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BMRB: 34217

6F98

Solution structure of the RING domain of the E3 ubiquitin ligase HRD1

Authors

Kniss, A., Kazemi, S., Lohr, F., Guntert, P., Dotsch, V.

Assembly

E3 ubiquitin-protein ligase

Entity

1. E3 ubiquitin-protein ligase, entity 1 (polymer, Thiol state: all other bound), 78 monomers, 8972.277 Da Detail

GAEQLQNSAN DDNICIICMD ELIHSPNQQT WKNKNKKPKR LPCGHILHLS CLKNWMERSQ TCPICRLPVF DEKGNVVQ

2. E3 ubiquitin-protein ligase, entity ZN (non-polymer), 65.409 × 2 Da

Total weight

9103.096 Da

Max. entity weight

8972.277 Da

Entity Connection

na 8 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS15:SG	2:ZN1:ZN
2	na	sing	1:CYS18:SG	2:ZN1:ZN
3	na	sing	1:HIS48:ND1	2:ZN1:ZN
4	na	sing	1:CYS51:SG	2:ZN1:ZN
5	na	sing	1:CYS43:SG	2:ZN1:ZN
6	na	sing	1:HIS45:ND1	2:ZN1:ZN
7	na	sing	1:CYS62:SG	2:ZN1:ZN
8	na	sing	1:CYS65:SG	2:ZN1:ZN

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 89.3 %, Completeness (bb): 94.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.3 % (837 of 937)	88.2 % (439 of 498)	94.0 % (329 of 350)	77.5 % (69 of 89)
Backbone	94.3 % (432 of 458)	93.5 % (144 of 154)	96.1 % (222 of 231)	90.4 % (66 of 73)
Sidechain	86.3 % (478 of 554)	85.8 % (295 of 344)	92.8 % (180 of 194)	18.8 % (3 of 16)
Aromatic	95.7 % (44 of 46)	100.0 % (23 of 23)	90.5 % (19 of 21)	100.0 % (2 of 2)
Methyl	97.2 % (70 of 72)	100.0 % (36 of 36)	94.4 % (34 of 36)

1. entity 1

GAEQLQNSAN DDNICIICMD ELIHSPNQQT WKNKNKKPKR LPCGHILHLS CLKNWMERSQ TCPICRLPVF DEKGNVVQ

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.8 mM [U-98% 13C; U-98% 15N] E3 ubiquitin ligase Hrd1, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	E3 ubiquitin ligase Hrd1	[U-98% 13C; U-98% 15N]		0.8 mM

LACS Plot; CA

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

Referencing offset: -0.2 ppm, Outliers: 3 Detail

LACS Plot; CB

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

Referencing offset: -0.2 ppm, Outliers: 3 Detail

LACS Plot; HA

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

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.09 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6F98, Strand ID: A Detail

Release date

2019-01-21

Citation

Unique RING finger structure from the human HRD1 protein
Kniss, A.
Protein Sci. (2018), PubMed 30345569 , DOI 10.1002/pro.3532 , Abstract

Related entities 1. E3 ubiquitin-protein ligase, entity 1, : 1 : 7 : 101 entities Detail

Interaction partners 1. E3 ubiquitin-protein ligase, entity 1, : 53 interactors Detail

More details for 53 interactors identified by 8 citations

Experiments performed 12 experiments Detail

1 3D 1H-15N NOESY