BMRB: 11342

Solution Structure of the RING domain of the human RING-box protein 2

Authors

Miyamoto, K., Tomizawa, T., Koshiba, S., Watanabe, S., Harada, T., Kigawa, T., Yokoyama, S.

Assembly

RING-box protein 2

Entity

1. RING domain (polymer, Thiol state: free and other bound), 81 monomers, 9231.458 Da Detail

GSSGSSGMWS WDVECDTCAI CRVQVMDACL RCQAENKQED CVVVWGECNH SFHNCCMSLW VKQNNRCPLC QQDWVVQRIG K

2. ZN (non-polymer), 65.409 × 3 Da

Total weight

9427.685 Da

Max. entity weight

9231.458 Da

Entity Connection

na 12 Detail

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ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS18:SG	2:ZN1:ZN
2	na	sing	1:CYS21:SG	2:ZN1:ZN
3	na	sing	1:HIS53:ND1	2:ZN1:ZN
4	na	sing	1:CYS56:SG	2:ZN1:ZN
5	na	sing	1:CYS29:SG	2:ZN1:ZN
6	na	sing	1:CYS32:SG	2:ZN1:ZN
7	na	sing	1:CYS41:SG	2:ZN1:ZN
8	na	sing	1:CYS55:SG	2:ZN1:ZN
9	na	sing	1:HIS50:ND1	2:ZN1:ZN
10	na	sing	1:CYS48:SG	2:ZN1:ZN
11	na	sing	1:CYS67:SG	2:ZN1:ZN
12	na	sing	1:CYS70:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.1 %, Completeness: 96.1 %, Completeness (bb): 94.6 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	96.1 % (878 of 914)	95.8 % (455 of 475)	96.8 % (331 of 342)	94.8 % (92 of 97)
Backbone	94.6 % (458 of 484)	94.0 % (156 of 166)	95.4 % (227 of 238)	93.8 % (75 of 80)
Sidechain	97.4 % (493 of 506)	96.8 % (299 of 309)	98.3 % (177 of 180)	100.0 % (17 of 17)
Aromatic	100.0 % (78 of 78)	100.0 % (39 of 39)	100.0 % (34 of 34)	100.0 % (5 of 5)
Methyl	100.0 % (64 of 64)	100.0 % (32 of 32)	100.0 % (32 of 32)

1. RING domain

GSSGSSGMWS WDVECDTCAI CRVQVMDACL RCQAENKQED CVVVWGECNH SFHNCCMSLW VKQNNRCPLC QQDWVVQRIG K

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.001) atm, Temperature 296 (±0.1) K, pH 7.0 (±0.05), Details 1.11mM RING domain {U-13C,15N;} 20mM {d-Tris-HCl(pH7.0);} 100mM {NaCl;} 1mM {d-DTT;} 0.02% {NaN3;} 0.05mM {ZNCl2;} 1.0mM {IDA;} 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RING domain	[U-13C; U-15N]	protein	1.11 mM
2	d-Tris-HCl	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	100 mM
4	d-DTT	natural abundance	salt	1 mM
5	NaN3	natural abundance	salt	0.02 %
6	ZnCl2	natural abundance	salt	0.05 mM
7	IDA	natural abundance	salt	1.0 mM
8	H2O		solvent	90 %
9	D2O		solvent	10 %

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LACS Plot; CA

Referencing offset: -0.27 ppm, Outliers: 4 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CB

Referencing offset: -0.27 ppm, Outliers: 4 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; HA

Referencing offset: -0.07 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CO

Referencing offset: 0.28 ppm, Outliers: 3 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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Protein Blocks Logo

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

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Release date

2011-08-18

Citation

Molecular basis of cullin-3 (Cul3) ubiquitin ligase subversion by vaccinia virus protein A55
Miyamoto, K., Tomizawa, T., Koshiba, S., Watanabe, S., Harada, T., Kigawa, T., Yokoyama, S.
J. Biol. Chem. (2019), 294, 6416-6429, PubMed 30819806 , DOI 10.1074/jbc.RA118.006561 , Abstract

Related entities 1. RING domain, : 1 : 8 : 160 entities Detail

Interaction partners 1. RING domain, : 26 interactors Detail

Experiments performed 2 experiments Detail