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- PDB-2mj5: Structure of the UBA Domain of Human NBR1 in Complex with Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 2mj5
TitleStructure of the UBA Domain of Human NBR1 in Complex with Ubiquitin
Components
  • Next to BRCA1 gene 1 protein
  • Polyubiquitin-C
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 / negative regulation of osteoblast differentiation / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) ...regulation of bone mineralization / phagophore assembly site / M band / peroxisomal membrane / mitogen-activated protein kinase binding / regulation of stress-activated MAPK cascade / negative regulation of osteoblast differentiation / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / autophagosome / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / IKK complex recruitment mediated by RIP1 / ubiquitin binding / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / macroautophagy / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Hh mutants are degraded by ERAD / Regulation of TNFR1 signaling
Similarity search - Function
NBR1, PB1 domain / : / Next to BRCA1 gene 1 protein-like, C-terminal UBA domain / Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. ...NBR1, PB1 domain / : / Next to BRCA1 gene 1 protein-like, C-terminal UBA domain / Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / 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 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Polyubiquitin-C / Next to BRCA1 gene 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
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
DepositionDec 25, 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
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: Polyubiquitin-C
B: Next to BRCA1 gene 1 protein


Theoretical massNumber of molelcules
Total (without water)14,4962
Polymers14,4962
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)1 / 199structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 1 / Fragment: UNP residuses 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0CG48
#2: 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 916-959
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: Structure of the UBA Domain of Human NBR1 in Complex with Ubiquitin
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
11332D 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-8, 5 % D2O-9, 95% H2O/5% D2O95% H2O/5% D2O
220 mM potassium phosphate-10, 5 mM potassium chloride-11, 1 mM EDTA-12, 1 mM benzamidine-13, 1 mM DTT-14, 0.02 % sodium azide-15, 0.5 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-16, 12.5 mg/mL Pf1 phage-17, 150 mM sodium chloride-18, 95 % H2O-19, 5 % D2O-20, 0.5 mM [U-100% 13C; U-100% 15N] NBR1_UBA-21, 2 mM Ubiquitin-22, 12.5 mg/mL Pf1 phage-23, 95% H2O/5% D2O95% H2O/5% D2O
320 mM potassium phosphate-24, 5 mM potassium chloride-25, 1 mM EDTA-26, 1 mM benzamidine-27, 1 mM DTT-28, 0.02 % sodium azide-29, 0.5 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-30, 12.5 mg/mL Pf1 phage-31, 150 mM sodium chloride-32, 95 % H2O-33, 5 % D2O-34, 0.5 mM [U-100% 13C; U-100% 15N] NBR1_UBA-35, 2 mM Ubiquitin-36, 12.5 mg/mL Pf1 phage-37, 95% H2O/5% D2O95% H2O/5% D2O
42 mM NBR1_UBA-38, 0.5 mM [U-100% 13C; U-100% 15N] Ubiquitin-39, 12.5 mg/mL Pf1 phage-40, 95% H2O/5% D2O95% H2O/5% D2O
51 mM [U-100% 15N] NBR1_UBA-41, 4.5 mM Ubiquitin-42, 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
95 %H2O-81
5 %D2O-91
20 mMpotassium phosphate-102
5 mMpotassium chloride-112
1 mMEDTA-122
1 mMbenzamidine-132
1 mMDTT-142
0.02 %sodium azide-152
0.5 mMNBR1 residues 913-959-16[U-100% 13C; U-100% 15N]2
12.5 mg/mLPf1 phage-172
150 mMsodium chloride-182
95 %H2O-192
5 %D2O-202
0.5 mMNBR1_UBA-21[U-100% 13C; U-100% 15N]2
2 mMUbiquitin-222
12.5 mg/mLPf1 phage-232
20 mMpotassium phosphate-243
5 mMpotassium chloride-253
1 mMEDTA-263
1 mMbenzamidine-273
1 mMDTT-283
0.02 %sodium azide-293
0.5 mMNBR1 residues 913-959-30[U-100% 13C; U-100% 15N]3
12.5 mg/mLPf1 phage-313
150 mMsodium chloride-323
95 %H2O-333
5 %D2O-343
0.5 mMNBR1_UBA-35[U-100% 13C; U-100% 15N]3
2 mMUbiquitin-363
12.5 mg/mLPf1 phage-373
2 mMNBR1_UBA-384
0.5 mMUbiquitin-39[U-100% 13C; U-100% 15N]4
12.5 mg/mLPf1 phage-404
1 mMNBR1_UBA-41[U-100% 15N]5
4.5 mMUbiquitin-425
Sample conditionspH: 6.6 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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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
HADDOCKrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 199 / Conformers submitted total number: 1 / Representative conformer: 1

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