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- PDB-2mgw: Solution Structure of the UBA Domain of Human NBR1 -

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Basic information

Entry
Database: PDB / ID: 2mgw
TitleSolution Structure of the UBA Domain of Human NBR1
ComponentsNext to BRCA1 gene 1 protein
KeywordsPROTEIN BINDING / autophagy / protein degradation / ubiquitin binding
Function / homology
Function and homology information


regulation of bone mineralization / phagophore assembly site / M band / peroxisomal membrane / mitogen-activated protein kinase binding / regulation of stress-activated MAPK cascade / autophagosome / negative regulation of osteoblast differentiation / Pexophagy / ubiquitin binding ...regulation of bone mineralization / phagophore assembly site / M band / peroxisomal membrane / mitogen-activated protein kinase binding / regulation of stress-activated MAPK cascade / autophagosome / negative regulation of osteoblast differentiation / Pexophagy / ubiquitin binding / macroautophagy / mitochondrial intermembrane space / late endosome / lysosome / nuclear body / receptor complex / intracellular membrane-bounded organelle / zinc ion binding / nucleoplasm / membrane / cytosol
Similarity search - Function
NBR1, PB1 domain / Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Ubiquitin-associated (UBA) domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. ...NBR1, PB1 domain / Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Ubiquitin-associated (UBA) domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Helicase, Ruva Protein; domain 3 / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Next to BRCA1 gene 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsWalinda, E. / Morimoto, D. / Sugase, K. / Komatsu, M. / Tochio, H. / Shirakawa, M.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Solution structure of the ubiquitin-associated (UBA) domain of human autophagy receptor NBR1 and its interaction with ubiquitin and polyubiquitin.
Authors: Walinda, E. / Morimoto, D. / Sugase, K. / Konuma, T. / Tochio, H. / Shirakawa, M.
History
DepositionNov 9, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Aug 24, 2022Group: Data collection / Database references
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _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: Next to BRCA1 gene 1 protein


Theoretical massNumber of molelcules
Total (without water)5,9191
Polymers5,9191
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)20 / 100all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Next to BRCA1 gene 1 protein / Cell migration-inducing gene 19 protein / Membrane component chromosome 17 surface marker 2 / ...Cell migration-inducing gene 19 protein / Membrane component chromosome 17 surface marker 2 / Neighbor of BRCA1 gene 1 protein / Protein 1A1-3B


Mass: 5918.783 Da / Num. of mol.: 1 / Fragment: UNP residues 913-959
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NBR1, 1A13B, KIAA0049, M17S2, MIG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14596

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Solution Structure of the UBA Domain of Human NBR1
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D H(CCO)NH
1813D C(CO)NH
1913D (H)CCH-TOCSY
11013D 1H-13C NOESY aliphatic
11113D 1H-13C NOESY aromatic
11213D 1H-15N NOESY
11322D 1H-15N HSQC IPAP
11412D 1H-15N HSQC IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM potassium phosphate-1, 5 mM potassium chloride-2, 1 mM EDTA-3, 1 mM benzamidine-4, 1 mM DTT-5, 0.02 % sodium azide-6, 1.2 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-7, 95% H2O/5% D2O95% H2O/5% D2O
220 mM potassium phosphate-8, 5 mM potassium chloride-9, 1 mM EDTA-10, 1 mM benzamidine-11, 1 mM DTT-12, 0.02 % sodium azide-13, 0.5 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-14, 12.5 mg/mL Pf1 phage-15, 150 mM sodium chloride-16, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMpotassium phosphate-11
5 mMpotassium chloride-21
1 mMEDTA-31
1 mMbenzamidine-41
1 mMDTT-51
0.02 %sodium azide-61
1.2 mMNBR1 residues 913-959-7[U-100% 13C; U-100% 15N]1
20 mMpotassium phosphate-82
5 mMpotassium chloride-92
1 mMEDTA-102
1 mMbenzamidine-112
1 mMDTT-122
0.02 %sodium azide-132
0.5 mMNBR1 residues 913-959-14[U-100% 13C; U-100% 15N]2
12.5 mg/mLPf1 phage-152
150 mMsodium chloride-162
Sample conditionspH: 6.6 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospincollection
TALOSCornilescu, Delaglio and Baxstructure solution
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MAGRODr. Naohiro Kobayashichemical shift assignment
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1055 / NOE long range total count: 190 / NOE medium range total count: 323
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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