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- PDB-7aan: Crystal structure of the F-BAR domain of PSTIPIP1 -

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Basic information

Entry
Database: PDB / ID: 7aan
TitleCrystal structure of the F-BAR domain of PSTIPIP1
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 / FOURIER SYNTHESIS / Resolution: 2.14 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
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: Refinement description / Structure summary / Category: audit_author / software / 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)68,5212
Polymers68,5212
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9910 Å2
ΔGint-79 kcal/mol
Surface area29090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.334, 71.867, 204.589
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 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 5 - 289 / Label seq-ID: 8 - 292

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and (resid 5 through 159 or (resid 160...AA
22(chain 'B' and resid 5 through 289)BB

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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: 34260.531 Da / Num. of mol.: 2
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.: 79 / 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: 2.59 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM Bis-Tris-propane (pH=6.0), 17% (w/v) PEG 3350, 150 mM sodium citrate

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.14→102.295 Å / Num. obs: 18546 / % possible obs: 46.1 % / Redundancy: 19.1 % / Biso Wilson estimate: 27.47 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.391 / Rrim(I) all: 0.401 / Net I/σ(I): 7.5
Reflection shellResolution: 2.14→2.332 Å / Redundancy: 17.7 % / Rmerge(I) obs: 3.109 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 927 / CC1/2: 0.54 / Rpim(I) all: 0.736 / Rrim(I) all: 3.198 / % possible all: 10.4

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Processing

Software
NameVersionClassification
XDSJan 31, 2020data reduction
Aimless0.7.4data scaling
STARANISO2.3.28data scaling
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7AAL

7aal


Resolution: 2.14→102.29 Å / SU ML: 0.2431 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.0304
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2405 956 5.16 %
Rwork0.2088 17579 -
obs0.2105 18535 46.03 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.17 Å2
Refinement stepCycle: LAST / Resolution: 2.14→102.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4637 0 0 79 4716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00134701
X-RAY DIFFRACTIONf_angle_d0.29266306
X-RAY DIFFRACTIONf_chiral_restr0.0257668
X-RAY DIFFRACTIONf_plane_restr0.0016841
X-RAY DIFFRACTIONf_dihedral_angle_d21.07951834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.250.4111180.3224301X-RAY DIFFRACTION5.65
2.25-2.40.3016670.32241095X-RAY DIFFRACTION20.5
2.4-2.580.3245650.30111545X-RAY DIFFRACTION28.42
2.58-2.840.3677960.29142216X-RAY DIFFRACTION40.65
2.84-3.250.29741540.25842906X-RAY DIFFRACTION53.38
3.25-4.10.23452070.18994068X-RAY DIFFRACTION73.87
4.1-102.290.20413490.17415448X-RAY DIFFRACTION95.83
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)
10.01533042402910.006850616145330.00403957358279-0.0004151098318-0.001012385062710.0399317509954-0.01178622587870.008894984490680.004222830312320.01179092311720.008125544333850.00309404551489-0.0300788581556-0.0607649299117-0.0180349865450.02393367123370.0162908334051-0.07124967110250.04554451853290.0900845728162-0.0112964592317-33.103481858831.2836738743-37.7125995148
20.0170056549692-0.0295325943434-0.02826245582580.06361393878490.03534716144940.0625792911919-0.0523100037364-0.03099761656760.03899266091420.0153012432601-0.06786093008740.0681885323139-0.0349486762867-0.0116917584537-0.1842860561760.08065352752140.00338598939992-0.04390981068280.149877831125-0.006770225018850.0648804026336-44.930428507332.97646034-49.7721402765
30.0566326419015-0.002964627697790.02577983554410.02591205417950.0639540710960.03734661048520.100635784583-0.0868509150111-0.0851879086494-0.00668682581233-0.03192775924710.01085993680370.0647633366354-0.0486106466899-0.02296188227690.165922448667-0.0250575487922-0.06052082405070.1419450566020.03819915384220.142140367982-33.382184618727.5598784847-39.8394040352
40.00131894818383-0.0009537541198790.001271565328890.00100467201786-0.001908753589310.001935887439386.56775957019E-6-0.0301744312655-0.0338625642966-0.01264089330290.03916167346320.0021483113991-0.007008408777860.0189805003496-1.41369629373E-50.1195200839550.043092359199-0.05345664766980.2899188945910.03358031316080.22651093136725.323804149928.65176651552.86019707228
50.00766453294040.0154447276525-0.00203223179625-0.00322707161861-0.01222385428830.00585194113099-0.0619047655954-0.01903573543970.0133101332032-0.07214268469560.06385697312830.0915864068910.025510346287-0.01857175361730.02500520125240.03808315387410.0180987334263-0.07798335615980.1071176293790.07286550225720.0282948030837-9.0418662075435.5079429347-15.343714755
60.02935290169870.00397461603170.01990102007480.0937405150053-0.07019779651680.0535739822723-0.0549014468219-0.00745737557220.0113885270342-0.02299469113820.0208693148815-0.0269278710464-0.0850700869986-0.07090665289180.03550214849980.1304639925470.04810922043510.004300865022070.3354656416240.03884400005080.13757448504310.649020826937.99463230960.81430820094
70.159111544899-0.07525113843070.08135362970280.0520640722099-0.06837613256190.04275260916010.0209278782613-0.0399751651550.0174653892697-0.02799709226980.06442663842710.01979362695070.0301174229792-0.05973190419730.3788414245050.100497410281-0.0323484785382-0.02186534214250.1958990238070.1329632678320.0529434064086-1.9635071574230.481277254-8.12348967824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 161 )
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 289 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 19 )
5X-RAY DIFFRACTION5chain 'B' and (resid 20 through 70 )
6X-RAY DIFFRACTION6chain 'B' and (resid 71 through 161 )
7X-RAY DIFFRACTION7chain 'B' and (resid 162 through 289 )

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