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- PDB-2mq1: Phosphotyrosine binding domain -

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Basic information

Entry
Database: PDB / ID: 2mq1
TitlePhosphotyrosine binding domain
ComponentsE3 ubiquitin-protein ligase Hakai
KeywordsLIGASE / phosphotyrosine binding
Function / homology
Function and homology information


RNA N6-methyladenosine methyltransferase complex / Antigen processing: Ubiquitination & Proteasome degradation / : / negative regulation of cell adhesion / positive regulation of endocytosis / regulation of cell adhesion / RING-type E3 ubiquitin transferase / cell-cell adhesion / ubiquitin protein ligase activity / protein ubiquitination ...RNA N6-methyladenosine methyltransferase complex / Antigen processing: Ubiquitination & Proteasome degradation / : / negative regulation of cell adhesion / positive regulation of endocytosis / regulation of cell adhesion / RING-type E3 ubiquitin transferase / cell-cell adhesion / ubiquitin protein ligase activity / protein ubiquitination / positive regulation of cell migration / nuclear speck / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
HAKAI-like, RING finger, HC subclass / E3 ubiquitin-protein ligase HAKAI/CBLL2 / Hakai, C2H2 zinc finger domain / C2H2 Hakai zinc finger domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Hakai
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsMukherjee, M. / Jing-Song, F. / Sivaraman, J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Dimeric switch of Hakai-truncated monomers during substrate recognition: insights from solution studies and NMR structure.
Authors: Mukherjee, M. / Jing-Song, F. / Ramachandran, S. / Guy, G.R. / Sivaraman, J.
History
DepositionJun 11, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Database references
Category: citation / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase Hakai
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4154
Polymers10,2191
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1minimized average structure

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Components

#1: Protein E3 ubiquitin-protein ligase Hakai / Casitas B-lineage lymphoma-transforming sequence-like protein 1 / E-cadherin binding protein E7 / c- ...Casitas B-lineage lymphoma-transforming sequence-like protein 1 / E-cadherin binding protein E7 / c-Cbl-like protein 1


Mass: 10219.141 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 106-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cbll1, Hakai / Production host: Escherichia coli (E. coli)
References: UniProt: Q9JIY2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D (H)CCH-TOCSY
1513D HN(CA)CB
1613D HNCO
1713D HN(CO)CA
1813D HBHA(CO)NH
1913D 1H-15N NOESY
11013D HN(COCA)CB

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Sample preparation

DetailsContents: 50 mM [U-100% 13C; U-100% 15N; U-80% 2H] potassium phosphate-1, 5 mM DTT-2, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMpotassium phosphate-1[U-100% 13C; U-100% 15N; U-80% 2H]1
5 mMDTT-21
Sample conditionsIonic strength: 0.05 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1087 / NOE long range total count: 344 / NOE medium range total count: 193 / NOE sequential total count: 338
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Representative conformer: 1

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