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- PDB-8gxe: PTPN21 FERM PTP complex -

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Basic information

Entry
Database: PDB / ID: 8gxe
TitlePTPN21 FERM PTP complex
Components(Tyrosine-protein phosphatase non-receptor type 21) x 2
KeywordsPROTEIN BINDING/ HYDROLASE / PTPN21 / FERM / phosphotase domain / PTP / PTPD1 / HYDROLASE / PROTEIN BINDING- HYDROLASE complex
Function / homology
Function and homology information


protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoskeleton / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-14/21 / PTPN14/21, FERM domain C-lobe / 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 / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. ...Protein-tyrosine phosphatase, non-receptor type-14/21 / PTPN14/21, FERM domain C-lobe / 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 / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / 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 active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChen, L. / Zheng, Y.Y. / Zhou, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2024
Title: Structural analysis of PTPN21 reveals a dominant-negative effect of the FERM domain on its phosphatase activity.
Authors: Chen, L. / Qian, Z. / Zheng, Y. / Zhang, J. / Sun, J. / Zhou, C. / Xiao, H.
History
DepositionSep 19, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 21
B: Tyrosine-protein phosphatase non-receptor type 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4603
Polymers68,4252
Non-polymers351
Water28816
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.313, 228.246, 117.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 21 / Protein-tyrosine phosphatase D1


Mass: 34406.172 Da / Num. of mol.: 1 / Fragment: PTPN21 PTP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN21, PTPD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16825, protein-tyrosine-phosphatase
#2: Protein Tyrosine-protein phosphatase non-receptor type 21 / Protein-tyrosine phosphatase D1


Mass: 34018.484 Da / Num. of mol.: 1 / Fragment: PTPN21 FERM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN21, PTPD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16825, protein-tyrosine-phosphatase
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.64 Å3/Da / Density % sol: 66.24 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEGMME 2000, HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3→47.84 Å / Num. obs: 37344 / % possible obs: 99.69 % / Redundancy: 13.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.2893 / Rpim(I) all: 0.08139 / Net I/σ(I): 8.89
Reflection shellResolution: 3→3.107 Å / Rmerge(I) obs: 1.583 / Num. unique obs: 2494 / CC1/2: 0.809 / Rpim(I) all: 0.4333

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Processing

Software
NameVersionClassification
PHENIX1.20rc1_4392refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BZL

2bzl


Resolution: 3→47.84 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2631 1896 5.08 %
Rwork0.2174 35448 -
obs0.2197 37344 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 205.11 Å2 / Biso mean: 91.374 Å2 / Biso min: 20.74 Å2
Refinement stepCycle: final / Resolution: 3→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4580 0 1 16 4597
Biso mean--47.01 41.74 -
Num. residues----565
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.070.34531330.34422494262799
3.08-3.160.33341260.30462574270099
3.16-3.250.38181410.296224942635100
3.25-3.360.32081430.264125182661100
3.36-3.480.30311120.268625312643100
3.48-3.620.27071760.240125162692100
3.62-3.780.27641360.219325232659100
3.78-3.980.25711150.210325822697100
3.98-4.230.22311490.185324922641100
4.23-4.550.23251130.176425872700100
4.55-5.010.23631450.174525162661100
5.01-5.740.22851200.196325562676100
5.74-7.220.34441380.235125502688100
7.22-47.840.20511490.18442515266499
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)
16.0142-0.85531.36955.0259-1.73614.69460.08810.62970.3936-0.4003-0.0904-0.8480.16981.18920.03980.3816-0.04890.07411.0838-0.00340.3492-1.3754-49.915818.5525
25.01211.2903-0.6645.7051-0.00635.86270.10960.55580.759-0.31080.03230.2031-0.1854-0.1589-0.15050.29930.0024-0.01510.41730.03720.3091-27.7057-41.794112.6397
35.71530.2243-1.00183.76740.58725.69870.0992-0.0042-0.1382-0.0762-0.02780.18360.1257-0.13540.00660.30080.02570.05090.3460.02090.2167-32.7748-57.62219.2095
44.98090.1404-1.19084.1832-0.3712.32810.08380.32010.0464-0.6483-0.1055-0.13860.15630.5962-0.03870.36050.05560.01020.65210.01230.195-13.5308-56.100414.4255
51.18490.33290.59385.23821.47063.25540.08950.7235-1.1056-0.3712-0.42691.03860.5704-0.04990.24590.73570.1284-0.20360.508-0.20360.9859-34.1202-81.702910.8446
61.0356-0.8374-0.42093.139-1.78412.940.3118-0.1248-1.1238-0.288-0.3156-0.68241.07731.3946-0.00051.20.3765-0.18281.187-0.17661.5557-14.5382-98.87569.019
72.5971-0.58180.74771.67160.143.3751-0.05530.3149-0.9122-1.3136-0.49041.39791.1383-0.99930.42161.55540.0102-0.49790.8058-0.38842.1648-46.9887-99.1333-1.3282
81.7161.324-0.13337.3659-0.26121.02030.22510.21350.349-1.0321-0.52681.7344-0.2209-0.53190.06341.360.3161-0.82010.7835-0.56521.9742-44.9532-87.0633-1.2767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 878 through 912 )A878 - 912
2X-RAY DIFFRACTION2chain 'A' and (resid 913 through 987 )A913 - 987
3X-RAY DIFFRACTION3chain 'A' and (resid 988 through 1073 )A988 - 1073
4X-RAY DIFFRACTION4chain 'A' and (resid 1074 through 1171 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 20 through 130 )B20 - 130
6X-RAY DIFFRACTION6chain 'B' and (resid 131 through 213 )B131 - 213
7X-RAY DIFFRACTION7chain 'B' and (resid 214 through 286 )B214 - 286
8X-RAY DIFFRACTION8chain 'B' and (resid 287 through 307 )B287 - 307

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