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BMRB: 30590

6NXK

Structure of WHB in complex with Ubiquitin Variant

Authors

Edmond, R.W., Grace, C.R.

Assembly

Uncharacterized protein, Polyubiquitin-B, Anaphase-promoting complex subunit 2

Entity

1. Uncharacterized protein, Polyubiquitin-B, Anaphase-promoting complex subunit 2, entity 1 (polymer, Thiol state: not present), 75 monomers, 8541.689 Da Detail

GMQIFVDTVQ WKTITLEVEP SDTIENVKAK IQDKEGIPPD QQRLIFAGKQ LEDGRTLSDY NIQKESALIL LLTLR

2. Uncharacterized protein, Polyubiquitin-B, Anaphase-promoting complex subunit 2, entity 2 (polymer, Thiol state: not present), 75 monomers, 8543.619 Da Detail

GMQIFVDTVQ WKTITLEVEP SDTIENVKAK IQDKEGIPPD QQRLDFAGKQ LEDGRTLSDY NIQKESALIL LLTLR

3. Uncharacterized protein, Polyubiquitin-B, Anaphase-promoting complex subunit 2, entity 3 (polymer, Thiol state: all free), 90 monomers, 10251.59 Da Detail

GSESDSGMAS QADQKEEELL LFWTYIQAML TNLESLSLDR IYNMLRMFVV TGPALAEIDL QELQGYLQKK VRDQQLVYSA GVYRLPKNCS

Total weight

27336.898 Da

Max. entity weight

10251.59 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 87.1 %, Completeness: 73.0 %, Completeness (bb): 77.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	73.0 % (2099 of 2874)	73.1 % (1098 of 1502)	70.2 % (778 of 1108)	84.5 % (223 of 264)
Backbone	77.0 % (1096 of 1424)	78.8 % (382 of 485)	72.7 % (514 of 707)	86.2 % (200 of 232)
Sidechain	69.5 % (1165 of 1677)	70.4 % (716 of 1017)	67.8 % (426 of 628)	71.9 % (23 of 32)
Aromatic	67.8 % (103 of 152)	81.6 % (62 of 76)	52.1 % (38 of 73)	100.0 % (3 of 3)
Methyl	72.2 % (221 of 306)	73.9 % (113 of 153)	70.6 % (108 of 153)

1. entity 1

GMQIFVDTVQ WKTITLEVEP SDTIENVKAK IQDKEGIPPD QQRLIFAGKQ LEDGRTLSDY NIQKESALIL LLTLR

2. entity 2

GMQIFVDTVQ WKTITLEVEP SDTIENVKAK IQDKEGIPPD QQRLDFAGKQ LEDGRTLSDY NIQKESALIL LLTLR

3. entity 3

GSESDSGMAS QADQKEEELL LFWTYIQAML TNLESLSLDR IYNMLRMFVV TGPALAEIDL QELQGYLQKK VRDQQLVYSA GVYRLPKNCS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 0.5 mM [U-99% 13C; U-99% 15N] WHB, 0.6 mM Ubiquitin Variant, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.5 mM
2	entity_2	[U-99% 13C; U-99% 15N]	0.5 mM
3	entity_3	[U-99% 13C; U-99% 15N]	0.5 mM
4	Ubiquitin Variant	natural abundance	0.6 mM
5	NaCl	natural abundance	100 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	indirect	na	-6.625 Hz	external	indirect	0.25
¹H	DSS	protons	-26.5 Hz	external	direct	0.0
¹⁵N	indirect	na	0.265 Hz	external	indirect	-0.1

Referencing offset: -0.22 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	indirect	na	-6.625 Hz	external	indirect	0.25
¹H	DSS	protons	-26.5 Hz	external	direct	0.0
¹⁵N	indirect	na	0.265 Hz	external	indirect	-0.1

Referencing offset: -0.22 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	indirect	na	-6.625 Hz	external	indirect	0.25
¹H	DSS	protons	-26.5 Hz	external	direct	0.0
¹⁵N	indirect	na	0.265 Hz	external	indirect	-0.1

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	indirect	na	-6.625 Hz	external	indirect	0.25
¹H	DSS	protons	-26.5 Hz	external	direct	0.0
¹⁵N	indirect	na	0.265 Hz	external	indirect	-0.1

Referencing offset: -0.16 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6OB1, Strand ID: A, B, C Detail

Release date

2019-08-06

Citation

Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site
Watson, E.R., Grace, C.R.R., Zhang, W., Miller, D.J., Davidson, I.F., Prabu, J.R., Yu, S., Bolhuis, D.L., Kulko, E.T., Vollrath, R., Haselbach, D., Stark, H., Peters, J.M., Brown, N.G., Sidhu, S.S., Schulman, B.A.
Proc. Natl. Acad. Sci. U. S. A. (2019), 116, 17280-17289, PubMed 31350353 , DOI 10.1073/pnas.1902889116 , Abstract

Related entities 1. Uncharacterized protein, Polyubiquitin-B, Anaphase-promoting complex subunit 2, entity 1, : 322 entities Detail

Related entities 2. Uncharacterized protein, Polyubiquitin-B, Anaphase-promoting complex subunit 2, entity 2, : 322 entities Detail

Related entities 3. Uncharacterized protein, Polyubiquitin-B, Anaphase-promoting complex subunit 2, entity 3, : 1 : 2 : 12 : 18 entities Detail

Interaction partners 3. Uncharacterized protein, Polyubiquitin-B, Anaphase-promoting complex subunit 2, entity 3, : 34 interactors Detail

More details for 34 interactors identified by 11 citations

Experiments performed 23 experiments Detail

1 2D 1H-15N HSQC