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- PDB-4gs0: Crystal structure of SHP1 catalytic domain with JAK1 activation l... -

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Basic information

Entry
Database: PDB / ID: 4gs0
TitleCrystal structure of SHP1 catalytic domain with JAK1 activation loop peptide
Components
  • Tyrosine-protein kinase JAK1
  • Tyrosine-protein phosphatase non-receptor type 6
KeywordsHYDROLASE/TRANSFERASE / protein-protein complex / Phosphatase domain / Hydrolase / HYDROLASE-TRANSFERASE complex
Function / homology
Function and homology information


negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / regulation of B cell differentiation / negative regulation of peptidyl-tyrosine phosphorylation / epididymis development / phosphorylation-dependent protein binding / negative regulation of inflammatory response to wounding / protein localization to cell-cell junction / interleukin-11-mediated signaling pathway / positive regulation of homotypic cell-cell adhesion ...negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / regulation of B cell differentiation / negative regulation of peptidyl-tyrosine phosphorylation / epididymis development / phosphorylation-dependent protein binding / negative regulation of inflammatory response to wounding / protein localization to cell-cell junction / interleukin-11-mediated signaling pathway / positive regulation of homotypic cell-cell adhesion / transmembrane receptor protein tyrosine phosphatase activity / CCR5 chemokine receptor binding / T-helper 17 cell lineage commitment / type III interferon-mediated signaling pathway / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / interleukin-2-mediated signaling pathway / natural killer cell mediated cytotoxicity / alpha-beta T cell receptor complex / regulation of release of sequestered calcium ion into cytosol / CD22 mediated BCR regulation / interleukin-15-mediated signaling pathway / Interleukin-37 signaling / Interleukin-15 signaling / Interleukin-12 signaling / Interleukin-35 Signalling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / positive regulation of cell adhesion mediated by integrin / Interleukin-2 signaling / growth hormone receptor binding / Costimulation by the CD28 family / Signal regulatory protein family interactions / platelet formation / megakaryocyte development / negative regulation of T cell receptor signaling pathway / Regulation of KIT signaling / Signaling by ALK / Other interleukin signaling / IFNG signaling activates MAPKs / Platelet sensitization by LDL / Interleukin-20 family signaling / Interleukin-6 signaling / negative regulation of MAPK cascade / type I interferon-mediated signaling pathway / interleukin-6-mediated signaling pathway / positive regulation of sprouting angiogenesis / MAPK3 (ERK1) activation / regulation of G1/S transition of mitotic cell cycle / Interleukin-10 signaling / MAPK1 (ERK2) activation / PECAM1 interactions / cell surface receptor signaling pathway via JAK-STAT / negative regulation of interleukin-6 production / regulation of type I interferon-mediated signaling pathway / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of tumor necrosis factor production / peptidyl-tyrosine dephosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / PD-1 signaling / Regulation of IFNA/IFNB signaling / growth hormone receptor signaling pathway via JAK-STAT / Interleukin receptor SHC signaling / hematopoietic progenitor cell differentiation / T cell proliferation / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / Growth hormone receptor signaling / Signaling by CSF3 (G-CSF) / negative regulation of T cell proliferation / GPVI-mediated activation cascade / T cell costimulation / extrinsic component of cytoplasmic side of plasma membrane / Interleukin-7 signaling / cell adhesion molecule binding / SH2 domain binding / phosphotyrosine residue binding / protein dephosphorylation / regulation of ERK1 and ERK2 cascade / protein-tyrosine-phosphatase / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein tyrosine phosphatase activity / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / cytoplasmic side of plasma membrane / ISG15 antiviral mechanism / platelet aggregation / cellular response to virus / SH3 domain binding / cytokine-mediated signaling pathway / positive regulation of protein localization to nucleus / peptidyl-tyrosine phosphorylation / specific granule lumen / Interferon gamma signaling / MAPK cascade / cell-cell junction
Similarity search - Function
Tyrosine-protein kinase, non-receptor Jak1 / Protein-tyrosine phosphatase, non-receptor type-6, -11 / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / Jak1 pleckstrin homology-like domain / FERM F2 acyl-CoA binding protein-like domain / FERM F1 ubiquitin-like domain / FERM central domain ...Tyrosine-protein kinase, non-receptor Jak1 / Protein-tyrosine phosphatase, non-receptor type-6, -11 / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / Jak1 pleckstrin homology-like domain / FERM F2 acyl-CoA binding protein-like domain / FERM F1 ubiquitin-like domain / FERM central domain / Protein tyrosine phosphatase superfamily / FERM superfamily, second domain / FERM domain / FERM domain profile. / Protein-Tyrosine Phosphatase; Chain A / 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 / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase JAK1 / Tyrosine-protein phosphatase non-receptor type 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7961 Å
AuthorsAlicea-Velazquez, N.L. / Jakoncic, J. / Boggon, T.J.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Structure-guided studies of the SHP-1/JAK1 interaction provide new insights into phosphatase catalytic domain substrate recognition.
Authors: Alicea-Velazquez, N.L. / Jakoncic, J. / Boggon, T.J.
History
DepositionAug 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Mar 6, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 6
B: Tyrosine-protein phosphatase non-receptor type 6
C: Tyrosine-protein kinase JAK1


