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- PDB-6bcr: Complex of 14-3-3 theta with an IRSp53 peptide phosphorylated at T340 -

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Basic information

Entry
Database: PDB / ID: 6bcr
TitleComplex of 14-3-3 theta with an IRSp53 peptide phosphorylated at T340
Components
  • 14-3-3 protein theta
  • Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
KeywordsSIGNALING PROTEIN / phosphate binding protein / protein complex / cytoskeleton regulation / cell motility
Function / homology
Function and homology information


neuron projection branch point / dendritic spine cytoplasm / negative regulation of monoatomic ion transmembrane transport / plasma membrane organization / actin crosslink formation / positive regulation of dendritic spine morphogenesis / protein localization to synapse / cellular response to L-glutamate / cadherin binding involved in cell-cell adhesion / regulation of modification of postsynaptic actin cytoskeleton ...neuron projection branch point / dendritic spine cytoplasm / negative regulation of monoatomic ion transmembrane transport / plasma membrane organization / actin crosslink formation / positive regulation of dendritic spine morphogenesis / protein localization to synapse / cellular response to L-glutamate / cadherin binding involved in cell-cell adhesion / regulation of modification of postsynaptic actin cytoskeleton / cytoskeletal anchor activity / neuron projection terminus / presynaptic cytosol / proline-rich region binding / postsynaptic cytosol / small GTPase-mediated signal transduction / positive regulation of actin filament polymerization / dendrite development / postsynaptic density, intracellular component / actin filament bundle assembly / positive regulation of excitatory postsynaptic potential / CDC42 GTPase cycle / excitatory synapse / Regulation of localization of FOXO transcription factors / protein targeting / Activation of BAD and translocation to mitochondria / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / cellular response to epidermal growth factor stimulus / ruffle / RAC1 GTPase cycle / substantia nigra development / axonogenesis / dendritic shaft / 14-3-3 protein binding / filopodium / synaptic membrane / secretory granule / PDZ domain binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / transcription coregulator binding / regulation of actin cytoskeleton organization / TP53 Regulates Metabolic Genes / FCGR3A-mediated phagocytosis / adherens junction / regulation of synaptic plasticity / Schaffer collateral - CA1 synapse / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / lamellipodium / insulin receptor signaling pathway / regulation of cell shape / scaffold protein binding / microtubule / transmembrane transporter binding / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / neuronal cell body / glutamatergic synapse / synapse / signal transduction / protein-containing complex / extracellular exosome / nucleoplasm / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
14-3-3 theta / I-BAR domain containing protein IRSp53 / IRSp53, SH3 domain / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / 14-3-3 domain / AH/BAR domain superfamily / Delta-Endotoxin; domain 1 ...14-3-3 theta / I-BAR domain containing protein IRSp53 / IRSp53, SH3 domain / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / 14-3-3 domain / AH/BAR domain superfamily / Delta-Endotoxin; domain 1 / Variant SH3 domain / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
TRIFLUOROETHANOL / DI(HYDROXYETHYL)ETHER / 14-3-3 protein theta / Brain-specific angiogenesis inhibitor 1-associated protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.986 Å
AuthorsKast, D.J. / Dominguez, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01 MH087950 United States
CitationJournal: Nat Commun / Year: 2019
Title: Mechanism of IRSp53 inhibition by 14-3-3.
Authors: Kast, D.J. / Dominguez, R.
History
DepositionOct 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 8, 2019Group: Data collection / 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 / _citation_author.identifier_ORCID
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_ptnr1_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein theta
B: 14-3-3 protein theta
C: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
D: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
E: 14-3-3 protein theta
F: 14-3-3 protein theta
G: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
H: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,22924
Polymers117,7768
Non-polymers1,45316
Water9,314517
1
A: 14-3-3 protein theta
B: 14-3-3 protein theta
C: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
D: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
hetero molecules


