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- PDB-7pc8: The PDZ domain of SNTG1 complexed with the phosphomimetic mutant ... -

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Basic information

Entry
Database: PDB / ID: 7pc8
TitleThe PDZ domain of SNTG1 complexed with the phosphomimetic mutant PDZ-binding motif of RSK1
Components
  • Gamma-1-syntrophin,Annexin A2
  • Ribosomal protein S6 kinase alpha-1
KeywordsPEPTIDE BINDING PROTEIN / PDZ / complex / crystallization chaperone
Function / homology
Function and homology information


syntrophin complex / regulation of translation in response to stress / : / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / AnxA2-p11 complex / membrane raft assembly / dystrophin-associated glycoprotein complex / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance ...syntrophin complex / regulation of translation in response to stress / : / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / AnxA2-p11 complex / membrane raft assembly / dystrophin-associated glycoprotein complex / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of hepatic stellate cell activation / positive regulation of vesicle fusion / hepatocyte proliferation / CREB phosphorylation / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / myelin sheath adaxonal region / cell communication / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / cornified envelope / vesicle budding from membrane / osteoclast development / TORC1 signaling / Gastrin-CREB signalling pathway via PKC and MAPK / plasma membrane protein complex / calcium-dependent phospholipid binding / negative regulation of receptor internalization / RSK activation / Dissolution of Fibrin Clot / negative regulation of TOR signaling / S100 protein binding / collagen fibril organization / vesicle membrane / : / epithelial cell apoptotic process / phosphatidylserine binding / positive regulation of receptor recycling / ERK/MAPK targets / Recycling pathway of L1 / positive regulation of exocytosis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / Transcriptional and post-translational regulation of MITF-M expression and activity / cytoskeletal protein binding / fibrinolysis / lipid droplet / phosphatidylinositol-4,5-bisphosphate binding / protein serine/threonine/tyrosine kinase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cell-matrix adhesion / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / response to activity / adherens junction / positive regulation of cell differentiation / lung development / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / nuclear matrix / ruffle membrane / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / late endosome membrane / melanosome / actin binding / midbody / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / protease binding / angiogenesis / collagen-containing extracellular matrix / chemical synaptic transmission / basolateral plasma membrane / vesicle / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / early endosome / histone H3T6 kinase activity
Similarity search - Function
: / Syntrophin / Syntrophin C-terminal PH domain / Annexin A2 / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin ...: / Syntrophin / Syntrophin C-terminal PH domain / Annexin A2 / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Annexin V; domain 1 / Protein kinase, C-terminal / Protein kinase C terminal domain / PDZ domain / Pdz3 Domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PDZ domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Annexin A2 / Ribosomal protein S6 kinase alpha-1 / Gamma-1-syntrophin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

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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
C: Ribosomal protein S6 kinase alpha-1
D: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,88519
Polymers95,9724
Non-polymers91315
Water3,981221
1
A: Gamma-1-syntrophin,Annexin A2
C: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,46310
Polymers47,9862
Non-polymers4778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-46 kcal/mol
Surface area20740 Å2
MethodPISA
2
B: Gamma-1-syntrophin,Annexin A2
D: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4229
Polymers47,9862
Non-polymers4377
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-41 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.580, 59.820, 125.210
Angle α, β, γ (deg.)90.000, 117.840, 90.000
Int Tables number5
Space group name H-MC121

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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 Ribosomal protein S6 kinase alpha-1 / S6K-alpha-1 / 90 kDa ribosomal protein S6 kinase 1 / p90-RSK 1 / p90RSK1 / p90S6K / MAP kinase- ...S6K-alpha-1 / 90 kDa ribosomal protein S6 kinase 1 / p90-RSK 1 / p90RSK1 / p90S6K / MAP kinase-activated protein kinase 1a / MAPK-activated protein kinase 1a / MAPKAP kinase 1a / MAPKAPK-1a / Ribosomal S6 kinase 1 / RSK-1


Mass: 1215.465 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: Q15418, non-specific serine/threonine protein kinase
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 3.96 Å3/Da / Density % sol: 68.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Lithium sulfate, 0.05 M Magnesium chloride hexahydrate ,0.1 M HEPES 7.8, 20 % v/v PEG Smear High

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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: 2.5→48.334 Å / Num. obs: 51681 / % possible obs: 99.5 % / Redundancy: 6.83 % / CC1/2: 0.995 / Rrim(I) all: 0.198 / Net I/σ(I): 9.56
Reflection shellResolution: 2.5→2.56 Å / Mean I/σ(I) obs: 1.26 / Num. unique obs: 3761 / CC1/2: 0.532 / Rrim(I) all: 1.66

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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: 2.5→48.334 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 2584 5 %
Rwork0.2023 49085 -
obs0.2037 51669 99.68 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.84 Å2 / Biso mean: 61.7162 Å2 / Biso min: 29.78 Å2
Refinement stepCycle: final / Resolution: 2.5→48.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6638 0 45 221 6904
Biso mean--63.02 52.36 -
Num. residues----836
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.5480.41071420.32552698100
2.548-2.60.35251400.3404266399
2.6-2.65660.34531420.29942700100
2.6566-2.71840.29871430.269272499
2.7184-2.78630.29551410.25832675100
2.7863-2.86170.31541430.2516270999
2.8617-2.94590.31241420.24712708100
2.9459-3.04090.31471420.2487268799
3.0409-3.14960.24631440.22982749100
3.1496-3.27570.23361420.21372694100
3.2757-3.42470.28091430.20372714100
3.4247-3.60520.21671440.20612743100
3.6052-3.8310.20271440.18212718100
3.831-4.12670.23021450.1662759100
4.1267-4.54170.16551440.16042740100
4.5417-5.19820.20021450.16872753100
5.1982-6.54660.22691470.20732792100
6.5466-48.3340.16731510.1672859100
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)
18.34750.7909-1.33827.71832.79826.90280.69920.5084-1.6157-0.4324-0.68850.2230.8617-0.0947-0.02790.69720.1499-0.29380.4924-0.07780.843111.515930.330714.7046
20.5538-0.08950.060.96281.33282.9880.00730.00670.08480.0111-0.17340.068-0.072-0.23350.16630.3374-0.0336-0.05410.32840.02840.331818.4298-1.656938.6974
35.99893.7674.83672.35323.05133.88990.12970.8409-0.1915-0.27580.02160.02920.02830.3156-0.16650.6256-0.0399-0.11880.88050.24660.669411.812-14.4899-14.1916
43.2736-1.06810.05641.45960.22170.60550.19240.55030.2992-0.2944-0.1324-0.1769-0.03990.0117-0.06390.3720.01290.04870.4220.10580.356141.27394.0015-10.4242
54.98882.5670.76411.9381.92343.9127-0.24130.2998-0.6116-0.234-0.66592.0696-0.2677-0.13410.90431.58320.2796-0.43070.7785-0.17441.514111.343618.143712.082
67.1013-0.49359.04910.0342-0.628720.6045-0.263-0.57130.34880.1589-0.00630.4558-0.257-0.76181.03120.0966-0.19792.01370.17061.188317.1144-22.0985-20.3877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 138 )A50 - 138
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 462 )A139 - 462
3X-RAY DIFFRACTION3chain 'B' and (resid 54 through 157 )B54 - 157
4X-RAY DIFFRACTION4chain 'B' and (resid 158 through 462 )B158 - 462
5X-RAY DIFFRACTION5chain 'C' and (resid 182 through 189 )C182 - 189
6X-RAY DIFFRACTION6chain 'D' and (resid 184 through 189 )D184 - 189

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