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- PDB-7p74: The PDZ domain of SYNJ2BP complexed with the phosphorylated PDZ-b... -

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Basic information

Entry
Database: PDB / ID: 7p74
TitleThe PDZ domain of SYNJ2BP complexed with the phosphorylated PDZ-binding motif of RSK1
Components
  • Ribosomal protein S6 kinase alpha-1
  • Synaptojanin-2-binding protein,Annexin A2
KeywordsPEPTIDE BINDING PROTEIN / PDZ / complex
Function / homology
Function and homology information


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 / negative regulation of sprouting angiogenesis / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity ...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 / negative regulation of sprouting angiogenesis / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / 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 / regulation of Notch signaling pathway / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / myelin sheath adaxonal region / embryo development / receptor localization to synapse / 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 / establishment or maintenance of epithelial cell apical/basal polarity / 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 / negative regulation of endothelial cell migration / osteoclast development / epithelial cell apoptotic process / positive regulation of receptor recycling / phosphatidylserine binding / ERK/MAPK targets / receptor clustering / Recycling pathway of L1 / positive regulation of exocytosis / negative regulation of endothelial cell proliferation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Rho protein signal transduction / regulation of endocytosis / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / protein targeting / 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 / negative regulation of angiogenesis / cell-matrix adhesion / response to activity / positive regulation of cell differentiation / adherens junction / postsynaptic density membrane / 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 / neuromuscular junction / negative regulation of ERK1 and ERK2 cascade / sarcolemma / nuclear matrix / cell-cell adhesion / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / melanosome / late endosome membrane / 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 / mitochondrial outer membrane / early endosome / non-specific serine/threonine protein kinase / intracellular signal transduction / endosome / neuron projection / cell cycle / lysosomal membrane
Similarity search - Function
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 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 / Synaptojanin-2-binding protein / Ribosomal protein S6 kinase alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGogl, G. / Cousido-Siah, A. / Trave, G.
CitationJournal: Nat Commun / Year: 2022
Title: Quantitative fragmentomics allow affinity mapping of interactomes.
Authors: Gogl, G. / Zambo, B. / Kostmann, C. / Cousido-Siah, A. / Morlet, B. / Durbesson, F. / Negroni, L. / Eberling, P. / Jane, P. / Nomine, Y. / Zeke, A. / Ostergaard, S. / Monsellier, E. / Vincentelli, R. / Trave, G.
History
DepositionJul 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 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
A: Synaptojanin-2-binding protein,Annexin A2
B: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8208
Polymers49,4762
Non-polymers3456
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-41 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.620, 75.150, 108.460
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 Synaptojanin-2-binding protein,Annexin A2 / Mitochondrial outer membrane protein 25 / Annexin II / Annexin-2 / Calpactin I heavy chain / ...Mitochondrial outer membrane protein 25 / 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: 47646.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYNJ2BP, OMP25, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Production host: Escherichia coli (E. coli) / References: UniProt: P57105, 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: 1828.959 Da / Num. of mol.: 1 / Mutation: N-terminal biotin-ttds label / Source method: obtained synthetically / 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.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM ammonium sulfate, 100mM sodium formate, 25% PEG smear broad

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→47 Å / Num. obs: 39032 / % possible obs: 99.5 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rrim(I) all: 0.17 / Net I/σ(I): 11.16
Reflection shellResolution: 1.9→1.95 Å / Mean I/σ(I) obs: 1.46 / Num. unique obs: 2825 / CC1/2: 0.593 / Rrim(I) all: 2.55

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Processing

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

5n7d

2jik


Resolution: 1.9→46.707 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2107 1949 5 %
Rwork0.181 37020 -
obs0.1825 38969 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.09 Å2 / Biso mean: 46.2206 Å2 / Biso min: 21.65 Å2
Refinement stepCycle: final / Resolution: 1.9→46.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 16 232 3597
Biso mean--43.07 48.93 -
Num. residues----422
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.94750.33021360.31258299
1.9475-2.00020.30421360.2741259399
2.0002-2.0590.29371370.2446258899
2.059-2.12550.28421380.21812616100
2.1255-2.20140.25941370.20792622100
2.2014-2.28960.22341360.1972260999
2.2896-2.39380.23691370.1833260699
2.3938-2.520.23881390.17782639100
2.52-2.67790.23031390.18092623100
2.6779-2.88460.21390.16962654100
2.8846-3.17480.20571410.16892661100
3.1748-3.63410.21411410.16792677100
3.6341-4.57790.15881430.1492717100
4.5779-46.7070.19881500.18632833100
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)
13.3276-1.1191-3.07170.98731.60434.3847-0.23260.1837-0.2004-0.37220.106-0.15980.20.18170.02480.5385-0.09860.02920.43550.06550.415-2.618-2.201122.5426
23.5417-1.08240.11732.27180.28031.7281-0.036-0.0434-0.33980.10510.09930.03550.2613-0.0386-0.00230.2942-0.00370.00340.2320.00120.436828.0427-20.3299-0.2199
31.6469-1.1798-0.48452.32130.62010.7601-0.1966-0.29970.09690.35580.2332-0.09740.03810.0762-0.04670.22730.0318-0.0350.2497-0.03030.230226.37687.45399.0743
42.4505-2.80121.34954.08570.79046.8985-0.15890.0942-0.6327-0.09380.1774-0.97770.36540.5317-0.03970.89430.10460.1350.9210.2231.14273.4816-4.83330.691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 101 )A6 - 101
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 175 )A102 - 175
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 422 )A176 - 422
4X-RAY DIFFRACTION4chain 'B' and (resid 731 through 735 )B731 - 735

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