BMRB Entry 25070

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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/BMR25070
MolProbity Validation Chart

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Title:
NMR structure of the Rad18-UBZ/ubiquitin complex
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:
Ubiquitin, polymer, 79 residues, 8859.192 Da.
Ubiquitin-binding_zinc_finger_(UBZ)_domain_from_human_Rad18, 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: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Ubiquitin: GSHMQIFVKTLTGKTITLEV EPSDTIENVKAKIQDKEGIP PDQQRLIFAGKQLEDGRTLS DYNIQKESTLHLVLRLRGG
Ubiquitin-binding_zinc_finger_(UBZ)_domain_from_human_Rad18: GSRQVTKVDCPVCGVNIPES HINKHLDSCLSRE

Data sets:
Data typeCount
1H chemical shifts732
13C chemical shifts438
15N chemical shifts106

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Ubiquitin1
2Ubiquitin-binding_zinc_finger_(UBZ)_domain_from_human_Rad182
3ZINC ION3

Entities:

Entity 1, Ubiquitin 79 residues - 8859.192 Da.

the first three residues 'GSH' are remnants of the thrombin cleavage site and cloning vector

1   GLYSERHISMETGLNILEPHEVALLYSTHR
2   LEUTHRGLYLYSTHRILETHRLEUGLUVAL
3   GLUPROSERASPTHRILEGLUASNVALLYS
4   ALALYSILEGLNASPLYSGLUGLYILEPRO
5   PROASPGLNGLNARGLEUILEPHEALAGLY
6   LYSGLNLEUGLUASPGLYARGTHRLEUSER
7   ASPTYRASNILEGLNLYSGLUSERTHRLEU
8   HISLEUVALLEUARGLEUARGGLYGLY

Entity 2, Ubiquitin-binding_zinc_finger_(UBZ)_domain_from_human_Rad18 33 residues - 3628.145 Da.

GSR are remnants of the thrombin cleavage tag. Q198 is the first native residue

1   GLYSERARGGLNVALTHRLYSVALASPCYS
2   PROVALCYSGLYVALASNILEPROGLUSER
3   HISILEASNLYSHISLEUASPSERCYSLEU
4   SERARGGLU

Entity 3, ZINC ION - Zn - 65.409 Da.

1   ZN

Samples:

13C-15N-UBZ_saturated_with_unlabeled_ubiquitin: Ubiquitin-binding zinc finger (UBZ) domain from human Rad18, [U-13C; U-15N], 0.5 mM; Ubiquitin 5 mM; MOPS 25 mM; NaCl 50 mM; ZnCl2 0.05 mM; H2O 90%; D2O 10%

13C-15N-ubiquitin_saturated_with_unlabeled_UBZ: Ubiquitin, [U-13C; U-15N], 2 mM; Ubiquitin-binding zinc finger (UBZ) domain from human Rad187 – 10 mM; MOPS 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: 125 mM

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC13C-15N-UBZ_saturated_with_unlabeled_ubiquitinisotropicMOPS_NMR_buffer
3D HNCO13C-15N-UBZ_saturated_with_unlabeled_ubiquitinisotropicMOPS_NMR_buffer
3D HNCACB13C-15N-UBZ_saturated_with_unlabeled_ubiquitinisotropicMOPS_NMR_buffer
3D HBHA(CO)NH13C-15N-UBZ_saturated_with_unlabeled_ubiquitinisotropicMOPS_NMR_buffer
3D HCCH-TOCSY13C-15N-UBZ_saturated_with_unlabeled_ubiquitinisotropicMOPS_NMR_buffer
3D 1H-15N NOESY13C-15N-UBZ_saturated_with_unlabeled_ubiquitinisotropicMOPS_NMR_buffer
3D 1H-13C NOESY13C-15N-UBZ_saturated_with_unlabeled_ubiquitinisotropicMOPS_NMR_buffer
3D 15N/13C-filtered NOESY13C-15N-UBZ_saturated_with_unlabeled_ubiquitinisotropicMOPS_NMR_buffer
2D 1H-15N HSQC13C-15N-ubiquitin_saturated_with_unlabeled_UBZisotropicMOPS_NMR_buffer
3D HNCO13C-15N-ubiquitin_saturated_with_unlabeled_UBZisotropicMOPS_NMR_buffer
3D HNCACB13C-15N-ubiquitin_saturated_with_unlabeled_UBZisotropicMOPS_NMR_buffer
3D HCCH-TOCSY13C-15N-ubiquitin_saturated_with_unlabeled_UBZisotropicMOPS_NMR_buffer
3D HBHA(CO)NH13C-15N-ubiquitin_saturated_with_unlabeled_UBZisotropicMOPS_NMR_buffer
3D 1H-15N NOESY13C-15N-ubiquitin_saturated_with_unlabeled_UBZisotropicMOPS_NMR_buffer
3D 1H-13C NOESY13C-15N-ubiquitin_saturated_with_unlabeled_UBZisotropicMOPS_NMR_buffer
3D 15N/13C-filtered NOESY13C-15N-ubiquitin_saturated_with_unlabeled_UBZisotropicMOPS_NMR_buffer

Software:

Analysis, CCPN - chemical shift assignment

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

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

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

TALOS+, Cornilescu, Delaglio and Bax - dihedral angles

NMR spectrometers:

  • Varian VNMRS 600 MHz
  • Varian VNMRS 800 MHz

Related Database Links:

BMRB 11505 11547 15047 15410 15689 15907 16228 16582 16626 16895 17181 17439 17769 17919 18582 18583 18584 18610 18611 18737 19406 19412 25123 25601 26604 4245 4375 25071
PDB
DBJ BAA03983 BAA09860 BAA11842 BAA11843 BAA23486
EMBL CAA26488 CAA28495 CAA30183 CAA30815 CAA33466
GB AAA02769 AAA28154 AAA28997 AAA28998 AAA28999
PIR I50437 I51568 I65237 JN0790 S13928
PRF 0412265A 1212243A 1212243B 1212243C 1212243D
REF NP_001005123 NP_001006688 NP_001009117 NP_001009202 NP_001009286
SP P0C273 P0C275 P0C276 P0CG47 P0CG48
TPD FAA00319
TPE CEL68433 CEL70397 CEL75964 CEL78064
TPG DAA18802 DAA20663 DAA20672 DAA24675 DAA28295
AlphaFold P0C273 P0C275 P0C276 P0CG47 P0CG48

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