BMRB Entry 25071

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25071
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Title:
NMR structure of the ubiquitin-binding zinc finger (UBZ) domain from human Rad18
Deposition date:
2014-07-03
Original release date:
2014-09-19
Authors:
Rizzo, Alessandro; Salerno, Paige; Bezsonova, Irina; Korzhnev, Dmitry
Citation:

Citation: Rizzo, Alessandro; Salerno, Paige; Bezsonova, Irina; Korzhnev, Dmitry. "NMR Structure of the Human Rad18 Zinc Finger in Complex with Ubiquitin Defines a Class of UBZ Domains in Proteins Linked to the DNA Damage Response."  Biochemistry 53, 5895-5906 (2014).
PubMed: 25162118

Assembly members:

Assembly members:
Rad18-UBZ, polymer, 33 residues, 3628.145 Da.
ZINC ION, non-polymer, 65.409 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Rad18-UBZ: GSRQVTKVDCPVCGVNIPES HINKHLDSCLSRE

Data sets:
Data typeCount
1H chemical shifts168
13C chemical shifts102
15N chemical shifts27

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Rad18-UBZ1
2ZINC ION2

Entities:

Entity 1, Rad18-UBZ 33 residues - 3628.145 Da.

1   GLYSERARGGLNVALTHRLYSVALASPCYS
2   PROVALCYSGLYVALASNILEPROGLUSER
3   HISILEASNLYSHISLEUASPSERCYSLEU
4   SERARGGLU

Entity 2, ZINC ION - Zn - 65.409 Da.

1   ZN

Samples:

Rad18_UBZ_sample: Rad18_UBZ, [U-13C; U-15N], 0.5 – 1.5 mM; MOPS-NaOH 25 mM; NaCl 50 mM; ZnCl2 0.05 mM; H2O 90%; D2O 10%

MOPS_NMR_buffer: temperature: 273 K; pH: 6.5; pressure: 1 atm; ionic strength: 150 mM

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCRad18_UBZ_sampleisotropicMOPS_NMR_buffer
3D HNCORad18_UBZ_sampleisotropicMOPS_NMR_buffer
3D HNCACBRad18_UBZ_sampleisotropicMOPS_NMR_buffer
3D HCCH-TOCSYRad18_UBZ_sampleisotropicMOPS_NMR_buffer
3D HBHA(CO)NHRad18_UBZ_sampleisotropicMOPS_NMR_buffer
3D 1H-15N NOESYRad18_UBZ_sampleisotropicMOPS_NMR_buffer
3D 1H-13C NOESYRad18_UBZ_sampleisotropicMOPS_NMR_buffer
3D CBCA(CO)NHRad18_UBZ_sampleisotropicMOPS_NMR_buffer
3D CCH-TOCSYRad18_UBZ_sampleisotropicMOPS_NMR_buffer

Software:

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

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

CCPNmr_Analysis, CCPN - chemical shift assignment

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

  • Varian VNMRS 800 MHz
  • Varian VNMRS 600 MHz
  • Varian VNMRS 500 MHz

Related Database Links:

PDB
REF XP_012616146

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