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- PDB-2loz: The novel binding mode of DLC1 and Tensin2 PTB domain -

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Basic information

Entry
Database: PDB / ID: 2loz
TitleThe novel binding mode of DLC1 and Tensin2 PTB domain
Components
  • Rho GTPase-activating protein 7
  • Tensin-like C1 domain-containing phosphatase
KeywordsHYDROLASE/HYDROLASE ACTIVATOR / PTB / DLC1 / HYDROLASE-HYDROLASE ACTIVATOR complex
Function / homology
Function and homology information


hindbrain morphogenesis / multicellular organismal-level homeostasis / collagen metabolic process / negative regulation of focal adhesion assembly / cellular homeostasis / regulation of Rho protein signal transduction / focal adhesion assembly / response to muscle activity / regulation of small GTPase mediated signal transduction / negative regulation of stress fiber assembly ...hindbrain morphogenesis / multicellular organismal-level homeostasis / collagen metabolic process / negative regulation of focal adhesion assembly / cellular homeostasis / regulation of Rho protein signal transduction / focal adhesion assembly / response to muscle activity / regulation of small GTPase mediated signal transduction / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / positive regulation of execution phase of apoptosis / RHOB GTPase cycle / cortical actin cytoskeleton / RHOC GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / peptidyl-tyrosine dephosphorylation / RHOA GTPase cycle / heart morphogenesis / forebrain development / positive regulation of protein dephosphorylation / negative regulation of insulin receptor signaling pathway / RAC1 GTPase cycle / SH2 domain binding / GTPase activator activity / protein-tyrosine-phosphatase / negative regulation of cell migration / kidney development / protein tyrosine phosphatase activity / neural tube closure / caveola / regulation of actin cytoskeleton organization / multicellular organism growth / ruffle membrane / kinase binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of cell shape / actin cytoskeleton organization / membrane raft / negative regulation of cell population proliferation / focal adhesion / intracellular membrane-bounded organelle / lipid binding / apoptotic process / endoplasmic reticulum / signal transduction / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tensin, phosphotyrosine-binding domain / Tensin-like, SH2 domain / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein ...Tensin, phosphotyrosine-binding domain / Tensin-like, SH2 domain / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Phorbol esters/diacylglycerol binding domain (C1 domain) / Rho GTPase activation protein / START-like domain superfamily / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / SAM domain (Sterile alpha motif) / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / C1-like domain superfamily / PH-domain like / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / C2 domain superfamily / Protein-tyrosine phosphatase-like / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Tensin-2 / Rho GTPase-activating protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model 1
AuthorsLiu, C. / Chen, L. / Zhu, G.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Solution structure of the phosphotyrosine binding (PTB) domain of human tensin2 protein in complex with deleted in liver cancer 1 (DLC1) peptide reveals a novel peptide binding mode.
Authors: Chen, L. / Liu, C. / Ko, F.C. / Xu, N. / Ng, I.O. / Yam, J.W. / Zhu, G.
History
DepositionJan 29, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Data collection / Database references / Category: citation / citation_author / pdbx_nmr_software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tensin-like C1 domain-containing phosphatase
B: Rho GTPase-activating protein 7


Theoretical massNumber of molelcules
Total (without water)17,5412
Polymers17,5412
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Tensin-like C1 domain-containing phosphatase / C1 domain-containing phosphatase and tensin homolog / C1-TEN / Tensin-2


Mass: 15983.139 Da / Num. of mol.: 1 / Fragment: PTB domain, UNP residues 1263-1409
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TENC1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q63HR2, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Protein/peptide Rho GTPase-activating protein 7 / Deleted in liver cancer 1 protein / DLC-1 / HP protein / Rho-type GTPase-activating protein 7 / ...Deleted in liver cancer 1 protein / DLC-1 / HP protein / Rho-type GTPase-activating protein 7 / START domain-containing protein 12 / StARD12 / StAR-related lipid transfer protein 12


Mass: 1557.724 Da / Num. of mol.: 1 / Fragment: UNP residues 811-824
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96QB1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1312D 1H-13C HSQC
1422D 1H-13C HSQC
1513D HNCO
1613D HN(CA)CB
1713D CBCA(CO)NH
1833D (H)CCH-TOCSY
1913D 1H-15N NOESY
11033D 1H-13C NOESY
11123D HNCO
11223D CBCA(CO)NH
11323D HN(CA)CB
11423D 1H-15N NOESY
11543D 1H-13C NOESY
11643D (H)CCH-COSY
11733D13C/15N FILTERED-13C EDITED NOESY
11843D13C/15N FILTERED-13C EDITED NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6-0.8 mM [U-100% 13C; U-100% 15N] Tensin2-1, 1.2-1.4 mM DLC1-2, 100 mM potassium phosphate-3, 100 mM potassium chloride-4, 1 mM EDTA-5, 90% H2O/10% D2O90% H2O/10% D2O
21.2-1.4 mM Tensin2-6, 0.6-0.8 mM [U-100% 13C; U-100% 15N] DLC1-7, 100 mM potassium phosphate-8, 100 mM potassium chloride-9, 1 mM EDTA-10, 90% H2O/10% D2O90% H2O/10% D2O
30.6-0.8 mM [U-100% 13C] Tensin2-11, 1.2-1.4 mM DLC1-12, 100 mM potassium phosphate-13, 100 mM potassium chloride-14, 1 mM EDTA-15, 100% D2O100% D2O
41.2-1.4 mM Tensin2-16, 0.6-0.8 mM [U-100% 13C] DLC1-17, 100 mM potassium phosphate-18, 100 mM potassium chloride-19, 1 mM EDTA-20, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMTensin2-1[U-100% 13C; U-100% 15N]0.6-0.81
mMDLC1-21.2-1.41
100 mMpotassium phosphate-31
100 mMpotassium chloride-41
1 mMEDTA-51
mMTensin2-61.2-1.42
mMDLC1-7[U-100% 13C; U-100% 15N]0.6-0.82
100 mMpotassium phosphate-82
100 mMpotassium chloride-92
1 mMEDTA-102
mMTensin2-11[U-100% 13C]0.6-0.83
mMDLC1-121.2-1.43
100 mMpotassium phosphate-133
100 mMpotassium chloride-143
1 mMEDTA-153
mMTensin2-161.2-1.44
mMDLC1-17[U-100% 13C]0.6-0.84
100 mMpotassium phosphate-184
100 mMpotassium chloride-194
1 mMEDTA-204
Sample conditionsIonic strength: 0.2 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
ProcheckNMRLaskowski and MacArthurdata analysis
ProcheckNMRLaskowski and MacArthurgeometry optimization
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
HADDOCKAlexandre Bonvinrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1

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