[English] 日本語
Yorodumi
- PDB-7aam: Crystal structure of the F-BAR domain of PSTIPIP1 bound to the CT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7aam
TitleCrystal structure of the F-BAR domain of PSTIPIP1 bound to the CTH domain of the phosphatase LYP
Components
  • Proline-serine-threonine phosphatase-interacting protein 1
  • Tyrosine-protein phosphatase non-receptor type 22
KeywordsSIGNALING PROTEIN / pyogenic arthritis / pyoderma gangrenosum and acne (PAPA) / Inflammatory response / membrane binding
Function / homology
Function and homology information


phosphoanandamide dephosphorylation / positive regulation of granzyme B production / positive regulation of toll-like receptor 3 signaling pathway / regulation of natural killer cell proliferation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / regulation of non-canonical NF-kappaB signal transduction / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway ...phosphoanandamide dephosphorylation / positive regulation of granzyme B production / positive regulation of toll-like receptor 3 signaling pathway / regulation of natural killer cell proliferation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / regulation of non-canonical NF-kappaB signal transduction / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of toll-like receptor 9 signaling pathway / uropod / negative regulation of T cell activation / positive regulation of protein K63-linked ubiquitination / cellular response to muramyl dipeptide / negative regulation of interleukin-8 production / negative regulation of JUN kinase activity / negative regulation of T cell receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / regulation of innate immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / phosphatase activity / cleavage furrow / negative regulation of interleukin-6 production / The NLRP3 inflammasome / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of tumor necrosis factor production / T cell differentiation / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of type I interferon production / Purinergic signaling in leishmaniasis infection / lipopolysaccharide-mediated signaling pathway / positive regulation of defense response to virus by host / actin filament polymerization / protein dephosphorylation / negative regulation of autophagy / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / actin filament / lipid metabolic process / cytoplasmic side of plasma membrane / autophagy / SH3 domain binding / kinase binding / endocytosis / actin filament binding / positive regulation of type II interferon production / lamellipodium / T cell receptor signaling pathway / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / cell adhesion / inflammatory response / negative regulation of gene expression / innate immune response / ubiquitin protein ligase binding / positive regulation of gene expression / perinuclear region of cytoplasm / signal transduction / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PSTPIP1, SH3 domain / : / Non-receptor tyrosine-protein phosphatase 22 / : / 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 ...PSTPIP1, SH3 domain / : / Non-receptor tyrosine-protein phosphatase 22 / : / 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 / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / 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 / Tyrosine-protein phosphatase non-receptor type 22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 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 / _software.version
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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
C: Tyrosine-protein phosphatase non-receptor type 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0915
Polymers70,9073
Non-polymers1842
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation, assay for oligomerization, Titration of fluorescein-labeled LYP-CTH with the F-BAR of PSTPIP1 under saturation conditions (concentration of LYP-CTH high above the Kd) ...Evidence: immunoprecipitation, assay for oligomerization, Titration of fluorescein-labeled LYP-CTH with the F-BAR of PSTPIP1 under saturation conditions (concentration of LYP-CTH high above the Kd) by fluorescence anisotropy.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12150 Å2
ΔGint-84 kcal/mol
Surface area29520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.996, 72.037, 205.034
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-IDDetails
d_1ens_1(chain "A" and (resid 5 through 39 or resid 41...
d_2ens_1(chain "B" and (resid 5 through 39 or resid 41...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUMETA1 - 35
d_12ens_1GLUARGA37 - 188
d_13ens_1SERASPA190 - 285
d_21ens_1LEUMETB3 - 37
d_22ens_1GLUARGB40 - 191
d_23ens_1SERASPB194 - 289

-
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: Protein/peptide Tyrosine-protein phosphatase non-receptor type 22 / Hematopoietic cell protein-tyrosine phosphatase 70Z-PEP / Lymphoid phosphatase / LyP / PEST-domain ...Hematopoietic cell protein-tyrosine phosphatase 70Z-PEP / Lymphoid phosphatase / LyP / PEST-domain phosphatase / PEP


Mass: 2385.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y2R2, protein-tyrosine-phosphatase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 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), 20% (w/v) PEG 3350, 200 mM sodium citrate. LYP-CTH peptide was soaked into preformed crystals of the F-BAR domain of PSTPIP1.

-
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: 2.15→102.52 Å / Num. obs: 20328 / % possible obs: 51.5 % / Redundancy: 19.1 % / Biso Wilson estimate: 24.23 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.397 / Rrim(I) all: 0.407 / Net I/σ(I): 8
Reflection shellResolution: 2.154→2.316 Å / Redundancy: 17.8 % / Rmerge(I) obs: 3.036 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1016 / CC1/2: 0.521 / Rpim(I) all: 0.722 / % possible all: 13.4

-
Processing

Software
NameVersionClassification
XDSJan 21, 2020data reduction
Aimless0.7.4data scaling
STARANISO2.3.28data scaling
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7AAN

7aan


Resolution: 2.15→102.52 Å / SU ML: 0.2541 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.8806
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2409 1042 5.13 %
Rwork0.2049 19272 -
obs0.2068 20314 51.43 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.12 Å2
Refinement stepCycle: LAST / Resolution: 2.15→102.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4733 0 12 162 4907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00124835
X-RAY DIFFRACTIONf_angle_d0.3246496
X-RAY DIFFRACTIONf_chiral_restr0.0269688
X-RAY DIFFRACTIONf_plane_restr0.0019865
X-RAY DIFFRACTIONf_dihedral_angle_d18.99121879
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.22149842685 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.270.3399260.294547X-RAY DIFFRACTION10.27
2.27-2.410.3241870.28861377X-RAY DIFFRACTION26.37
2.41-2.60.3173930.281874X-RAY DIFFRACTION35.85
2.6-2.860.30111110.27432526X-RAY DIFFRACTION46.99
2.86-3.270.27541590.24093178X-RAY DIFFRACTION59.41
3.27-4.120.22382190.17784347X-RAY DIFFRACTION80.22
4.12-102.520.21383470.17685423X-RAY DIFFRACTION97.33
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)
10.172491876233-0.07103716722730.04157078532830.02674005776030.05826567875140.1631344405270.02573563478980.00438698506958-0.0196187259040.0396560423042-0.005969243275430.0311018903512-0.011101005795-0.05482583287730.058235845810.0482173105155-0.0164759698795-0.02997093437620.06718461743550.01376165624130.0580716351549-37.272506431231.0886773067-43.0466960336
20.2480691512050.1115088853140.04605987849860.0119313770052-0.02800272688990.007349940447380.0122658213025-0.1268805819270.04230306050330.00892584734438-0.00322189068291-0.008550836825080.0381934233699-0.02354222637610.07511302377590.0853597897314-0.0257127890222-0.009562728322730.136921999480.01008498076570.07251286285532.3160610251834.5373993072-6.05350144059
32.97247633674E-5-0.0004759693008120.0001650546872640.001432211071650.000123207658751-9.35577239523E-5-0.02255105575340.00467363235736-0.01429551096760.016793698197-0.0236095460649-0.003143575689030.000669691435288-0.003159417164532.29492516396E-50.2254406605610.0238040617401-0.0450880740040.206442487218-0.01018456668290.260771512571-25.796030183812.4908771133-31.347859523
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 289 )AA5 - 2891 - 285
22chain 'B' and (resid 3 through 289 )BB3 - 2891 - 289
33chain 'C' and (resid 793 through 806 )CC793 - 8061 - 14

+
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