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- PDB-7qql: The PDZ domain of SNTG2 complexed with the phosphorylated PDZ-bin... -

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Basic information

Entry
Database: PDB / ID: 7qql
TitleThe PDZ domain of SNTG2 complexed with the phosphorylated PDZ-binding motif of RSK1
Components
  • Gamma-2-syntrophin,Annexin A2
  • Ribosomal protein S6 kinase alpha-1
KeywordsPEPTIDE BINDING PROTEIN / PDZ / linear motif / crystallization chaperone
Function / homology
Function and homology information


syntrophin complex / regulation of translation in response to stress / positive regulation of low-density lipoprotein particle receptor binding / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / dystrophin-associated glycoprotein complex / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance ...syntrophin complex / regulation of translation in response to stress / positive regulation of low-density lipoprotein particle receptor binding / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / dystrophin-associated glycoprotein complex / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / ribosomal protein S6 kinase activity / CREB phosphorylation / hepatocyte proliferation / positive regulation of hepatic stellate cell activation / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / neuroligin family protein binding / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / myelin sheath adaxonal region / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / vesicle budding from membrane / cornified envelope / Gastrin-CREB signalling pathway via PKC and MAPK / plasma membrane protein complex / calcium-dependent phospholipid binding / negative regulation of receptor internalization / RSK activation / collagen fibril organization / Dissolution of Fibrin Clot / S100 protein binding / negative regulation of TOR signaling / virion binding / positive regulation of low-density lipoprotein receptor activity / osteoclast development / epithelial cell apoptotic process / positive regulation of receptor recycling / phosphatidylserine binding / 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 / fibrinolysis / cytoskeletal protein binding / phosphatidylinositol-4,5-bisphosphate binding / protein serine/threonine/tyrosine kinase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / cell-matrix adhesion / response to activity / central nervous system development / PDZ domain binding / positive regulation of cell differentiation / adherens junction / lung development / calcium channel activity / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / sarcolemma / nuclear matrix / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / melanosome / late endosome membrane / actin binding / midbody / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / chemical synaptic transmission / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / early endosome / cytoskeleton / non-specific serine/threonine protein kinase / intracellular signal transduction / endosome / cell cycle / lysosomal membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / synapse / calcium ion binding / Neutrophil degranulation / negative regulation of apoptotic process / structural molecule activity / positive regulation of DNA-templated transcription / cell surface / magnesium ion binding
Similarity search - Function
Syntrophin / Annexin A2 / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat ...Syntrophin / Annexin A2 / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / 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
Similarity search - Domain/homology
Annexin A2 / Ribosomal protein S6 kinase alpha-1 / Gamma-2-syntrophin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 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
DepositionJan 10, 2022Deposition 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

Downloads & links

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Assembly

Deposited unit
C: Gamma-2-syntrophin,Annexin A2
F: Ribosomal protein S6 kinase alpha-1
A: Gamma-2-syntrophin,Annexin A2
B: Gamma-2-syntrophin,Annexin A2
D: Ribosomal protein S6 kinase alpha-1
E: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,48423
Polymers142,6476
Non-polymers83717
Water4,017223
1
C: Gamma-2-syntrophin,Annexin A2
F: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8418
Polymers47,5492
Non-polymers2926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-55 kcal/mol
Surface area19540 Å2
MethodPISA
2
A: Gamma-2-syntrophin,Annexin A2
E: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8017
Polymers47,5492
Non-polymers2525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-43 kcal/mol
Surface area19820 Å2
MethodPISA
3
B: Gamma-2-syntrophin,Annexin A2
D: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8418
Polymers47,5492
Non-polymers2926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-54 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.460, 60.550, 135.210
Angle α, β, γ (deg.)90.000, 92.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gamma-2-syntrophin,Annexin A2 / G2SYN / Syntrophin-5 / SYN5 / Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy ...G2SYN / Syntrophin-5 / SYN5 / 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: 46138.352 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNTG2, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NY99, 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: 1410.602 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: biotin-ttds (Trioxatridecan-succinamic acid) tag at the N-terminus
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.: 14 / Source method: isolated from a natural source / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Succinic acid pH 7.0 15% w/v PEG 3350

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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: Oct 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→48.416 Å / Num. obs: 59163 / % possible obs: 99.9 % / Redundancy: 6.79 % / CC1/2: 0.998 / Rrim(I) all: 0.147 / Net I/σ(I): 11.3
Reflection shellResolution: 2.44→2.5 Å / Mean I/σ(I) obs: 1.18 / Num. unique obs: 4350 / CC1/2: 0.454 / Rrim(I) all: 1.655