Theoretical massNumber of molelcules
Total (without water)71,3243
Polymers71,3243
Non-polymers00
Water5,170287
1
A: Tyrosine-protein phosphatase non-receptor type 6


Theoretical massNumber of molelcules
Total (without water)35,3871
Polymers35,3871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 6
C: Tyrosine-protein kinase JAK1


Theoretical massNumber of molelcules
Total (without water)35,9372
Polymers35,9372
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-9 kcal/mol
Surface area12220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.935, 43.935, 258.112
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 6 / Hematopoietic cell protein-tyrosine phosphatase / Protein-tyrosine phosphatase 1C / PTP-1C / ...Hematopoietic cell protein-tyrosine phosphatase / Protein-tyrosine phosphatase 1C / PTP-1C / Protein-tyrosine phosphatase SHP-1 / SH-PTP1


Mass: 35386.887 Da / Num. of mol.: 2 / Fragment: Phosphatase domain (UNP Residues 242-528)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCP, PTP1C, PTPN6, SHP-1 / Plasmid: pET-32 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P29350, protein-tyrosine-phosphatase
#2: Protein/peptide Tyrosine-protein kinase JAK1 / Janus kinase 1 / JAK-1


Mass: 550.491 Da / Num. of mol.: 1
Fragment: JAK1 activation loop phophomimetic (UNP Residues 1032-1037)
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P23458, non-specific protein-tyrosine kinase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF CHAIN F IS KE(FTY)(FTY)TV. DUE TO UNCERTAINTY IN SEQUENCE REGISTRATION, MUCH OF ...THE SEQUENCE OF CHAIN F IS KE(FTY)(FTY)TV. DUE TO UNCERTAINTY IN SEQUENCE REGISTRATION, MUCH OF CHAIN F AS BUILT IS LABELLED UNK

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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 Å3/Da / Density % sol: 38.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M calcium acetate, 13% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.796→50 Å / Num. all: 51289 / Num. obs: 51289 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 23.3 Å2 / Rsym value: 0.086 / Net I/σ(I): 13.5
Reflection shellResolution: 1.796→1.86 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 5133 / Rsym value: 0.669 / % possible all: 99

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Processing

Software
NameVersionClassification
EXECUTORdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FPR

