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- PDB-5n7g: MAGI-1 complexed with a synthetic pRSK1 peptide -

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Basic information

Entry
Database: PDB / ID: 5n7g
TitleMAGI-1 complexed with a synthetic pRSK1 peptide
Components
  • Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
  • Ribosomal protein S6 kinase alpha-1
KeywordsSIGNALING PROTEIN / docking / signaling / complex
Function / homology
Function and homology information


regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / ribosomal protein S6 kinase activity / phospholipase A2 inhibitor activity / positive regulation of low-density lipoprotein particle clearance / positive regulation of vesicle fusion ...regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / ribosomal protein S6 kinase activity / phospholipase A2 inhibitor activity / positive regulation of low-density lipoprotein particle clearance / positive regulation of vesicle fusion / hepatocyte proliferation / CREB phosphorylation / positive regulation of hepatic stellate cell activation / myelin sheath adaxonal region / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / positive regulation of cell-cell adhesion / cadherin binding involved in cell-cell adhesion / cornified envelope / endothelial cell morphogenesis / Schmidt-Lanterman incisure / vesicle budding from membrane / Gastrin-CREB signalling pathway via PKC and MAPK / TORC1 signaling / plasma membrane protein complex / calcium-dependent phospholipid binding / osteoclast development / negative regulation of receptor internalization / RSK activation / Dissolution of Fibrin Clot / S100 protein binding / collagen fibril organization / negative regulation of TOR signaling / vesicle membrane / epithelial cell apoptotic process / phosphatidylserine binding / ERK/MAPK targets / alpha-actinin binding / Recycling pathway of L1 / positive regulation of receptor recycling / basement membrane / positive regulation of exocytosis / Smooth Muscle Contraction / regulation of neurogenesis / bicellular tight junction / cytoskeletal protein binding / fibrinolysis / phosphatidylinositol-4,5-bisphosphate binding / lipid droplet / protein serine/threonine/tyrosine kinase activity / Transcriptional and post-translational regulation of MITF-M expression and activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lung development / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / response to activity / cell periphery / cell projection / adherens junction / positive regulation of cell differentiation / serine-type endopeptidase inhibitor activity / mRNA transcription by RNA polymerase II / sarcolemma / RNA polymerase II transcription regulator complex / nuclear matrix / calcium-dependent protein binding / azurophil granule lumen / cell-cell junction / late endosome membrane / cell junction / melanosome / : / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / protease binding / protein-containing complex assembly / midbody / angiogenesis / basolateral plasma membrane / vesicle / chemical synaptic transmission / early endosome / cell surface receptor signaling pathway / protein phosphorylation / non-specific serine/threonine protein kinase / cell adhesion / endosome / lysosomal membrane / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / synapse / Neutrophil degranulation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleolus / magnesium ion binding / cell surface
Similarity search - Function
Unstructured region on MAGI / Unstructured region on MAGI / Annexin A2 / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin ...Unstructured region on MAGI / Unstructured region on MAGI / 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 / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Protein kinase, C-terminal / Protein kinase C terminal domain / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW 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 / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Annexin A2 / Ribosomal protein S6 kinase alpha-1 / Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsGogl, G. / Nyitray, L.
CitationJournal: FEBS J. / Year: 2018
Title: Dynamic control of RSK complexes by phosphoswitch-based regulation.
Authors: Gogl, G. / Biri-Kovacs, B. / Poti, A.L. / Vadaszi, H. / Szeder, B. / Bodor, A. / Schlosser, G. / Acs, A. / Turiak, L. / Buday, L. / Alexa, A. / Nyitray, L. / Remenyi, A.
History
DepositionFeb 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
B: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
C: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,86117
Polymers97,0403
Non-polymers82114
Water00
1
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
C: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,45611
Polymers48,9402
Non-polymers5179
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-64 kcal/mol
Surface area20980 Å2
MethodPISA
2
B: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4046
Polymers48,1001
Non-polymers3045
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-27 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.930, 60.230, 99.350
Angle α, β, γ (deg.)90.00, 98.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2 / Atrophin-1-interacting protein 3 / AIP-3 / BAI1-associated protein 1 / BAP-1 / Membrane-associated ...Atrophin-1-interacting protein 3 / AIP-3 / BAI1-associated protein 1 / BAP-1 / Membrane-associated guanylate kinase inverted 1 / MAGI-1 / Trinucleotide repeat-containing gene 19 protein / WW domain-containing protein 3 / WWP3 / 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: 48099.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: MAGI1, AIP3, BAIAP1, BAP1, TNRC19, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D
Production host: Escherichia coli (E. coli) / References: UniProt: Q96QZ7, UniProt: P07355
#2: Protein/peptide Ribosomal protein S6 kinase alpha-1 / S6K-alpha-1 / 90 kDa ribosomal protein S6 kinase 1 / p90S6K / MAP kinase-activated protein kinase ...S6K-alpha-1 / 90 kDa ribosomal protein S6 kinase 1 / p90S6K / MAP kinase-activated protein kinase 1a / MAPKAPK-1a / Ribosomal S6 kinase 1 / RSK-1


