780.22581350.19752578
2.4778-2.53980.24181390.19692628
2.5398-2.60850.25781360.19772577
2.6085-2.68520.22331370.19222604
2.6852-2.77190.24721370.1922601
2.7719-2.87090.19221380.18362620
2.8709-2.98590.23591370.18592604
2.9859-3.12170.20371360.17692597
3.1217-3.28630.20031380.17762614
3.2863-3.49210.21791390.17672635
3.4921-3.76160.21251400.17842670
3.7616-4.140.17711400.15932648
4.14-4.73850.19171410.14712683
4.7385-5.96810.241440.192709
5.9681-46.6870.19621510.18192855
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.2981-2.3372-2.1622.33211.65413.20140.00341.2701-0.2467-0.4952-0.45630.2806-0.2836-0.09420.36860.75310.0166-0.08410.88480.00490.575115.1036-8.0596179.3181
21.10960.33730.27530.77820.52060.97850.0448-0.07230.01870.0447-0.07360.06450.0157-0.07550.03660.2570.00920.0030.17220.03930.309311.06210.4239216.9087
34.0032-1.12750.78852.72021.54422.08010.07030.18830.0335-0.1912-0.04110.0341-0.13440.0969-0.0490.22620.00150.0190.19220.05170.258816.1479-5.9772201.7297
42.2909-2.3715-1.08872.40761.10370.5020.1440.7087-0.0045-0.1157-0.47150.3292-0.4863-0.98720.2980.75890.16090.00481.1616-0.13640.584237.7217-26.4529174.1023
50.6957-0.13080.38780.75670.37712.3586-0.14780.22680.1464-0.1359-0.01770.0279-0.18310.23510.16710.4285-0.10880.0040.57310.00990.33859.7055-34.418156.5471
60.3083-0.22090.07780.1576-0.0560.01930.44860.3382-0.17350.0029-0.07550.3165-0.37690.2755-0.341.69290.0585-0.27981.3731-0.07270.850112.6788-1.1865168.7527
74.5198-2.72033.64272.834-2.64823.19390.4206-0.26090.21950.4547-0.06120.1213-0.5135-0.6625-0.32860.9830.2010.37681.53140.2521.379442.8414-18.7948169.2164
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 54 through 156 )A54 - 156
2X-RAY DIFFRACTION2chain 'A' and (resid 157 through 400 )A157 - 400
3X-RAY DIFFRACTION3chain 'A' and (resid 401 through 461 )A401 - 461
4X-RAY DIFFRACTION4chain 'B' and (resid 54 through 156 )B54 - 156
5X-RAY DIFFRACTION5chain 'B' and (resid 157 through 461 )B157 - 461
6X-RAY DIFFRACTION6chain 'E' and (resid 91 through 100 )E91 - 100
7X-RAY DIFFRACTION7chain 'F' and (resid 63 through 66 )F63 - 66

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