[English] 日本語
Yorodumi
- PDB-7xty: Crystal Structure of the second PDZ domain from human PTPN13 in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xty
TitleCrystal Structure of the second PDZ domain from human PTPN13 in complex with APC peptide
Components
  • APC-peptide
  • Tyrosine-protein phosphatase non-receptor type 13
KeywordsPEPTIDE BINDING PROTEIN / protein-protein complex
Function / homology
Function and homology information


negative regulation of excitatory synapse assembly / APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / cellular response to toxic substance / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome / pattern specification process ...negative regulation of excitatory synapse assembly / APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / cellular response to toxic substance / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome / pattern specification process / bicellular tight junction assembly / protein kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / negative regulation of microtubule depolymerization / negative regulation of cyclin-dependent protein serine/threonine kinase activity / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / microtubule plus-end binding / beta-catenin destruction complex / regulation of microtubule-based process / heart valve development / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / catenin complex / Interleukin-37 signaling / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cell fate specification / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / endocardial cushion morphogenesis / dynein complex binding / negative regulation of G1/S transition of mitotic cell cycle / mitotic spindle assembly checkpoint signaling / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / Synthesis of PIPs at the plasma membrane / mitotic cytokinesis / peptidyl-tyrosine dephosphorylation / bicellular tight junction / lateral plasma membrane / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of protein phosphorylation / protein tyrosine phosphatase activity / Deactivation of the beta-catenin transactivating complex / adherens junction / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / kinetochore / fibrillar center / ruffle membrane / beta-catenin binding / Wnt signaling pathway / positive regulation of protein catabolic process / cell migration / Ovarian tumor domain proteases / lamellipodium / insulin receptor signaling pathway / cell body / nervous system development / positive regulation of cold-induced thermogenesis / microtubule binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / microtubule / cytoskeleton / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / negative regulation of cell population proliferation / centrosome / DNA damage response / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP ...Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family / Adenomatous polyposis coli protein / Adenomatous polyposis coli, N-terminal dimerisation domain / APC, N-terminal coiled-coil domain superfamily / Adenomatous polyposis coli (APC) repeat / APC repeat / SAMP Motif / EB-1 Binding Domain / APC basic domain / APC 15 residue motif / Coiled-coil N-terminus of APC, dimerisation domain / Adenomatous polyposis coli (APC) repeat / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Armadillo/beta-catenin-like repeats / Armadillo / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / 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 domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Armadillo-like helical / PH-like domain superfamily / Armadillo-type fold / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Adenomatous polyposis coli protein / Tyrosine-protein phosphatase non-receptor type 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJing, L.Q. / Sun, X.N. / Ma, W.H. / Zhou, W.J. / Wu, D.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177063 China
CitationJournal: to be published
Title: Targeting PTPN13 with 11 amino acid peptides of C-terminal APC prevents immune evasion of colorectal cancer
Authors: Jing, L.Q. / Sun, X.N. / Ma, W.H. / Zhou, W.J. / Wu, D.L.
History
DepositionMay 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Tyrosine-protein phosphatase non-receptor type 13
B: Tyrosine-protein phosphatase non-receptor type 13
C: APC-peptide
D: APC-peptide


Theoretical massNumber of molelcules
Total (without water)22,2614
Polymers22,2614
Non-polymers00
Water2,360131
1
A: Tyrosine-protein phosphatase non-receptor type 13
C: APC-peptide


Theoretical massNumber of molelcules
Total (without water)11,1302
Polymers11,1302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-4 kcal/mol
Surface area5410 Å2
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 13
D: APC-peptide


Theoretical massNumber of molelcules
Total (without water)11,1302
Polymers11,1302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-5 kcal/mol
Surface area5390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.462, 32.407, 69.917
Angle α, β, γ (deg.)90.000, 108.860, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 13 / Fas-associated protein-tyrosine phosphatase 1 / FAP-1 / PTP-BAS / Protein-tyrosine phosphatase 1E / ...Fas-associated protein-tyrosine phosphatase 1 / FAP-1 / PTP-BAS / Protein-tyrosine phosphatase 1E / PTP-E1 / hPTPE1 / Protein-tyrosine phosphatase PTPL1


Mass: 9923.138 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN13, PNP1, PTP1E, PTPL1 / Plasmid: pET28as / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12923, protein-tyrosine-phosphatase
#2: Protein/peptide APC-peptide / Protein APC / Deleted in polyposis 2.5


Mass: 1207.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P25054
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.35 Å3/Da / Density % sol: 47.59 % / Mosaicity: 0.315 °
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.8 / Details: 0.1M citric acid (pH 3.5), 3M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: SIEMENS-NICOLET / Detector: PIXEL / Date: Jul 18, 2021 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 12152 / % possible obs: 98 % / Redundancy: 6 % / Biso Wilson estimate: 23.51 Å2 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.074 / Rrim(I) all: 0.189 / Χ2: 0.845 / Net I/σ(I): 3.1 / Num. measured all: 72771
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.144.20.3745620.8830.1860.4190.54487.4
2.14-2.184.50.3635190.910.1750.4050.57289
2.18-2.224.60.3795830.8980.180.4210.61392.4
2.22-2.264.60.3435700.8840.1640.3820.63295.3
2.26-2.3150.3466000.8990.1610.3830.6497.6
2.31-2.375.40.3455920.9160.1550.3790.61298.2
2.37-2.4260.3166070.9480.1350.3440.57299.5
2.42-2.496.40.3146290.9420.1330.3420.59199.8
2.49-2.566.50.3296230.9510.1380.3570.59100
2.56-2.656.50.2635990.9710.1110.2860.61100
2.65-2.746.30.266120.9670.1120.2840.746100
2.74-2.856.30.2356230.9630.1010.2560.709100
2.85-2.986.80.2176200.9690.0890.2350.802100
2.98-3.146.90.2026040.970.0830.2190.841100
3.14-3.336.70.1756210.9770.0730.190.982100
3.33-3.596.40.1536300.9670.0660.1671.087100
3.59-3.956.60.1386230.9840.0580.151.179100
3.95-4.526.80.1296350.9870.0530.1391.361100
4.52-5.76.20.1236300.9770.0540.1351.224100
5.7-506.20.1266700.9780.0560.1391.323100

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LNY

3lny


Resolution: 2.1→33.14 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 1215 10 %
Rwork0.1935 10929 -
obs0.1983 12144 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.09 Å2 / Biso mean: 27.2849 Å2 / Biso min: 9.74 Å2
Refinement stepCycle: final / Resolution: 2.1→33.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1432 0 0 131 1563
Biso mean---31.09 -
Num. residues----195
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.18360.24071200.219107988
2.1836-2.28290.26721290.2079116594
2.2829-2.40320.26271330.1965119498
2.4032-2.55380.26781370.21631225100
2.5538-2.75090.22421370.20681237100
2.7509-3.02750.24241380.19721237100
3.0275-3.46520.27511360.18361230100

+
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