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- PDB-6twy: MAGI1_2 complexed with a phosphomimetic RSK1 peptide -

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Basic information

Entry
Database: PDB / ID: 6twy
TitleMAGI1_2 complexed with a phosphomimetic RSK1 peptide
Components
  • Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
  • Phosphomimetic RSK1 peptide
KeywordsPEPTIDE BINDING PROTEIN / phosphorylation / motif / PDZ domain
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 / positive regulation of exocytosis / Recycling pathway of L1 / alpha-actinin binding / 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 / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cytoskeletal protein binding / 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 / sarcolemma / mRNA transcription by RNA polymerase II / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / serine-type endopeptidase inhibitor activity / calcium channel activity / 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 / angiogenesis / protein-containing complex assembly / collagen-containing extracellular matrix / vesicle / protease binding / cell surface receptor signaling pathway / early endosome / 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
CITRIC ACID / 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. / Cousido-Siah, A. / Trave, G.
CitationJournal: Structure / Year: 2020
Title: Dual Specificity PDZ- and 14-3-3-Binding Motifs: A Structural and Interactomics Study.
Authors: Gogl, G. / Jane, P. / Caillet-Saguy, C. / Kostmann, C. / Bich, G. / Cousido-Siah, A. / Nyitray, L. / Vincentelli, R. / Wolff, N. / Nomine, Y. / Sluchanko, N.N. / Trave, G.
History
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 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
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_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_asym_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.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.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

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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: Phosphomimetic RSK1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,86620
Polymers97,5723
Non-polymers1,29417
Water2,180121
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A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6779
Polymers48,1001
Non-polymers5778
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-34 kcal/mol
Surface area20570 Å2
MethodPISA
2
B: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
C: Phosphomimetic RSK1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,18911
Polymers49,4722
Non-polymers7179
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-53 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.450, 96.380, 198.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#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 Phosphomimetic RSK1 peptide


Mass: 1372.659 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15418*PLUS

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Non-polymers , 4 types, 138 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.01 Å3/Da / Density % sol: 59.16 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 22% PEG3000, 100mM Na-citrate (pH 5.5), 100mM Na-citrate

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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: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48.3 Å / Num. obs: 52853 / % possible obs: 99 % / Redundancy: 13.5 % / Biso Wilson estimate: 57.3 Å2 / CC1/2: 1 / Net I/σ(I): 19.97
Reflection shellResolution: 2.3→2.36 Å / Mean I/σ(I) obs: 1.18 / Num. unique obs: 3836 / CC1/2: 0.477

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Processing

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

5n7d


Resolution: 2.3→48.19 Å / SU ML: 0.3363 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3064
RfactorNum. reflection% reflection
Rfree0.2502 2556 4.84 %
Rwork0.2046 --
obs0.2068 52773 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 85.34 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6663 0 68 121 6852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00456859
X-RAY DIFFRACTIONf_angle_d0.62599242
X-RAY DIFFRACTIONf_chiral_restr0.04151027
X-RAY DIFFRACTIONf_plane_restr0.00351201
X-RAY DIFFRACTIONf_dihedral_angle_d23.33782613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.35211330.3142735X-RAY DIFFRACTION98.69
2.34-2.390.32551240.3022735X-RAY DIFFRACTION98.21
2.39-2.440.33791530.29252744X-RAY DIFFRACTION98.64
2.44-2.50.33191540.28072698X-RAY DIFFRACTION98.62
2.5-2.560.30541340.27452748X-RAY DIFFRACTION97.73
2.56-2.630.32081480.27542766X-RAY DIFFRACTION100
2.63-2.710.33831340.26822713X-RAY DIFFRACTION98.1
2.71-2.80.30141400.24092777X-RAY DIFFRACTION98.51
2.8-2.90.29471410.22862786X-RAY DIFFRACTION99.97
2.9-3.010.28351340.2292777X-RAY DIFFRACTION98.71
3.01-3.150.29391290.23352783X-RAY DIFFRACTION98.98
3.15-3.320.30991340.22732788X-RAY DIFFRACTION99.19
3.32-3.520.271470.21952783X-RAY DIFFRACTION99.29
3.52-3.80.26041660.19682798X-RAY DIFFRACTION99.43
3.8-4.180.2141370.17312825X-RAY DIFFRACTION99.3
4.18-4.780.19991380.16162863X-RAY DIFFRACTION99.54
4.78-6.020.21351630.19152881X-RAY DIFFRACTION99.8
6.02-48.190.21881470.1813017X-RAY DIFFRACTION99.28
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)
15.05878358862-0.461785706675-0.006618918417750.0432640115517-0.05061961404750.04434291593370.0734087186305-0.242573212160.07100075859790.304715575712-0.120412844809-0.6166927831760.09998658002140.822526542879-0.06432591901271.441212491840.0227315489804-0.2316508434021.50892303448-0.2057597693381.36262063833-1.2551947692169.607312061-24.1869287614
21.29791339661-0.694072006199-0.2384753574081.171902124940.9124440387173.48149853962-0.160788910912-0.214472399678-0.03291476361980.2378657828180.09682823114290.0239180645104-0.0371353267819-0.05724439436370.06897882240960.4515878417080.0330197317282-0.07112041237410.356117707976-0.001449705612930.540441838118-27.5467257856.5638195953-36.3682263808
35.74197655691-2.31607012841-3.830428612261.590675005550.8395402459413.195444911950.03068641477430.2234305247690.0393061496834-0.9215099281130.0328518311341-0.424406735955-0.3727446228070.210061419644-0.1210519636590.852153504693-0.3000192254160.1958308286691.0144455855-0.1500758331610.608599082117-28.0339964449.32932149459-7.36697022366
43.13229027699-0.3792839054551.085763854871.222958842-0.3889446980542.35679011817-0.201463973581-0.782193041150.2702727188980.276339078910.0551907988246-0.037418921873-0.463788536185-0.02170245965720.1650360514270.479874021179-0.0717606997321-0.03903025455680.624079705806-0.05064897404840.462458043588-2.9761238476419.0909089786-27.6091048428
50.0163597249530.1083301478550.02368878887573.063779519611.219487608010.538821580122-0.1068903454410.1561596277960.113009026448-0.8291582584350.0396272537178-0.578112719145-0.6585883404440.5628873133930.03599019623931.78518602762-0.2528431860070.06855479738020.838209211918-0.2122257209620.660781383119-33.028693596918.868315712-12.9411112239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 458 through 573 )
2X-RAY DIFFRACTION2chain 'A' and (resid 574 through 878 )
3X-RAY DIFFRACTION3chain 'B' and (resid 458 through 573 )
4X-RAY DIFFRACTION4chain 'B' and (resid 574 through 878 )
5X-RAY DIFFRACTION5chain 'C' and (resid 731 through 735 )

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