1fpr


Resolution: 1.7961→43.019 Å / SU ML: 0.42 / σ(F): 1.98 / Phase error: 18.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 2618 5.11 %RANDOM
Rwork0.1617 ---
obs0.1634 51204 98.42 %-
all-51204 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.983 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8746 Å2-0 Å2-0 Å2
2---0.8746 Å20 Å2
3---1.7492 Å2
Refinement stepCycle: LAST / Resolution: 1.7961→43.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 0 287 4645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074555
X-RAY DIFFRACTIONf_angle_d1.0626195
X-RAY DIFFRACTIONf_dihedral_angle_d16.381760
X-RAY DIFFRACTIONf_chiral_restr0.074672
X-RAY DIFFRACTIONf_plane_restr0.004807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7961-1.82870.33091300.26132516X-RAY DIFFRACTION94
1.8287-1.86390.28541460.24272511X-RAY DIFFRACTION100
1.8639-1.90190.27361480.2182645X-RAY DIFFRACTION99
1.9019-1.94330.23721610.19642481X-RAY DIFFRACTION99
1.9433-1.98850.23351480.18772578X-RAY DIFFRACTION99
1.9885-2.03820.23751230.1782577X-RAY DIFFRACTION98
2.0382-2.09330.20331280.16422597X-RAY DIFFRACTION98
2.0933-2.15490.20661280.15812500X-RAY DIFFRACTION99
2.1549-2.22450.18251500.15762593X-RAY DIFFRACTION99
2.2245-2.3040.20051450.15132603X-RAY DIFFRACTION99
2.304-2.39620.19271340.15542473X-RAY DIFFRACTION98
2.3962-2.50530.20141340.15622518X-RAY DIFFRACTION98
2.5053-2.63740.20591520.15652584X-RAY DIFFRACTION99
2.6374-2.80260.23461130.16582587X-RAY DIFFRACTION99
2.8026-3.01890.18911400.16142523X-RAY DIFFRACTION98
3.0189-3.32260.16781230.15232614X-RAY DIFFRACTION98
3.3226-3.80310.18581450.14572499X-RAY DIFFRACTION98
3.8031-4.79050.14671360.1362598X-RAY DIFFRACTION99
4.7905-43.0310.19731340.17622589X-RAY DIFFRACTION100
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)
14.60014.1593-2.46273.9898-2.79412.7056-0.27090.6287-1.30.1481-0.03840.3124-0.0683-0.06950.24170.5384-0.0618-0.04150.295-0.07630.562937.9094-15.3626-15.0191
22.9805-0.4864-0.01424.34941.89993.91590.06810.3509-0.439-0.382-0.08650.1150.15990.1768-0.00660.33150.1895-0.00480.0933-0.04510.213126.9136-13.71765.9683
33.47660.86381.26791.9284-0.21263.9946-0.04910.2605-0.0611-0.29030.0234-0.22740.20630.18180.01410.20930.08230.04350.0975-0.00140.162723.8798-5.87611.7211
40.95360.35880.6351.4683-0.43871.6875-0.0566-0.03780.0838-0.027-0.0925-0.0243-0.05480.0050.13750.2070.05420.01210.1204-0.00550.18420.05462.3226.6239
57.63344.068-5.33474.0235-4.09028.5655-0.07-0.2667-0.0252-0.1223-0.07340.23830.1356-0.28910.12280.19020.0533-0.00120.138-0.04040.20298.17750.62337.1912
60.7431-0.7658-0.051.63-0.24750.55790.0015-0.0970.26090.115-0.15070.4638-0.1849-0.30360.03010.20320.1119-0.02690.1469-0.06450.253112.772611.35211.946
73.42181.77961.66522.27410.66932.1327-0.1067-0.07510.4099-0.1386-0.08010.379-0.2353-0.20210.15810.21690.09990.00030.1316-0.0010.22857.5817.79040.6191
83.46920.18630.33122.5540.39893.5905-0.00220.50820.0679-0.3668-0.00590.02630.1831-0.1153-0.01620.24240.05080.00230.14710.0150.1310.9162-5.0236-8.7671
