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BMRB: 17024

2L00

Solution structure of the non-covalent complex of the ZNF216 A20 domain with ubiquitin

Authors

Garner, T.P., Long, J.E., Searle, M.S., Layfield, R.

Assembly

Znf A20:ubiquitin complex

Entity

1. ZNF216-A20 (polymer, Thiol state: all other bound), 62 monomers, 6533.223 Da Detail

GSMAQETNQT PGPMLCSTGC GFYGNPRTNG MCSVCYKEHL QRQQNSGRMS PMGTASGSNS PT

2. ubiquitin (polymer, Thiol state: not present), 76 monomers, 8556.668 Da Detail

MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

3. ZN (non-polymer, Thiol state: not present), 65.409 Da

Total weight

15155.3 Da

Max. entity weight

8556.668 Da

Entity Connection

na 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS16:SG	3:ZN1:ZN
2	na	sing	1:CYS20:SG	3:ZN1:ZN
3	na	sing	1:CYS32:SG	3:ZN1:ZN
4	na	sing	1:CYS35:SG	3:ZN1:ZN

Source organism

Rattus norvegicus , Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

Rigid Body Docking, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 45.7 %, Completeness: 30.0 %, Completeness (bb): 39.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	30.0 % (467 of 1556)	26.7 % (218 of 818)	30.9 % (182 of 589)	45.0 % (67 of 149)
Backbone	39.7 % (323 of 814)	35.9 % (102 of 284)	41.1 % (164 of 399)	43.5 % (57 of 131)
Sidechain	22.4 % (194 of 865)	21.7 % (116 of 534)	21.7 % (68 of 313)	55.6 % (10 of 18)
Aromatic	19.4 % (12 of 62)	38.7 % (12 of 31)	0.0 % (0 of 31)
Methyl	19.4 % (24 of 124)	17.7 % (11 of 62)	21.0 % (13 of 62)

1. ZNF216-A20

GSMAQETNQT PGPMLCSTGC GFYGNPRTNG MCSVCYKEHL QRQQNSGRMS PMGTASGSNS PT

2. ubiquitin

MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.05) K, pH 7 (±0.1), Details 50uM ZnCl2 used 0.1 mM DSS used for referencing

#	Name	Isotope labeling	Concentration
1	ZNF216-A20	natural abundance	4 (±0.1) mM
2	ZnCl2	natural abundance	50 (±0.2) uM
3	DSS	natural abundance	0.1 (±0.01) mM
4	TRIS	natural abundance	5 (±0.5) mM
5	sodium chloride	natural abundance	50 (±5.0) mM
6	ubiquitin	[U-100% 15N]	1 (±0.1) mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.05) K, pH 7 (±0.1), Details The spin label MTSL was covalently attached to a K48C mutant of ubiquitin to measure inter molecular PRE

#	Name	Isotope labeling	Concentration
9	ZNF216-A20	[U-100% 15N]	1.0 (±0.1) mM
10	ZnCl2	natural abundance	50 (±0.2) uM
11	MTSL	natural abundance	4 (±0.1) mM
12	TRIS	natural abundance	5 (±0.5) mM
13	sodium chloride	natural abundance	50 (±5.0) mM
14	ubiquitin	natural abundance	4 (±0.1) mM
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.05) K, pH 7 (±0.1), Details 50 uM ZnCl2 added 0.1 mM DSS used

#	Name	Isotope labeling	Concentration
17	ZNF216-A20	[U-100% 13C; U-100% 15N]	0.8 (±0.2) mM
18	ZnCl2	natural abundance	50 (±0.2) uM
19	DSS	natural abundance	0.1 (±0.01) mM
20	TRIS	natural abundance	5 (±0.5) mM
21	sodium chloride	natural abundance	50 (±5.0) mM
22	ubiquitin	natural abundance	2 (±0.1) mM
23	H2O	natural abundance	90 %
24	D2O	natural abundance	10 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.05) K, pH 7 (±0.1), Details Sample 2 soaked in 5% PAG gel

#	Name	Isotope labeling	Concentration
25	ZNF216-A20	[U-100% 15N]	1.0 (±0.1) mM
26	ZnCl2	natural abundance	50 (±0.2) uM
27	DSS	natural abundance	0.1 (±0.01) mM
28	TRIS	natural abundance	5 (±0.5) mM
29	sodium chloride	natural abundance	50 (±5.0) mM
30	Polyacrylamide gel	natural abundance	5 (±0.5) %
31	ubiquitin	natural abundance	4 (±0.1) mM
32	H2O	natural abundance	90 %
33	D2O	natural abundance	10 %

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.05) K, pH 7 (±0.1), Details Sample 2 soaked in 5% PAG gel

#	Name	Isotope labeling	Concentration
34	ZNF216-A20	natural abundance	4 (±0.1) mM
35	ZnCl2	natural abundance	50 (±0.2) uM
36	DSS	natural abundance	0.1 (±0.01) mM
37	TRIS	natural abundance	5 (±0.5) mM
38	sodium chloride	natural abundance	50 (±5.0) mM
39	Polyacrylamide gel	natural abundance	5 (±0.5) %
40	ubiquitin	[U-100% 15N]	1 (±0.1) mM
41	H2O	natural abundance	90 %
42	D2O	natural abundance	10 %

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.05) K, pH 7 (±0.1), Details 50 uM ZnCl2 added 0.1 mM DSS used

#	Name	Isotope labeling	Concentration
43	ZNF216-A20	natural abundance	2 (±0.2) mM
44	ZnCl2	natural abundance	50 (±0.2) uM
45	DSS	natural abundance	0.1 (±0.01) mM
46	TRIS	natural abundance	5 (±0.5) mM
47	sodium chloride	natural abundance	50 (±5.0) mM
48	ubiquitin	[U-100% 13C; U-100% 15N]	1 (±0.1) mM
49	H2O	natural abundance	90 %
50	D2O	natural abundance	10 %

Sample #7

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.05) K, pH 7 (±0.1), Details 50uM ZnCl2 used 0.1 mM DSS used for referencing

#	Name	Isotope labeling	Concentration
51	ZNF216-A20	[U-100% 15N]	1 (±0.1) mM
52	ZnCl2	natural abundance	50 (±0.2) uM
53	DSS	natural abundance	0.1 (±0.01) mM
54	TRIS	natural abundance	5 (±0.5) mM
55	sodium chloride	natural abundance	50 (±5.0) mM
56	ubiquitin	natural abundance	4 (±0.1) mM
57	H2O	natural abundance	90 %
58	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.14 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.14 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.15 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2L00, Strand ID: A, B Detail

Release date

2012-08-01

Citation

Co-localisation of ubiquitin receptors ZNF216 and p62 in a ubiquitin-mediated ternary complex
Garner, T.P., Strachan, J., Long, J.E., Layfield, R., Searle, M.S.
Nat. Struct. Biol.

Related entities 1. ZNF216-A20, : 1 : 1 : 6 : 22 entities Detail

Related entities 2. ubiquitin, : 21 : 119 : 186 entities Detail

Interaction partners 1. ZNF216-A20, : 8 interactors Detail

More details for 8 interactors identified by 6 citations