BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 25423

Title: Solution structure of NDP52 ubiquitin-binding zinc finger   PubMed: 26506893

Deposition date: 2015-01-12 Original release date: 2015-11-09

Authors: Pan, Lifeng; Xie, Xingqiao

Citation: Xie, Xingqiao; Wang, Yingli; Lin, Zhijie; Chen, Xiaofang; Liu, Jianping; Pan, Lifeng. "Molecular basis of ubiquitin recognition by the autophagy receptor CALCOCO2"  Autophagy 11, 1775-1789 (2015).

Assembly members:
entity_1, polymer, 33 residues, 3887.567 Da.
ZINC ION, non-polymer, 65.409 Da.

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

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
entity_1: QMQPLCFNCPICDKIFPATE KQIFEDHVFCHSL

Data sets:
Data typeCount
13C chemical shifts103
15N chemical shifts34
1H chemical shifts241

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2ZINC ION2

Entities:

Entity 1, entity_1 33 residues - 3887.567 Da.

1   GLNMETGLNPROLEUCYSPHEASNCYSPRO
2   ILECYSASPLYSILEPHEPROALATHRGLU
3   LYSGLNILEPHEGLUASPHISVALPHECYS
4   HISSERLEU

Entity 2, ZINC ION - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: entity_1, [U-100% 13C; U-100% 15N], 1 mM; entity_1, [U-100% 15N], 1 mM; D2O 10%; H2O 90%; Potassium phosphate buffer 50 mM; NaCl 50 mM; DTT 1 mM

sample_2: entity_1, [U-100% 13C; U-100% 15N], 1 mM; D2O 100%; Potassium phosphate buffer 50 mM; NaCl 50 mM; DTT 1 mM

sample_3: entity_1 1.2 mM; D2O 100%; Potassium phosphate buffer 50 mM; NaCl 50 mM; DTT 1 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.1 M; pH: 6.5; pressure: 2 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_2
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_2
2D 1H-1H NOESYsample_3isotropicsample_conditions_2

Software:

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

PIPP, Garrett - chemical shift assignment, data analysis

SPARKY, Goddard - chemical shift assignment, data analysis

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMR spectrometers:

  • Agilent INOVA 800 MHz

Related Database Links:

PDB
DBJ BAD96947 BAG37327 BAG56685 BAG56845 BAG60448
EMBL CAG33044 CAH92289
GB AAA75297 AAH04130 AAH15893 ADQ32739 ADZ15727
REF NP_001126338 NP_001233315 NP_001248319 NP_001248320 NP_001248322
SP Q13137 Q5R7H1

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts