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- PDB-7aal: Crystal structure of the F-BAR domain of PSTIPIP1, G258A mutant -

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Basic information

Entry
Database: PDB / ID: 7aal
TitleCrystal structure of the F-BAR domain of PSTIPIP1, G258A mutant
ComponentsProline-serine-threonine phosphatase-interacting protein 1
KeywordsSIGNALING PROTEIN / pyogenic arthritis / pyoderma gangrenosum and acne (PAPA) / Inflammatory response / membrane binding
Function / homology
Function and homology information


uropod / cleavage furrow / The NLRP3 inflammasome / Purinergic signaling in leishmaniasis infection / actin filament polymerization / actin filament / endocytosis / actin filament binding / lamellipodium / cell adhesion ...uropod / cleavage furrow / The NLRP3 inflammasome / Purinergic signaling in leishmaniasis infection / actin filament polymerization / actin filament / endocytosis / actin filament binding / lamellipodium / cell adhesion / inflammatory response / innate immune response / perinuclear region of cytoplasm / signal transduction / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
PSTPIP1, SH3 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH3 domain / Src homology 3 domains / SH3-like domain superfamily ...PSTPIP1, SH3 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Proline-serine-threonine phosphatase-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsManso, J.A. / Alcon, P. / Bayon, Y. / Alonso, A. / de Pereda, J.M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Other private Spain
CitationJournal: Cell.Mol.Life Sci. / Year: 2022
Title: PSTPIP1-LYP phosphatase interaction: structural basis and implications for autoinflammatory disorders.
Authors: Manso, J.A. / Marcos, T. / Ruiz-Martin, V. / Casas, J. / Alcon, P. / Sanchez Crespo, M. / Bayon, Y. / de Pereda, J.M. / Alonso, A.
History
DepositionSep 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / pdbx_related_exp_data_set
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 8, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proline-serine-threonine phosphatase-interacting protein 1
B: Proline-serine-threonine phosphatase-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)68,5492
Polymers68,5492
Non-polymers00
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint-77 kcal/mol
Surface area28990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.191, 73.023, 205.248
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUMETMET(chain 'A' and (resid 5 through 35 or resid 37...AA5 - 358 - 38
12LYSLYSMETMET(chain 'A' and (resid 5 through 35 or resid 37...AA37 - 12340 - 126
13ARGARGARGARG(chain 'A' and (resid 5 through 35 or resid 37...AA125 - 228128 - 231
14ALAALAASPASP(chain 'A' and (resid 5 through 35 or resid 37...AA230 - 289233 - 292
25LEULEUMETMET(chain 'B' and (resid 5 through 35 or resid 37...BB5 - 358 - 38
26LYSLYSMETMET(chain 'B' and (resid 5 through 35 or resid 37...BB37 - 12340 - 126
27ARGARGARGARG(chain 'B' and (resid 5 through 35 or resid 37...BB125 - 228128 - 231
28ALAALAASPASP(chain 'B' and (resid 5 through 35 or resid 37...BB230 - 289233 - 292

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Components

#1: Protein Proline-serine-threonine phosphatase-interacting protein 1 / PEST phosphatase-interacting protein 1 / CD2-binding protein 1 / H-PIP


Mass: 34274.559 Da / Num. of mol.: 2 / Mutation: G258A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSTPIP1, CD2BP1 / Plasmid: pETEV15b / Details (production host): Based on pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43586
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.63 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Bis-Tris-propane (pH 6.5), 15% (w/v) PEG 3350, 0.25 M sodium citrate

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.97→102.62 Å / Num. obs: 30894 / % possible obs: 59.4 % / Redundancy: 12.3 % / Biso Wilson estimate: 30.46 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.039 / Rrim(I) all: 0.13 / Net I/σ(I): 13.1
Reflection shellResolution: 1.974→2.172 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.477 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1545 / CC1/2: 0.481 / Rsym value: 1.477 / % possible all: 12.1

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Processing

Software
NameVersionClassification
XDSJan 31, 2020data reduction
Aimless0.7.4data scaling
STARANISO2.3.28data scaling
PHASERphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WPE

4wpe


Resolution: 1.97→102.62 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.8754
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2189 1568 5.08 %
Rwork0.1861 29314 -
obs0.1879 30882 59.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.58 Å2
Refinement stepCycle: LAST / Resolution: 1.97→102.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4659 0 0 310 4969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00134756
X-RAY DIFFRACTIONf_angle_d0.36846385
X-RAY DIFFRACTIONf_chiral_restr0.0276676
X-RAY DIFFRACTIONf_plane_restr0.0017852
X-RAY DIFFRACTIONf_dihedral_angle_d20.96621865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.030.381460.298265X-RAY DIFFRACTION6.05
2.11-2.190.30271050.26271712X-RAY DIFFRACTION39.18
2.2-2.290.2859830.26371766X-RAY DIFFRACTION39.54
2.29-2.420.26161360.25412507X-RAY DIFFRACTION56.73
2.42-2.570.25431350.24122848X-RAY DIFFRACTION63.68
2.57-2.770.27431190.26022383X-RAY DIFFRACTION53.69
2.77-3.040.25782020.21814038X-RAY DIFFRACTION89.43
3.04-3.480.24142320.19414525X-RAY DIFFRACTION100
3.48-4.390.2022440.14534567X-RAY DIFFRACTION99.96
4.39-102.620.17763060.15594703X-RAY DIFFRACTION99.8
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)
10.113064770275-0.00849510041110.129662570751-0.003882564914830.06529507362170.150316840550.0171774192853-0.003792885403860.0003159600846160.0147803279396-0.017023136202-0.0008328932556010.0142016132788-0.0247507671717-0.03217109377270.170932717871-0.0208536920869-0.03574519421720.1441629095350.06554835102130.153934602526-37.267386197430.662993937-42.76970694
20.388976301284-0.01762019522290.3211740961040.0545110538905-0.07202106582470.3637201845730.000820726885176-0.1263783480270.0242295489097-0.029172543420.0263386667053-0.0125182771831-0.0173788393959-0.1655059309130.157810787880.09071950190.00744679663454-0.01181015626020.1811226104220.04231429443320.08456807168532.6436168173133.8923197015-5.8608212491
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 289 )
2X-RAY DIFFRACTION2chain 'B' and (resid 5 through 289 )

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