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- PDB-7xty: Crystal Structure of the second PDZ domain from human PTPN13 in c... -

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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 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of protein localization to centrosome ...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 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of protein localization to centrosome / bicellular tight junction assembly / pattern specification process / phosphatidylinositol 3-kinase regulatory subunit binding / negative regulation of microtubule depolymerization / catenin complex / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / heart valve development / cellular response to toxic substance / regulation of microtubule-based process / microtubule plus-end binding / 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 / Interleukin-37 signaling / protein kinase regulator activity / 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 / negative regulation of G1/S transition of mitotic cell cycle / mitotic spindle assembly checkpoint signaling / Apoptotic cleavage of cellular proteins / dynein complex binding / Synthesis of PIPs at the plasma membrane / mitotic cytokinesis / peptidyl-tyrosine dephosphorylation / negative regulation of protein phosphorylation / bicellular tight junction / lateral plasma membrane / protein dephosphorylation / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / adherens junction / Deactivation of the beta-catenin transactivating complex / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / Degradation of beta-catenin by the destruction complex / kinetochore / Wnt signaling pathway / ruffle membrane / positive regulation of protein catabolic process / Ovarian tumor domain proteases / insulin receptor signaling pathway / cell migration / nervous system development / lamellipodium / positive regulation of cold-induced thermogenesis / cell body / protein-containing complex assembly / microtubule binding / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / cytoskeleton / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / negative regulation of cell population proliferation / centrosome / ubiquitin protein ligase binding / DNA damage response / 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 protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain ...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 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 / 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 / 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 / PDZ domain / Pdz3 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 / Roll / Mainly Beta
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.35 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

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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

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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

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