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- PDB-6uzj: NMR structure of the HACS1 SH3 domain -

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Basic information

Entry
Database: PDB / ID: 6uzj
TitleNMR structure of the HACS1 SH3 domain
ComponentsSAM domain-containing protein SAMSN-1
KeywordsSIGNALING PROTEIN / adaptor protein SH3 domain protein-protein interaction
Function / homology
Function and homology information


negative regulation of adaptive immune response / negative regulation of B cell activation / negative regulation of peptidyl-tyrosine phosphorylation / ruffle / phosphotyrosine residue binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
SAMSN1, SAM domain / SAM/SH3 domain-containing / SLy Proteins Associated Disordered Region / Variant SH3 domain / SAM domain (Sterile alpha motif) / SH3 Domains / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily ...SAMSN1, SAM domain / SAM/SH3 domain-containing / SLy Proteins Associated Disordered Region / Variant SH3 domain / SAM domain (Sterile alpha motif) / SH3 Domains / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
SAM domain-containing protein SAMSN-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDonaldson, L.W.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Commun Biol / Year: 2020
Title: HACS1 signaling adaptor protein recognizes a motif in the paired immunoglobulin receptor B cytoplasmic domain.
Authors: Kwan, J.J. / Slavkovic, S. / Piazza, M. / Wang, D. / Dieckmann, T. / Johnson, P.E. / Wen, X.Y. / Donaldson, L.W.
History
DepositionNov 15, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionNov 27, 2019ID: 2KEA
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 2, 2020Group: 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
Revision 1.3Jun 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
Revision 1.4May 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: SAM domain-containing protein SAMSN-1


Theoretical massNumber of molelcules
Total (without water)9,6571
Polymers9,6571
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein SAM domain-containing protein SAMSN-1 / Hematopoietic adaptor containing SH3 and SAM domains 1 / Nash1 / SAM domain / SH3 domain and ...Hematopoietic adaptor containing SH3 and SAM domains 1 / Nash1 / SAM domain / SH3 domain and nuclear localization signals protein 1 / SH3-SAM adaptor protein


Mass: 9656.987 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMSN1, HACS1 / Plasmid: pGEX2T / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9NSI8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic13D CBCA(CO)NH
141isotropic13D HN(CA)CB
151isotropic12D 1H-13C HSQC aliphatic
1101isotropic13D HNCO
191isotropic13D C(CO)NH
181isotropic13D H(CCO)NH
171isotropic13D (H)CCH-TOCSY
161isotropic13D 1H-15N NOESY
1111isotropic13D 1H-13C NOESY aliphatic
1121isotropic13D 1H-13C NOESY aromatic
1132anisotropic12D 1H-15N IPAP HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution120 mM sodium phosphate, 150 mM sodium chloride, 0.05 % w/v sodium azide, 90% H2O/10% D2Omain sample for NMR13C15N_sample90% H2O/10% D2O
filamentous virus220 mM sodium phosphate, 150 mM sodium chloride, 0.05 % w/v sodium azide, 10 mg/mL Pf1 phage, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
0.05 % w/vsodium azidenatural abundance1
20 mMsodium phosphatenatural abundance2
150 mMsodium chloridenatural abundance2
0.05 % w/vsodium azidenatural abundance2
10 mg/mLPf1 phagenatural abundance2
Sample conditionsIonic strength: 150 mM / Label: main_conditions / pH: 7.7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNdata analysis
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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