BMRB Entry 17824

Name: Rbx1
Published: 2012-03-26

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PDB ID: 2lgv
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17824
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Rbx1

Deposition date:

2011-08-02

Original release date:

2012-03-26

Authors:

Spratt, Donald; Shaw, Gary

Citation:

Citation: Spratt, Donald; Wu, Kenneth; Kovacev, Jordan; Pan, Zhen-Qiang; Shaw, Gary. "Selective recruitment of an E2~ubiquitin complex by an E3 ubiquitin ligase." J. Biol. Chem. 287, 17374-17385 (2012).
PubMed: 22433864

Assembly members:

Assembly members:
Rbx1, polymer, 100 residues, 11159.5 Da.
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Rbx1: GGGGTNSGAGKKRFEVKKSN ASAQSAWDIVVDNCAICRNH IMDLCIECQANQASATSEEC TVAWGVCNHAFHFHCISRWL KTRQVCPLDNREWEFQKYGH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	321
15N chemical shifts	76
1H chemical shifts	451

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Rbx1	1
2	ZINC ION_1	2
3	ZINC ION_2	2
4	ZINC ION_3	2

Entities:

Entity 1, Rbx1 100 residues - 11159.5 Da.

Residues G9-G11 represent the non-native N-terminus of the protein after TEV cleavage to remove a 6His affinity tag. Residues G1-G8 are spacer residues that were added to maintain proper sequence numbering.

1	GLY	GLY	GLY	GLY	THR	ASN	SER	GLY	ALA	GLY
2	LYS	LYS	ARG	PHE	GLU	VAL	LYS	LYS	SER	ASN
3	ALA	SER	ALA	GLN	SER	ALA	TRP	ASP	ILE	VAL
4	VAL	ASP	ASN	CYS	ALA	ILE	CYS	ARG	ASN	HIS
5	ILE	MET	ASP	LEU	CYS	ILE	GLU	CYS	GLN	ALA
6	ASN	GLN	ALA	SER	ALA	THR	SER	GLU	GLU	CYS
7	THR	VAL	ALA	TRP	GLY	VAL	CYS	ASN	HIS	ALA
8	PHE	HIS	PHE	HIS	CYS	ILE	SER	ARG	TRP	LEU
9	LYS	THR	ARG	GLN	VAL	CYS	PRO	LEU	ASP	ASN
10	ARG	GLU	TRP	GLU	PHE	GLN	LYS	TYR	GLY	HIS

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: sodium phosphate 20 mM; sodium chloride 100 mM; DTT 1 mM; entity_1, [U-98% 15N], 700 uM; H2O 90%; D2O 10%

sample_2: sodium phosphate 20 mM; sodium chloride 100 mM; DTT 1 mM; Rbx1, [U-98% 13C; U-98% 15N], 700 uM; H2O 90%; D2O 10%

sample_3: sodium phosphate 20 mM; sodium chloride 100 mM; DTT 1 mM; Rbx1, [U-98% 13C; U-98% 15N], 700 uM; D2O 100%

sample_conditions_1: ionic strength: 0.120 M; pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_3	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HN(CO)CA	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNHA	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_2	isotropic	sample_conditions_1

Software:

VNMRJ vVarian VnmrJ 2.2D, Varian - collection

NMRPipe v2009.015.15.35, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRDraw vVer 5.0 Rev 2009.244.15.09, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v8.0.rc47 with Java 1.6.0_26, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

TALOS vTALOSPlus, Cornilescu, Delaglio and Bax - geometry optimization

Procheck, Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Tho - refinement

NMR spectrometers:

Varian INOVA 600 MHz

PDB	2LGV
GB	EAW60402 EKC33263 KFM64926 KFP48973 KFQ68825
REF	XP_004063570 XP_008474369 XP_010219658 XP_011232809 XP_011232810

1	GLY	GLY	GLY	GLY	THR	ASN	SER	GLY	ALA	GLY
2	LYS	LYS	ARG	PHE	GLU	VAL	LYS	LYS	SER	ASN
3	ALA	SER	ALA	GLN	SER	ALA	TRP	ASP	ILE	VAL
4	VAL	ASP	ASN	CYS	ALA	ILE	CYS	ARG	ASN	HIS
5	ILE	MET	ASP	LEU	CYS	ILE	GLU	CYS	GLN	ALA
6	ASN	GLN	ALA	SER	ALA	THR	SER	GLU	GLU	CYS
7	THR	VAL	ALA	TRP	GLY	VAL	CYS	ASN	HIS	ALA
8	PHE	HIS	PHE	HIS	CYS	ILE	SER	ARG	TRP	LEU
9	LYS	THR	ARG	GLN	VAL	CYS	PRO	LEU	ASP	ASN
10	ARG	GLU	TRP	GLU	PHE	GLN	LYS	TYR	GLY	HIS

1	GLY	GLY	GLY	GLY	THR	ASN	SER	GLY	ALA	GLY
2	LYS	LYS	ARG	PHE	GLU	VAL	LYS	LYS	SER	ASN
3	ALA	SER	ALA	GLN	SER	ALA	TRP	ASP	ILE	VAL
4	VAL	ASP	ASN	CYS	ALA	ILE	CYS	ARG	ASN	HIS
5	ILE	MET	ASP	LEU	CYS	ILE	GLU	CYS	GLN	ALA
6	ASN	GLN	ALA	SER	ALA	THR	SER	GLU	GLU	CYS
7	THR	VAL	ALA	TRP	GLY	VAL	CYS	ASN	HIS	ALA
8	PHE	HIS	PHE	HIS	CYS	ILE	SER	ARG	TRP	LEU
9	LYS	THR	ARG	GLN	VAL	CYS	PRO	LEU	ASP	ASN
10	ARG	GLU	TRP	GLU	PHE	GLN	LYS	TYR	GLY	HIS