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Processing

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

5n7d


Resolution: 2.44→48.416 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2295 2957 5 %
Rwork0.1953 56189 -
obs0.197 59146 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 215.35 Å2 / Biso mean: 66.7492 Å2 / Biso min: 26.31 Å2
Refinement stepCycle: final / Resolution: 2.44→48.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9583 0 32 223 9838
Biso mean--67.16 54.54 -
Num. residues----1204
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.44-2.480.321390.29732624
2.48-2.52270.35531400.27792670
2.5227-2.56860.29941380.28752623
2.5686-2.6180.34261400.27612663
2.618-2.67140.3341400.27072663
2.6714-2.72950.29861410.25752674
2.7295-2.7930.27851390.24532645
2.793-2.86290.28721420.24032680
2.8629-2.94020.29951390.23612656
2.9402-3.02680.24861410.22242673
3.0268-3.12440.2891370.21422607
3.1244-3.23610.2631420.20432696
3.2361-3.36560.23811420.20912700
3.3656-3.51880.251390.21312631
3.5188-3.70420.23941420.19672701
3.7042-3.93620.2131400.17122650
3.9362-4.23990.18941420.15972711
4.2399-4.66630.19011420.15462693
4.6663-5.34080.20071420.17012694
5.3408-6.7260.21351430.20172747
6.726-48.4160.16091470.15342788
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)
16.7285-1.9732.0498.45381.97315.53450.1773-0.46850.50020.3264-0.3175-0.060.2109-0.11090.10690.425-0.06310.10970.5823-0.10490.519165.42592.010925.8575
23.71840.4353-1.76381.5310.6421.74670.10950.63680.1283-0.1111-0.11730.11740.2212-0.34390.01660.52880.0399-0.10930.67940.02270.376942.0702-4.920227.8432
33.4519-0.3560.30681.17861.79054.5666-0.05340.2072-0.34860.2414-0.56130.5940.4823-0.9520.54940.4932-0.20810.05250.7203-0.14460.557224.6715-0.859753.6242
41.4811-0.9287-0.53012.99792.16683.3683-0.0626-0.06320.02380.6563-0.14010.06340.5317-0.15770.22080.5362-0.1163-0.05760.40370.02270.336839.7454-1.319661.8927
58.04572.0259-3.2994.2514-4.68015.3125-0.1676-0.88751.19611.3035-0.5210.9605-1.4329-1.01390.70011.05240.27140.23661.4753-0.21530.87565.95452.248335.517
64.34372.1209-2.86756.75253.29886.0342-0.7036-0.1588-1.4617-0.2986-0.2720.3741.1989-0.10940.91221.26160.08090.150.9909-0.10851.529928.4817-19.848-1.4582
71.59290.3763-0.16040.8122-0.27920.99080.0365-0.0696-0.0820.0143-0.0676-0.07960.02310.1280.03040.28980.0052-0.02980.2772-0.02480.322116.03057.74399.8023
86.81662.8729-1.578.31451.52498.9919-0.0338-0.160.0580.9684-0.34720.8410.9974-0.42060.36370.59270.03310.08240.5267-0.09230.4574-38.843639.353817.367
93.1701-1.74132.11461.6681-1.69431.8713-0.10110.0268-0.05-0.1486-0.0895-0.0615-0.24820.0210.23630.555-0.02410.05010.4213-0.04410.3331-2.650230.593931.8193
101.77870.03940.17041.9152-1.58273.5171-0.116-0.00210.04620.147-0.0998-0.2177-0.12450.54020.25790.4011-0.00850.0160.42620.02190.45813.666118.240261.9729
112.544-1.23831.38381.6489-1.33363.31010.0780.1193-0.0105-0.0531-0.08750.0404-0.0453-0.02490.02840.4457-0.01760.0540.3240.00020.3449-5.166329.099752.7631
122.0038-1.17231.1090.7482-0.69250.6491-0.19070.4990.3068-0.48250.58990.79030.9207-0.0708-0.32331.7754-0.5050.36861.88970.00422.0061-47.126436.618521.0979
138.5499-3.72274.62876.309-6.28087.29290.2717-0.5072-0.0802-0.5644-1.02460.2439-0.0606-0.91670.5311.33720.24140.07181.5346-0.08831.619725.258-14.11037.5725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 70 through 142 )C70 - 142
2X-RAY DIFFRACTION2chain 'C' and (resid 143 through 238 )C143 - 238
3X-RAY DIFFRACTION3chain 'C' and (resid 239 through 320 )C239 - 320
4X-RAY DIFFRACTION4chain 'C' and (resid 321 through 472 )C321 - 472
5X-RAY DIFFRACTION5chain 'F' and (resid 731 through 735 )F731 - 735
6X-RAY DIFFRACTION6chain 'A' and (resid 70 through 154 )A70 - 154
7X-RAY DIFFRACTION7chain 'A' and (resid 155 through 472 )A155 - 472
8X-RAY DIFFRACTION8chain 'B' and (resid 70 through 143 )B70 - 143
9X-RAY DIFFRACTION9chain 'B' and (resid 144 through 269 )B144 - 269
10X-RAY DIFFRACTION10chain 'B' and (resid 270 through 382 )B270 - 382
11X-RAY DIFFRACTION11chain 'B' and (resid 383 through 472 )B383 - 472
12X-RAY DIFFRACTION12chain 'D' and (resid 731 through 735 )D731 - 735
13X-RAY DIFFRACTION13chain 'E' and (resid 731 through 735 )E731 - 735

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