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BMRB: 25071

2MRF

NMR structure of the ubiquitin-binding zinc finger (UBZ) domain from human Rad18

Authors

Rizzo, A.A., Salerno, P.E., Bezsonova, I., Korzhnev, D.M.

Assembly

Rad18-UBZ

Entity

1. Rad18-UBZ (polymer), 33 monomers, 3622.074 Da Detail

GSRQVTKVDC PVCGVNIPES HINKHLDSCL SRE

2. ZINC ION (non-polymer), 65.409 Da

Total weight

3687.483 Da

Max. entity weight

3622.074 Da

Entity Connection

metal coordination 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:CYS10:SG	2:ZN1:ZN
2	metal coordination	sing	1:CYS13:SG	2:ZN1:ZN
3	metal coordination	sing	1:HIS25:SG	2:ZN1:ZN
4	metal coordination	sing	1:CYS29:SG	2:ZN1:ZN

Source organism

Exptl. method

Refine. method

simulated annealing/torsian angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 87.9 %, Completeness: 76.3 %, Completeness (bb): 82.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.3 % (277 of 363)	75.8 % (144 of 190)	75.5 % (105 of 139)	82.4 % (28 of 34)
Backbone	82.0 % (159 of 194)	83.3 % (55 of 66)	80.4 % (78 of 97)	83.9 % (26 of 31)
Sidechain	72.5 % (145 of 200)	71.8 % (89 of 124)	74.0 % (54 of 73)	66.7 % (2 of 3)
Aromatic	0.0 % (0 of 8)	0.0 % (0 of 4)	0.0 % (0 of 4)
Methyl	76.5 % (26 of 34)	76.5 % (13 of 17)	76.5 % (13 of 17)

1. Rad18-UBZ

GSRQVTKVDC PVCGVNIPES HINKHLDSCL SRE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details residues 198-227

#	Name	Isotope labeling	Type	Concentration
1	Rad18_UBZ	[U-13C; U-15N]		0.5 ~ 1.5 mM
2	MOPS-NaOH	natural abundance		25 mM
3	NaCl	natural abundance		50 mM
4	ZnCl2	natural abundance		0.05 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2MRF, Strand ID: A Detail

Release date

2014-09-18

Citation

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
Rizzo, A.A., Salerno, P.E., Bezsonova, I., Korzhnev, D.M.
Biochemistry (2014), 53, 5895-5906, PubMed 25162118 , DOI 10.1021/bi500823h , Abstract

Related entities 1. Rad18-UBZ, : 1 : 1 : 1 : 25 entities Detail

Interaction partners 1. Rad18-UBZ, : 28 interactors Detail

More details for 28 interactors identified by 13 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details residues 198-227

#	Name	Isotope labeling	Type	Concentration
1	Rad18_UBZ	[U-13C; U-15N]		0.5 ~ 1.5 mM
2	MOPS-NaOH	natural abundance		25 mM
3	NaCl	natural abundance		50 mM
4	ZnCl2	natural abundance		0.05 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 3D HNCO

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details residues 198-227

#	Name	Isotope labeling	Type	Concentration
1	Rad18_UBZ	[U-13C; U-15N]		0.5 ~ 1.5 mM
2	MOPS-NaOH	natural abundance		25 mM
3	NaCl	natural abundance		50 mM
4	ZnCl2	natural abundance		0.05 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details residues 198-227

#	Name	Isotope labeling	Type	Concentration
1	Rad18_UBZ	[U-13C; U-15N]		0.5 ~ 1.5 mM
2	MOPS-NaOH	natural abundance		25 mM
3	NaCl	natural abundance		50 mM
4	ZnCl2	natural abundance		0.05 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

4 3D HCCH-TOCSY

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details residues 198-227

#	Name	Isotope labeling	Type	Concentration
1	Rad18_UBZ	[U-13C; U-15N]		0.5 ~ 1.5 mM
2	MOPS-NaOH	natural abundance		25 mM
3	NaCl	natural abundance		50 mM
4	ZnCl2	natural abundance		0.05 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 3D HBHA(CO)NH

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details residues 198-227

#	Name	Isotope labeling	Type	Concentration
1	Rad18_UBZ	[U-13C; U-15N]		0.5 ~ 1.5 mM
2	MOPS-NaOH	natural abundance		25 mM
3	NaCl	natural abundance		50 mM
4	ZnCl2	natural abundance		0.05 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

6 3D 1H-15N NOESY

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details residues 198-227

#	Name	Isotope labeling	Type	Concentration
1	Rad18_UBZ	[U-13C; U-15N]		0.5 ~ 1.5 mM
2	MOPS-NaOH	natural abundance		25 mM
3	NaCl	natural abundance		50 mM
4	ZnCl2	natural abundance		0.05 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 3D 1H-13C NOESY

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details residues 198-227

#	Name	Isotope labeling	Type	Concentration
1	Rad18_UBZ	[U-13C; U-15N]		0.5 ~ 1.5 mM
2	MOPS-NaOH	natural abundance		25 mM
3	NaCl	natural abundance		50 mM
4	ZnCl2	natural abundance		0.05 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

8 3D CBCA(CO)NH

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details residues 198-227

#	Name	Isotope labeling	Type	Concentration
1	Rad18_UBZ	[U-13C; U-15N]		0.5 ~ 1.5 mM
2	MOPS-NaOH	natural abundance		25 mM
3	NaCl	natural abundance		50 mM
4	ZnCl2	natural abundance		0.05 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

9 3D CCH-TOCSY

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details residues 198-227

#	Name	Isotope labeling	Type	Concentration
1	Rad18_UBZ	[U-13C; U-15N]		0.5 ~ 1.5 mM
2	MOPS-NaOH	natural abundance		25 mM
3	NaCl	natural abundance		50 mM
4	ZnCl2	natural abundance		0.05 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

nullKeywords translesion synthesis, DNA repair