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BMRB: 15160

2I5O

Solution Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Y-Polymerase Eta

Authors

Bomar, M.G., Zhou, P.

Assembly

polymerase eta UBZ domain

Entity

1. UBZ domain (polymer, Thiol state: all other bound), 39 monomers, 4416.960 Da Detail

GSHMAAEDQV PCEKCGSLVP VWDMPEHMDY HFALELQKS

2. ZN (non-polymer), 65.409 Da

Total weight

4482.369 Da

Max. entity weight

4416.96 Da

Entity Connection

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	2:ZN1:ZN	1:CYS12:SG
2	na	sing	2:ZN1:ZN	1:CYS15:SG
3	na	sing	2:ZN1:ZN	1:HIS27:NE2
4	na	sing	2:ZN1:ZN	1:HIS31:NE2

Source organism

Exptl. method

Refine. method

Structure originally calculated by torsion angle dynamics and refined by water refinement.

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 87.6 %, Completeness (bb): 79.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.6 % (388 of 443)	97.0 % (223 of 230)	74.1 % (129 of 174)	92.3 % (36 of 39)
Backbone	79.8 % (182 of 228)	93.5 % (72 of 77)	67.0 % (77 of 115)	91.7 % (33 of 36)
Sidechain	96.4 % (243 of 252)	98.7 % (151 of 153)	92.7 % (89 of 96)	100.0 % (3 of 3)
Aromatic	78.6 % (33 of 42)	90.5 % (19 of 21)	65.0 % (13 of 20)	100.0 % (1 of 1)
Methyl	100.0 % (30 of 30)	100.0 % (15 of 15)	100.0 % (15 of 15)

1. UBZ domain

GSHMAAEDQV PCEKCGSLVP VWDMPEHMDY HFALELQKS

Show sample condition

Sample #1

Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	UBZ domain	[U-100% 15N]		2 mM
2	phosphate	natural abundance		25 mM
3	KCL	natural abundance		100 mM

Sample #2

Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	UBZ domain	[U-100% 13C; U-100% 15N]		2 mM
5	phosphate	natural abundance		25 mM
6	KCL	natural abundance		100 mM

Sample #3

Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	UBZ domain	[U-10% 13C; U-100% 15N]		2 mM
8	phosphate	natural abundance		25 mM
9	KCL	natural abundance		100 mM

Protein Blocks Logo

Calculated from 15 models in PDB: 2I5O, Strand ID: A Detail

Release date

2007-03-05

Citation

Structure of the ubiquitin-binding zinc finger domain of human DNA Y-polymerase eta
Bomar, M.G., Pai, M., Tzeng, S., Li, S., Zhou, P.
EMBO Rep. (2007), 8, 247-251, PubMed 17304240 , DOI 10.1038/sj.embor.7400901 , Abstract

Related entities 1. UBZ domain, : 1 : 9 entities Detail

Interaction partners 1. UBZ domain, : 8 interactors Detail

More details for 8 interactors identified by 4 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	UBZ domain	[U-100% 15N]		2 mM
2	phosphate	natural abundance		25 mM
3	KCL	natural abundance		100 mM

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	UBZ domain	[U-10% 13C; U-100% 15N]		2 mM
8	phosphate	natural abundance		25 mM
9	KCL	natural abundance		100 mM

3 2D 1H-1H NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	UBZ domain	[U-100% 15N]		2 mM
2	phosphate	natural abundance		25 mM
3	KCL	natural abundance		100 mM

4 3D HCCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	UBZ domain	[U-100% 13C; U-100% 15N]		2 mM
5	phosphate	natural abundance		25 mM
6	KCL	natural abundance		100 mM

5 3D HNCO

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	UBZ domain	[U-100% 13C; U-100% 15N]		2 mM
5	phosphate	natural abundance		25 mM
6	KCL	natural abundance		100 mM

6 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	UBZ domain	[U-100% 13C; U-100% 15N]		2 mM
5	phosphate	natural abundance		25 mM
6	KCL	natural abundance		100 mM

7 3D HNCA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	UBZ domain	[U-100% 13C; U-100% 15N]		2 mM
5	phosphate	natural abundance		25 mM
6	KCL	natural abundance		100 mM

8 3D HN(CO)CA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	UBZ domain	[U-100% 13C; U-100% 15N]		2 mM
5	phosphate	natural abundance		25 mM
6	KCL	natural abundance		100 mM

9 2D 1H-13C HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	UBZ domain	[U-10% 13C; U-100% 15N]		2 mM
8	phosphate	natural abundance		25 mM
9	KCL	natural abundance		100 mM

10 3D HN(COCA)CB

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	UBZ domain	[U-100% 13C; U-100% 15N]		2 mM
5	phosphate	natural abundance		25 mM
6	KCL	natural abundance		100 mM

11 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	UBZ domain	[U-100% 15N]		2 mM
2	phosphate	natural abundance		25 mM
3	KCL	natural abundance		100 mM

12 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	UBZ domain	[U-100% 13C; U-100% 15N]		2 mM
5	phosphate	natural abundance		25 mM
6	KCL	natural abundance		100 mM

nullKeywords polymerase eta, translesion synthesis, ubiquitin-binding, UBZ domain, zinc finger