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- PDB-1sj6: NMR Structure and Regulated Expression in APL Cell of Human SH3BGRL3 -

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Basic information

Entry
Database: PDB / ID: 1sj6
TitleNMR Structure and Regulated Expression in APL Cell of Human SH3BGRL3
ComponentsSH3 domain-binding glutamic acid-rich-like protein 3
KeywordsPROTEIN BINDING / thioredoxin / Nuclear protein
Function / homology
Function and homology information


protein-disulfide reductase activity / electron transfer activity / nuclear body / extracellular exosome / cytoplasm
Similarity search - Function
SH3-binding, glutamic acid-rich protein / SH3-binding, glutamic acid-rich protein / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SH3 domain-binding glutamic acid-rich-like protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsXu, C. / Tang, Y. / Xu, Y. / Wu, J. / Shi, Y. / Zhang, Q. / Zheng, P. / Du, Y.
CitationJournal: Febs Lett. / Year: 2005
Title: NMR structure and regulated expression in APL cell of human SH3BGRL3.
Authors: Xu, C. / Zheng, P. / Shen, S. / Xu, Y. / Wei, L. / Gao, H. / Wang, S. / Zhu, C. / Tang, Y. / Wu, J. / Zhang, Q. / Shi, Y.
History
DepositionMar 3, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 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: SH3 domain-binding glutamic acid-rich-like protein 3


Theoretical massNumber of molelcules
Total (without water)11,5191
Polymers11,5191
Non-polymers00
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein SH3 domain-binding glutamic acid-rich-like protein 3 / SH3 domain-binding protein SH3BP-1 / P1725 / TNF inhibitory protein / SH3BGRL3-like protein


Mass: 11518.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHEBGRL3 / Plasmid: PET22B(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H299

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D (H)CCH-COSY
1313D 13C-separated NOESY
1413D 15N-separated NOESY
1513D CBCA(CO)NH
1613D CBCANH
1713D HNCO
1813D H(CCO)NH TOCSY
1913D C(CO)NH TOCSY
11013D (H)CCH-TOCSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 2mM SH3BGRL3 U-15N, 13C; 20mM phosphate buffer NA; 100mM NaCl, pH7.0; 90% H2O, 10% D2O
Solvent system: 90% H20, 10% D20
Sample conditionsIonic strength: 100mM NaCl, 20mM phosphate buffer / pH: 7.0 / Pressure: 1 atm / Temperature: 295 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2F.Delaglioprocessing
CNS1.1A.T.Brungerstructure solution
SparkySPARKY3T.D.Goddard&D.G.Knellerdata analysis
CNS1.1A.T.Brungerrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: the structures are based on a total of 1463 restraints, 1306 are NOE-derived distance constraints, 101 dihedral angle restraints, 56 distance restraints from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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