BMRB Entry 16114

Name: Solution structure of a Ubiquitin/UIM fusion protein
Published: 2010-02-11

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PDB ID: 2kdi
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16114
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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:

Solution structure of a Ubiquitin/UIM fusion protein

Deposition date:

2009-01-09

Original release date:

2010-02-11

Authors:

Sgourakis, Nikolaos; Patel, Mayank; Garcia, Angel; Makhatadze, George; McCallum, Scott

Citation:

Citation: Sgourakis, Nikolaos; Patel, Mayank; Garcia, Angel; Makhatadze, George; McCallum, Scott. "Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain." J. Mol. Biol. 396, 1128-1144 (2010).
PubMed: 20053359

Assembly members:

Assembly members:
Ubiquitin/UIM_fusion_protein, polymer, 114 residues, Formula weight is not available

Natural source:

Natural source: Common Name: baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Ubiquitin/UIM_fusion_protein: MHHHHHHGEFQIFAKTLTGK TITLEVESSDTIDNVKSKIQ DKEGIPPDQQRLIWAGKQLE DGRTLSDYNIQRESTLHLVL RLRGGSMGGAADEEELIRKA IELSLKESRNSGGY

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
RDCs

Data type	Count
13C chemical shifts	324
15N chemical shifts	105
1H chemical shifts	684

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Ubiquitin/UIM fusion protein	1

Entities:

Entity 1, Ubiquitin/UIM fusion protein 114 residues - Formula weight is not available

1

MET

HIS

GLY

GLU

PHE

2

GLN

ILE

PHE

ALA

LYS

THR

LEU

THR

GLY

LYS

3

THR

ILE

THR

LEU

GLU

VAL

GLU

SER

ASP

4

THR

ILE

ASP

ASN

VAL

LYS

SER

LYS

ILE

GLN

5

ASP

LYS

GLU

GLY

ILE

PRO

ASP

GLN

6

ARG

LEU

ILE

TRP

ALA

GLY

LYS

GLN

LEU

GLU

7

ASP

GLY

ARG

THR

LEU

SER

ASP

TYR

ASN

ILE

8

GLN

ARG

GLU

SER

THR

LEU

HIS

LEU

VAL

LEU

9

ARG

LEU

ARG

GLY

SER

MET

GLY

ALA

10

ALA

ASP

GLU

LEU

ILE

ARG

LYS

ALA

11

ILE

GLU

LEU

SER

LEU

LYS

GLU

SER

ARG

ASN

12

SER

GLY

TYR

Samples:

sample_1: Ubiquitin/UIM fusion protein, [U-100% 13C; U-100% 15N], 1.24 mM; sodium azide 3 mM; sodium phosphate 20 mM; sodium chloride 50 mM; H2O 95%; D2O 5%

sample_2: Ubiquitin/UIM fusion protein, [U-100% 15N], 1.1 mM; sodium azide 3 mM; sodium phosphate 20 mM; sodium chloride 50 mM; H2O 95%; D2O 5%

sample_3: Ubiquitin/UIM fusion protein, [U-100% 15N], 0.5 mM; sodium azide 3 mM; sodium phosphate 20 mM; sodium chloride 50 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 0.103 M; pH: 6; pressure: 1 atm; temperature: 300 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HN(CO)CACB	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
2D HN-IPAP	sample_3	anisotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D (H)C(CCO)NH-TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	anisotropic	sample_conditions_1
2D HN-IPAP	sample_2	anisotropic	sample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - processing

SPARKY v3.111, Goddard - chemical shift assignment, data analysis, peak picking

X-PLOR v2.18, Brunger - data analysis, geometry optimization, refinement, structure solution

TALOS v2003.027.13.05, Cornilescu, Delaglio and Bax - data analysis, structure solution

PALES, Markus Zweckstetter and Ad Bax - data analysis

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 600 MHz

PDB	2KDI
DBJ	BAO40007
EMBL	CDO91688
GB	KGQ91175 KGR10456 KGT69098 KGU29735 KHC54981