Mass: 839.890 Da / Num. of mol.: 1 / Fragment: UNP residues 88-94 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q15418, non-specific serine/threonine protein kinase
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
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: 3.38 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 14% PEG 8000, 200 mM MgCl2, 100 mM TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→49.105 Å / Num. obs: 24379 / % possible obs: 99.9 % / Redundancy: 6.86 % / Rrim(I) all: 0.268 / Net I/σ(I): 8.36
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.49 / Num. unique all: 1785 / Rrim(I) all: 0.897 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2420: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xjl

1xjl


Resolution: 2.95→49.105 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2635 1195 4.9 %
Rwork0.2102 --
obs0.2129 24374 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→49.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5900 0 39 0 5939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046010
X-RAY DIFFRACTIONf_angle_d0.4998083
X-RAY DIFFRACTIONf_dihedral_angle_d17.7422297
X-RAY DIFFRACTIONf_chiral_restr0.038905
X-RAY DIFFRACTIONf_plane_restr0.0031037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9501-3.06820.31061110.28122567X-RAY DIFFRACTION100
3.0682-3.20780.32021200.26592557X-RAY DIFFRACTION100
3.2078-3.37690.30761260.24232570X-RAY DIFFRACTION100
3.3769-3.58840.29981310.22682547X-RAY DIFFRACTION100
3.5884-3.86540.27281610.2032528X-RAY DIFFRACTION100
3.8654-4.25420.25571370.18022583X-RAY DIFFRACTION100
4.2542-4.86930.22361500.16582555X-RAY DIFFRACTION100
4.8693-6.13290.23121230.20212603X-RAY DIFFRACTION100
6.1329-49.11180.23371360.19782669X-RAY DIFFRACTION100
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)
10.74520.8953-0.02251.70180.55980.48730.06160.04650.0888-0.12690.0782-0.03350.00910.0788-0.15730.2763-0.0108-0.04510.1814-0.02690.5276332.7092-46.715434.9963
21.6761-0.60380.20571.08290.08440.51720.03930.1943-0.0471-0.1078-0.09530.1993-0.02940.00050.03730.09340.0199-0.02720.0546-0.00340.156355.8144-21.462431.5919
32.0053-0.14050.91581.54360.17392.0134-0.0525-0.27260.5076-0.0877-0.23990.5127-0.1592-0.29350.26180.3912-0.0498-0.12690.4881-0.06650.4618343.337-48.1492377.7091
41.00320.59860.72881.53030.73460.98540.3543-0.53250.16960.7193-0.58420.37890.3235-0.32820.17260.6596-0.3330.07321.0771-0.1210.4275361.2447-40.9901404.9415
51.02730.45620.37551.86260.22270.24050.31920.02850.09770.2989-0.4007-0.2880.11170.10570.06980.4408-0.0587-0.04120.7496-0.00970.2213368.8423-47.2247389.6754
64.39932.14573.36711.05451.64982.5833-0.24490.11320.25270.20980.0092-0.347-0.24510.66720.13620.8402-0.2454-0.42241.0022-0.1031.562341.57-51.3013428.116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 456 through 573 )
2X-RAY DIFFRACTION2chain 'A' and (resid 574 through 878 )
3X-RAY DIFFRACTION3chain 'B' and (resid 561 through 644 )
4X-RAY DIFFRACTION4chain 'B' and (resid 645 through 760 )
5X-RAY DIFFRACTION5chain 'B' and (resid 761 through 878 )
6X-RAY DIFFRACTION6chain 'C' and (resid 730 through 735 )

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