[English] 日本語
Yorodumi
- PDB-7aal: Crystal structure of the F-BAR domain of PSTIPIP1, G258A mutant -

+
Open data


ID or keywords:

Loading...

-
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 / endocytosis / lamellipodium / cytoskeleton / cell adhesion / inflammatory response / innate immune response ...uropod / cleavage furrow / The NLRP3 inflammasome / Purinergic signaling in leishmaniasis infection / endocytosis / lamellipodium / cytoskeleton / 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 / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / SH3 domain ...PSTPIP1, SH3 domain / Fes/CIP4, and EFC/F-BAR homology domain / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / SH3 domain / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more