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- PDB-5n7d: MAGI-1 complexed with a RSK1 peptide -

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Basic information

Entry
Database: PDB / ID: 5n7d
TitleMAGI-1 complexed with a RSK1 peptide
Components
  • Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
  • Ribosomal protein S6 kinase alpha-1Ribosome
KeywordsSIGNALING PROTEIN / docking / signaling / 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 / S100 protein binding / Dissolution of Fibrin Clot / negative regulation of TOR signaling / virion binding / osteoclast development / positive regulation of low-density lipoprotein receptor activity / epithelial cell apoptotic process / positive regulation of receptor recycling / phosphatidylserine binding / ERK/MAPK targets / alpha-actinin binding / positive regulation of exocytosis / Recycling pathway of L1 / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / bicellular tight junction / fibrinolysis / phosphatidylinositol-4,5-bisphosphate binding / cytoskeletal protein binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / protein serine/threonine/tyrosine kinase activity / 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 / chemical synaptic transmission / basolateral plasma membrane / protein-containing complex assembly / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / early endosome / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / cell adhesion / endosome / intracellular signal transduction / 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
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_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_symmetry / _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.pdbx_dist_value / _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_symmetry

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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)102,20115
Polymers101,4603
Non-polymers74112
Water3,963220
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)53,7979
Polymers53,3602
Non-polymers4377
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-38 kcal/mol
Surface area20720 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
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-30 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.810, 60.680, 99.710
Angle α, β, γ (deg.)90.00, 98.81, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1097-

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 / Ribosome / 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: 5260.097 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 8% PEG 400, 100 mM acetate buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.3→49.267 Å / Num. obs: 51873 / % possible obs: 100 % / Redundancy: 12.8 % / Net I/σ(I): 18
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.36 / Num. unique all: 3854 / Rrim(I) all: 0.773 / % 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→49.267 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2271 2466 4.76 %
Rwork0.1906 --
obs0.1923 51850 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→49.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6493 0 37 220 6750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036612
X-RAY DIFFRACTIONf_angle_d0.5698910
X-RAY DIFFRACTIONf_dihedral_angle_d17.6672468
X-RAY DIFFRACTIONf_chiral_restr0.0371009
X-RAY DIFFRACTIONf_plane_restr0.0031152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2999-2.34410.25731430.26142782X-RAY DIFFRACTION100
2.3441-2.3920.29951370.23632700X-RAY DIFFRACTION100
2.392-2.4440.2481420.22782703X-RAY DIFFRACTION100
2.444-2.50090.25861430.22592728X-RAY DIFFRACTION100
2.5009-2.56340.24771280.21912705X-RAY DIFFRACTION100
2.5634-2.63270.26241540.23122736X-RAY DIFFRACTION100
2.6327-2.71020.28921310.22812715X-RAY DIFFRACTION100
2.7102-2.79760.27641350.22112706X-RAY DIFFRACTION100
2.7976-2.89760.2941270.22112759X-RAY DIFFRACTION100
2.8976-3.01360.25541260.2252750X-RAY DIFFRACTION100
3.0136-3.15070.25611300.20812726X-RAY DIFFRACTION100
3.1507-3.31680.27261360.2062729X-RAY DIFFRACTION100
3.3168-3.52460.27411330.20052741X-RAY DIFFRACTION100
3.5246-3.79660.2131410.19032757X-RAY DIFFRACTION100
3.7966-4.17850.17671540.15852729X-RAY DIFFRACTION100
4.1785-4.78270.18351480.15172761X-RAY DIFFRACTION100
4.7827-6.0240.21561380.18222788X-RAY DIFFRACTION100
6.024-49.27850.19331200.16962869X-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)
12.91094.74151.30198.79153.11352.64840.1717-0.0670.0662-0.11010.08750.09330.14770.0561-0.22960.4534-0.01-0.15620.40530.02330.7902152.7941-29.6942338.0991
22.4141-0.9514-0.11421.71960.32610.67120.1020.2583-0.1416-0.2027-0.1510.394-0.0707-0.07880.02880.26940.0032-0.01470.2465-0.00690.3252176.1114-4.2798334.5251
39.0777-5.1565-2.30217.94782.77160.99471.66691.171-1.5764-1.1519-0.6503-0.0271-0.3348-0.3346-1.00072.029-0.0117-0.28431.2949-0.08261.5341172.4839-1.9095277.8009
45.84483.02463.09065.43134.12883.2899-0.8237-0.99891.29690.4545-0.7625-0.4273-0.4943-0.80921.21932.3625-0.0411-0.57771.6160.02282.1581175.75281.1455279.2168
52.3389-0.79040.76557.19270.75621.4746-0.536-0.00141.765-0.4127-0.41180.2859-0.98930.12490.8941.04130.0252-0.4040.95330.05361.2626167.9971-13.4227277.4859
63.18551.40241.6152.52070.57661.31080.5035-0.54070.15680.3715-0.61510.20820.1527-0.16110.09180.5917-0.10130.06820.8555-0.02370.3085181.1368-28.4331296.1621
72.41842.2031-0.82362.2072-1.20161.3133-0.04831.14750.12791.56990.6795-4.9512-1.77916.9868-0.58410.9474-0.2497-0.18761.7494-0.03592.2704158.9506-34.8326329.5903
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 509 )
4X-RAY DIFFRACTION4chain 'B' and (resid 510 through 535 )
5X-RAY DIFFRACTION5chain 'B' and (resid 536 through 585 )
6X-RAY DIFFRACTION6chain 'B' and (resid 586 through 878 )
7X-RAY DIFFRACTION7chain 'C' and (resid 732 through 735 )

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