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- PDB-5n7f: MAGI-1 complexed with a pRSK1 peptide -

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Basic information

Entry
Database: PDB / ID: 5n7f
TitleMAGI-1 complexed with a 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 / 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 / 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 ...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 / 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 / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / positive regulation of cell-cell adhesion / 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 / alpha-actinin binding / 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 / bicellular tight junction / 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 / cell projection / cell periphery / 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 / cell-cell junction / melanosome / cell junction / late endosome membrane / midbody / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / protein-containing complex assembly / chemical synaptic transmission / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / cell surface receptor signaling pathway / early endosome / non-specific serine/threonine protein kinase / cell adhesion / 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 / nucleolus / negative regulation of apoptotic process
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 repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats ...Unstructured region on MAGI / Unstructured region on MAGI / 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. / 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
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: 2.3 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 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr1_symmetry / _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

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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)102,45318
Polymers101,5403
Non-polymers91315
Water11,422634
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)53,91710
Polymers53,4402
Non-polymers4778
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-41 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)48,5368
Polymers48,1001
Non-polymers4377
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-32 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.150, 98.560, 200.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-1226-

HOH

21A-1240-

HOH

31A-1306-

HOH

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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: 5340.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KA1, MAPKAPK1A, RSK1 / Production host: Escherichia coli (E. coli)
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.: 6 / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.93 %
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: 2.3→49.73 Å / Num. obs: 53922 / % possible obs: 100 % / Redundancy: 19.87 % / Rrim(I) all: 0.219 / Net I/σ(I): 15.42
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 18.6 % / Mean I/σ(I) obs: 3 / Num. unique all: 3925 / % 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: 2.3→49.73 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.27
RfactorNum. reflection% reflection
Rfree0.2401 2613 4.85 %
Rwork0.1862 --
obs0.1889 53845 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6623 0 45 634 7302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076761
X-RAY DIFFRACTIONf_angle_d0.8719097
X-RAY DIFFRACTIONf_dihedral_angle_d21.4922566
X-RAY DIFFRACTIONf_chiral_restr0.0471019
X-RAY DIFFRACTIONf_plane_restr0.0051171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2999-2.34170.36141280.29242654X-RAY DIFFRACTION100
2.3417-2.38680.33411220.26912662X-RAY DIFFRACTION100
2.3868-2.43550.31361400.25812646X-RAY DIFFRACTION100
2.4355-2.48840.30651400.25292652X-RAY DIFFRACTION100
2.4884-2.54630.30141610.24212644X-RAY DIFFRACTION100
2.5463-2.610.2591320.2212692X-RAY DIFFRACTION100
2.61-2.68050.28251330.21782657X-RAY DIFFRACTION100
2.6805-2.75940.30661380.21482670X-RAY DIFFRACTION100
2.7594-2.84850.28671300.19912668X-RAY DIFFRACTION100
2.8485-2.95030.25691290.19722666X-RAY DIFFRACTION100
2.9503-3.06840.23371390.18982700X-RAY DIFFRACTION100
3.0684-3.2080.26661330.19082686X-RAY DIFFRACTION100
3.208-3.37710.22761280.17482708X-RAY DIFFRACTION100
3.3771-3.58860.24961330.16612691X-RAY DIFFRACTION100
3.5886-3.86560.19971360.15782697X-RAY DIFFRACTION100
3.8656-4.25440.18121450.14192738X-RAY DIFFRACTION100
4.2544-4.86960.21651550.13612723X-RAY DIFFRACTION100
4.8696-6.13340.20181460.17412770X-RAY DIFFRACTION100
6.1334-49.74750.19681450.17692908X-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)
12.68220.3262-1.57550.64730.21491.20690.03720.0847-0.0020.1828-0.13440.04990.0561-0.27070.11650.1956-0.02310.01250.4710.03420.2849-32.1812-285.9643809.1224
22.69030.08491.91820.98490.03482.4855-0.46480.17590.45050.09420.1520.0008-0.60140.19330.18580.2966-0.0076-0.06980.2148-00.2854-57.4987-276.0702830.2321
30.5578-0.20130.30730.17670.25921.45-0.13570.66050.0957-0.4156-0.24570.2082-0.58990.32550.36281.53050.1585-0.00231.69630.11421.323-62.92-226.4638823.478
40.69130.3181-0.76750.7792-1.18684.0307-0.20160.1495-0.0341-0.1271-0.069-0.07630.219-0.23190.24310.3123-0.05940.02190.1965-0.03740.2949-33.3237-236.9605836.4785
50.390.0821-1.60030.0202-0.31446.68520.3167-0.92880.38971.33230.51291.1217-1.6438-1.3975-0.81811.18090.35560.151.2658-0.11180.9207-27.953-276.6594815.3942
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 459 through 554 )
4X-RAY DIFFRACTION4chain 'B' and (resid 555 through 878 )
5X-RAY DIFFRACTION5chain 'C' and (resid 730 through 735 )

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