  • defined by author&software
  • Evidence: light scattering, The assembly has a determined mass of 58 kDa, consistent with the theoretical mass of a single 14-3-3 dimer bound to two singly-phosphorylated IRSp53 peptides., isothermal ...Evidence: light scattering, The assembly has a determined mass of 58 kDa, consistent with the theoretical mass of a single 14-3-3 dimer bound to two singly-phosphorylated IRSp53 peptides., isothermal titration calorimetry, Stoichiometry determined from ITC is consistent with one 14-3-3 dimer binding to two singly-phosphorylated IRSp53 peptides.
  • 59.5 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)59,47311
Polymers58,8884
Non-polymers5867
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-47 kcal/mol
Surface area23110 Å2
MethodPISA
2
E: 14-3-3 protein theta
F: 14-3-3 protein theta
G: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
H: Insulin receptor substrate protein of 53 kDa, peptide (IRSp53)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,75513
Polymers58,8884
Non-polymers8679
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-24 kcal/mol
Surface area23370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.007, 69.114, 84.560
Angle α, β, γ (deg.)105.250, 95.720, 115.040
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABEFCDGH

#1: Protein
14-3-3 protein theta / 14-3-3 protein T-cell / 14-3-3 protein tau / Protein HS1


Mass: 27795.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAQ / Plasmid: pTYB11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27348
#2: Protein/peptide
Insulin receptor substrate protein of 53 kDa, peptide (IRSp53) /


Mass: 1648.709 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UQB8*PLUS

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Non-polymers , 6 types, 533 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-ETF / TRIFLUOROETHANOL / 2,2,2-Trifluoroethanol


Mass: 100.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3F3O
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.15 M Magnesium Formate, 18% PEG3350, 4% TFE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 17, 2012 / Details: Oxford Danfysik toroidal focusing mirror
RadiationMonochromator: channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.986→31.29 Å / Num. obs: 76071 / % possible obs: 95.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 32.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Net I/σ(I): 21.8
Reflection shellResolution: 1.986→2.06 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 6527 / CC1/2: 0.888 / % possible all: 92

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BR9

2br9


Resolution: 1.986→31.288 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.81
RfactorNum. reflection% reflection
Rfree0.2291 3820 5.02 %
Rwork0.1946 --
obs0.1963 76054 95.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.83 Å2 / Biso mean: 46.5178 Å2 / Biso min: 17.43 Å2
Refinement stepCycle: final / Resolution: 1.986→31.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7712 0 195 517 8424
Biso mean--57.81 42.64 -
Num. residues----959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038065
X-RAY DIFFRACTIONf_angle_d0.54510886
X-RAY DIFFRACTIONf_chiral_restr0.0331228
X-RAY DIFFRACTIONf_plane_restr0.0021392
X-RAY DIFFRACTIONf_dihedral_angle_d14.1155056
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9863-2.01150.3551870.29131656174360
2.0115-2.03790.28971330.27472424255787
2.0379-2.06590.37591370.25962734287197
2.0659-2.09540.29131230.25292710283396
2.0954-2.12660.29571360.23732722285897
2.1266-2.15990.26031260.23252743286997
2.1599-2.19530.26041570.21942664282197
2.1953-2.23310.26561430.21982753289697
2.2331-2.27370.26991520.23082662281497
2.2737-2.31740.26951500.21422726287697
2.3174-2.36470.26031490.20842712286197
2.3647-2.41610.26671400.20732751289197
2.4161-2.47230.26461230.19572747287098
2.4723-2.53410.22891190.20052723284298
2.5341-2.60260.21381480.20132770291898
2.6026-2.67910.24911490.21332701285098
2.6791-2.76550.25711420.21262735287798
2.7655-2.86430.24571750.20292692286798
2.8643-2.97890.2631460.2092770291698
2.9789-3.11440.23511470.21672717286498
3.1144-3.27840.27151380.21632748288698
3.2784-3.48360.22251580.19892753291198
3.4836-3.75210.17881590.17122730288998
3.7521-4.12890.20671560.15972738289498
4.1289-4.72470.15981430.14242758290198
4.7247-5.94590.18071420.17132771291399
5.9459-31.29210.24551420.19962624276694

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