94.8445-2.64922.35599.231-4.63892.95190.09770.67990.0157-0.54180.17830.35320.3334-0.3064-0.29160.2558-0.03720.00070.28150.02670.1489-2.8285-2.9716-15.4756
103.0619-1.7837-0.9474.73960.85463.4432-0.2016-0.15460.23770.3061-0.06770.0833-0.1462-0.07190.10170.24290.2266-0.06590.0753-0.08150.197218.495611.599728.249
112.3923-0.1691-1.39644.43741.62763.3574-0.1378-0.16880.48470.17890.0833-0.15-0.229-0.30160.00480.26810.1621-0.05710.2059-0.02710.157121.44966.728233.1096
122.87590.36950.25362.7321-1.18035.8957-0.0186-0.2890.3430.317-0.1054-0.1865-0.31970.43240.1050.19970.089-0.05490.149-0.05890.188829.0467.441734.4015
130.9859-0.1146-0.1860.6726-0.18571.3817-0.1785-0.070.12420.00120.089-0.0209-0.1423-0.09590.07380.18950.0879-0.00810.1425-0.02030.182228.9033-1.390829.6148
141.56872.8061.04545.39470.81983.8568-0.1372-0.28050.5211-0.088-0.04040.71650.2204-0.54810.12730.24590.0801-0.01820.2376-0.03280.262322.1857-10.596534.1342
153.2204-1.5701-0.54372.8753-0.11081.5279-0.0952-0.0074-0.36590.066-0.03240.03820.3387-0.00830.11080.25170.05410.02670.1464-0.03250.179330.9597-13.606225.5289
166.02843.3093-3.20216.8034-4.3496.3261-0.184-0.3651-0.55690.2619-0.0391-0.04230.57470.21490.2910.31570.09080.03110.1168-0.00620.201432.4698-16.108234.0719
173.431.1095-2.42092.3848-2.72056.237-0.1443-0.3798-0.20530.0375-0.2151-0.45940.18770.80920.37570.21050.0915-0.03260.1837-0.03990.193938.1821-9.290930.6977
186.23451.4865-2.06244.4108-0.45755.2291-0.1307-0.3101-0.75380.14160.11230.10260.387-0.45240.01360.27970.0703-0.01190.2740.04090.175825.2651-14.082246.0181
190.06770.33790.37144.1507-0.46844.1826-0.2078-0.2625-0.24370.21020.0335-0.3234-0.11720.18780.15130.20770.0919-0.00710.1784-0.00090.146131.1523-4.265139.0525
201.96770.0743-0.15012.9914-0.59010.1464-0.1664-0.8655-0.03471.03010.1528-0.0599-0.6567-0.67270.02440.45240.22330.0390.4998-0.04380.11723.5317-453.8696
213.8862-4.08514.0234.5204-4.25124.1674-0.0928-0.1013-0.0715-0.35660.25570.20510.2562-0.779-0.46070.46030.01230.01261.10420.14580.30610.7162-1.818835.9366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 243:257)
2X-RAY DIFFRACTION2chain 'A' and (resseq 258:273)
3X-RAY DIFFRACTION3chain 'A' and (resseq 274:320)
4X-RAY DIFFRACTION4chain 'A' and (resseq 321:342)
5X-RAY DIFFRACTION5chain 'A' and (resseq 343:359)
6X-RAY DIFFRACTION6chain 'A' and (resseq 360:386)
7X-RAY DIFFRACTION7chain 'A' and (resseq 387:441)
8X-RAY DIFFRACTION8chain 'A' and (resseq 442:501)
9X-RAY DIFFRACTION9chain 'A' and (resseq 502:527)
10X-RAY DIFFRACTION10chain 'B' and (resseq 260:273)
11X-RAY DIFFRACTION11chain 'B' and (resseq 274:290)
12X-RAY DIFFRACTION12chain 'B' and (resseq 291:320)
13X-RAY DIFFRACTION13chain 'B' and (resseq 321:342)
14X-RAY DIFFRACTION14chain 'B' and (resseq 343:359)
15X-RAY DIFFRACTION15chain 'B' and (resseq 360:386)
16X-RAY DIFFRACTION16chain 'B' and (resseq 387:399)
17X-RAY DIFFRACTION17chain 'B' and (resseq 400:414)
18X-RAY DIFFRACTION18chain 'B' and (resseq 415:441)
19X-RAY DIFFRACTION19chain 'B' and (resseq 442:457)
20X-RAY DIFFRACTION20chain 'B' and (resseq 458:523)
21X-RAY DIFFRACTION21chain 'C'

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