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- PDB-7mm1: PTP1B in complex with TCS401 by Native S-SAD at Room Temperature -

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Basic information

Entry
Database: PDB / ID: 7mm1
TitlePTP1B in complex with TCS401 by Native S-SAD at Room Temperature
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE/HYDROLASE inhibitor / Protein Tyrosine Phosphatase 1B / Hydrolase / Inhibitor / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane ...regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / mitochondrial crista / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / non-membrane spanning protein tyrosine phosphatase activity / positive regulation of protein tyrosine kinase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of signal transduction / Regulation of IFNG signaling / MECP2 regulates neuronal receptors and channels / Growth hormone receptor signaling / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / Insulin receptor recycling / negative regulation of insulin receptor signaling pathway / ephrin receptor binding / Integrin signaling / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of MAP kinase activity / protein phosphatase 2A binding / protein tyrosine phosphatase activity / endosome lumen / insulin receptor binding / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / insulin receptor signaling pathway / actin cytoskeleton organization / early endosome / mitochondrial matrix / cadherin binding / protein kinase binding / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-1/2 / 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 ...Protein-tyrosine phosphatase, non-receptor type-1/2 / 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
Similarity search - Domain/homology
Chem-OTA / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsGreisman, J.B. / Dalton, K.M. / Hekstra, D.R.
Funding support United States, 3items
OrganizationGrant numberCountry
Other privateSearle Scholars Program (SSP-2018-3240) United States
Other privateGeorge W. Merck Fund in the New York Community Trust (338034) United States
National Science Foundation (NSF, United States)DGE1745303 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Native SAD phasing at room temperature.
Authors: Greisman, J.B. / Dalton, K.M. / Sheehan, C.J. / Klureza, M.A. / Kurinov, I. / Hekstra, D.R.
History
DepositionApr 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Aug 3, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8604
Polymers37,3461
Non-polymers5153
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.341, 89.341, 105.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 1 / Protein-tyrosine phosphatase 1B / PTP-1B


Mass: 37345.562 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: C32S, C92V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical ChemComp-OTA / 2-(OXALYL-AMINO)-4,5,6,7-TETRAHYDRO-THIENO[2,3-C]PYRIDINE-3-CARBOXYLIC ACID


Mass: 270.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N2O5S
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.26 Å3/Da / Density % sol: 62.29 % / Description: Hexagonal rod
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100mM HEPES (pH 6.8 - 7.6), 250mM magnesium acetate, 11-15% PEG8000 (w/v), 10% glycerol (v/v), 6% ethanol (v/v), 0.1% BME (v/v). TCS401 was co-crystallized using a >5-fold molar excess.
PH range: 6.8 - 7.6

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Data collection

DiffractionMean temperature: 295 K / Ambient temp details: Ambient / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.892 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 17, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.892 Å / Relative weight: 1
ReflectionResolution: 1.85→77.37 Å / Num. obs: 79832 / % possible obs: 99 % / Redundancy: 26.3 % / Biso Wilson estimate: 25.49 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1381 / Rpim(I) all: 0.0257 / Rrim(I) all: 0.1406 / Net I/σ(I): 16.6
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.748 / Mean I/σ(I) obs: 2.21 / Num. unique obs: 7532 / CC1/2: 0.675 / CC star: 0.898 / Rpim(I) all: 0.4928 / % possible all: 93.15

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Processing

Software
NameVersionClassification
DIALS3.2.0data reduction
Aimless0.7.4data scaling
AutoSolphasing
PHENIX1.18.2_3874model building
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: SAD / Resolution: 1.85→77.37 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.1097
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1385 3899 4.88 %
Rwork0.129 75932 -
obs0.1295 79831 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.16 Å2
Refinement stepCycle: LAST / Resolution: 1.85→77.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2435 0 34 159 2628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012704
X-RAY DIFFRACTIONf_angle_d1.07393666
X-RAY DIFFRACTIONf_chiral_restr0.0647377
X-RAY DIFFRACTIONf_plane_restr0.0069482
X-RAY DIFFRACTIONf_dihedral_angle_d18.55461055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.26631430.2622508X-RAY DIFFRACTION91.63
1.87-1.90.24781200.23342611X-RAY DIFFRACTION93.43
1.9-1.920.20511660.20842539X-RAY DIFFRACTION94.78
1.92-1.950.1941490.18772646X-RAY DIFFRACTION96.88
1.95-1.980.16391450.16932671X-RAY DIFFRACTION98.29
1.98-20.16111870.152666X-RAY DIFFRACTION98.89
2-2.040.17191340.14032760X-RAY DIFFRACTION99.48
2.04-2.070.15071060.13712746X-RAY DIFFRACTION99.79
2.07-2.110.1291240.1312761X-RAY DIFFRACTION99.69
2.11-2.140.14061430.12772688X-RAY DIFFRACTION99.75
2.14-2.180.14591320.1232756X-RAY DIFFRACTION99.97
2.18-2.230.17511120.12082789X-RAY DIFFRACTION99.83
2.23-2.280.1181100.12222716X-RAY DIFFRACTION99.96
2.28-2.330.12581360.11752725X-RAY DIFFRACTION99.97
2.33-2.390.15581480.12272776X-RAY DIFFRACTION100
2.39-2.450.13541360.10792693X-RAY DIFFRACTION100
2.45-2.530.12571850.11162714X-RAY DIFFRACTION99.97
2.53-2.610.12811400.11552755X-RAY DIFFRACTION100
2.61-2.70.14851600.11992737X-RAY DIFFRACTION100
2.7-2.810.1641440.12182708X-RAY DIFFRACTION100
2.81-2.940.12061480.12432750X-RAY DIFFRACTION99.97
2.94-3.090.1131940.13222758X-RAY DIFFRACTION100
3.09-3.290.12522060.13342689X-RAY DIFFRACTION100
3.29-3.540.14221580.12132725X-RAY DIFFRACTION100
3.54-3.890.10511140.10952756X-RAY DIFFRACTION100
3.9-4.460.10881510.10792753X-RAY DIFFRACTION100
4.46-5.610.1311020.11172755X-RAY DIFFRACTION100
5.62-77.370.16581060.16762781X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: -7.33265748108 Å / Origin y: 47.8317139244 Å / Origin z: 50.8689757791 Å
111213212223313233
T0.168491695221 Å2-0.0629927402336 Å20.0157702005374 Å2-0.15489453561 Å2-0.00371100404911 Å2--0.167518517098 Å2
L1.70828185516 °20.224517437928 °20.289138344062 °2-1.94466221178 °2-0.179365723673 °2--1.72846609622 °2
S0.0493418463303 Å °-0.0185167137503 Å °-0.0288036420928 Å °0.0335372446582 Å °-0.00280945713692 Å °-0.0138621716294 Å °0.06272756823 Å °0.114830219863 Å °-0.0431180379278 Å °
Refinement TLS groupSelection details: all

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