BMRB Entry 19606

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19606
MolProbity Validation Chart

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Title:
Solution Structure of the UBA Domain of Human NBR1
Deposition date:
2013-11-09
Original release date:
2014-04-07
Authors:
Walinda, Erik; Morimoto, Daichi; Sugase, Kenji; Komatsu, Masaaki; Tochio, Hidehito; Shirakawa, Masahiro
Citation:

Citation: Walinda, Erik; Morimoto, Daichi; Sugase, Kenji; Konuma, Tsuyoshi; Tochio, Hidehito; Shirakawa, Masahiro. "Solution Structure of the Ubiquitin-associated (UBA) Domain of Human Autophagy Receptor NBR1 and its Interaction with Ubiquitin and Polyubiquitin."  J. Biol. Chem. ., .-. (2014).
PubMed: 24692539

Assembly members:

Assembly members:
entity, polymer, 52 residues, 5918.827 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pGEX-6P1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GPLGSSEDQTAALMAHLFEM GFCDRQLNLRLLKKHNYNIL QVVTELLQLNNN

Data sets:
Data typeCount
1H chemical shifts356
13C chemical shifts176
15N chemical shifts50

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1UBA Domain of Human NBR11

Entities:

Entity 1, UBA Domain of Human NBR1 52 residues - 5918.827 Da.

1   GLYPROLEUGLYSERSERGLUASPGLNTHR
2   ALAALALEUMETALAHISLEUPHEGLUMET
3   GLYPHECYSASPARGGLNLEUASNLEUARG
4   LEULEULYSLYSHISASNTYRASNILELEU
5   GLNVALVALTHRGLULEULEUGLNLEUASN
6   ASNASN

Samples:

sample_1: potassium phosphate 20 mM; potassium chloride 5 mM; EDTA 1 mM; benzamidine 1 mM; DTT 1 mM; sodium azide 0.02%; NBR1 residues 913-959, [U-100% 13C; U-100% 15N], 1.2 mM; H2O 95%; D2O 5%

aniso: potassium phosphate 20 mM; potassium chloride 5 mM; EDTA 1 mM; benzamidine 1 mM; DTT 1 mM; sodium azide 0.02%; NBR1 residues 913-959, [U-100% 13C; U-100% 15N], 0.5 mM; Pf1 phage 12.5 mg/mL; sodium chloride 150 mM; H2O 95%; D2O 5%

sample_conditions_1: pH: 6.6; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
2D 1H-15N HSQC IPAPanisoanisotropicsample_conditions_1
2D 1H-15N HSQC IPAPsample_1isotropicsample_conditions_1

Software:

TOPSPIN v2.0, Bruker Biospin - collection

TALOS, Cornilescu, Delaglio and Bax - structure solution

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

MAGRO, Dr. Naohiro Kobayashi - chemical shift assignment

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

PDB
DBJ BAA06417 BAF82694 BAG09582 BAH12580
EMBL CAA54274 CAH90613
GB AAI49980 AAS15047 EAW60946 EAW60947 EAW60949
REF NP_001093837 NP_001127309 NP_005890 NP_114068 XP_001097043
SP Q14596 Q5RC94
TPG DAA18460
AlphaFold Q5RC94 Q14596

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks