BMRB Entry 15592

Name: NMR structure of the ubiquitin associated (UBA) domain of p62 (SQSTM1) in complex with ubiquitin. RDC refined
Published: 2008-01-16

Click here to enlarge.

PDB ID: 2jy8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15592
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

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

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

NMR structure of the ubiquitin associated (UBA) domain of p62 (SQSTM1) in complex with ubiquitin. RDC refined

Deposition date:

2007-12-12

Original release date:

2008-01-16

Authors:

Long, Jed; Layfield, Robert; Searle, Mark

Citation:

Citation: Long, Jed; Gallagher, Thomas; Cavey, James; Sheppard, Paul; Ralston, Stuart; Layfield, Robert; Searle, Mark. "Ubiquitin recognition by the ubiquitin-associated domain of p62 involves a novel conformational switch" J. Biol. Chem. 283, 5427-5440 (2008).
PubMed: 18083707

Assembly members:

Assembly members:
P62_UBA, polymer, 52 residues, Formula weight is not available
ubiquitin, polymer, 76 residues, Formula weight is not available

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: pGEX-4T-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
P62_UBA: GSPPEADPRLIESLSQMLSM GFSDEGGWLTRLLQTKNYDI GAALDTIQYSKH
ubiquitin: MQIFVKTLTGKTITLEVESS DTIDNVKSKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
RDCs
- RDC_list_1

Data type	Count
13C chemical shifts	227
15N chemical shifts	53
1H chemical shifts	339
residual dipolar couplings	45

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	P62_UBA	1
2	ubiquitin	2

Entities:

Entity 1, P62_UBA 52 residues - Formula weight is not available

P62_UBA

1

GLY

SER

PRO

GLU

ALA

ASP

PRO

ARG

LEU

2

ILE

GLU

SER

LEU

SER

GLN

MET

LEU

SER

MET

3

GLY

PHE

SER

ASP

GLU

GLY

TRP

LEU

THR

4

ARG

LEU

GLN

THR

LYS

ASN

TYR

ASP

ILE

5

GLY

ALA

LEU

ASP

THR

ILE

GLN

TYR

SER

6

LYS

HIS

Entity 2, ubiquitin 76 residues - Formula weight is not available

1

MET

GLN

ILE

PHE

VAL

LYS

THR

LEU

THR

GLY

2

LYS

THR

ILE

THR

LEU

GLU

VAL

GLU

SER

3

ASP

THR

ILE

ASP

ASN

VAL

LYS

SER

LYS

ILE

4

GLN

ASP

LYS

GLU

GLY

ILE

PRO

ASP

GLN

5

GLN

ARG

LEU

ILE

PHE

ALA

GLY

LYS

GLN

LEU

6

GLU

ASP

GLY

ARG

THR

LEU

SER

ASP

TYR

ASN

7

ILE

GLN

LYS

GLU

SER

THR

LEU

HIS

LEU

VAL

8

LEU

ARG

LEU

ARG

GLY

Samples:

sample_1: entity, [U-100% 15N], 1 mM; ubiquitin 6 mM; potassium phosphate 50 mM; sodium chloride 50 mM; sodium azide 0.04%; D2O, [U-100% 2H], 10%; H2O 90%

sample_2: entity, [U-100% 13C; U-100% 15N], 1 mM; ubiquitin 6 mM; potassium phosphate 50 mM; sodium chloride 50 mM; sodium azide 0.04%; D2O, [U-100% 2H], 10%; H2O 90%

sample_3: entity, [U-100% 15N], 1 mM; ubiquitin 6 mM; potassium phosphate 50 mM; sodium chloride 50 mM; sodium azide 0.04%; D2O, [U-100% 2H], 10%; H2O 90%

sample_conditions_1: pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

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

Software:

X-PLOR NIH v2.14, Schwieters, Kuszewski, Tjandra and Clore - structure solution

xwinnmr v3.5, Bruker Biospin - collection, processing

CcpNMR v1.0.10, CCPN - chemical shift assignment, data analysis, peak picking

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

NMR spectrometers:

Bruker Avance 600 MHz

Related Database Links:

BMRB	11149 11443 15591 17024 4769 4983
PDB	1Q02 2JY7 2JY8 2K0B 2KNV 2RRU 3B0F 1OTR 1Q0W 1VW8 1VW9 1VWU 1VWV 1VXV 1VXW 1VXY 1VXZ 1WR1 2G3Q 2JT4 2JWZ 2L00 3CMM 3J60 3J80 3J81 3L0W 3L10 3OLM 3U5C 3U5E 3U5G 3U5I 4B6A 4BYL 4BYN 4BYT 4BYU 4CUW 4HCN 4II3 4NNJ 4Q5E 4Q5H
DBJ	BAC26183 BAG35358 BAG53577 BAG65614 BAI46491 BAA02154 BAA03764 BAA05085 BAA05670 BAA76889
EMBL	CAA69642 CAH90955 CAA07773 CAA10056 CAA11267 CAA11268 CAA21278
GB	AAA93299 AAB02908 AAB17127 AAC50535 AAC52070 AAA03351 AAA19247 AAA32904 AAA32905 AAA32906
REF	NP_001125548 NP_001135770 NP_001135771 NP_001156515 NP_001253287 NP_001031585 NP_001031824 NP_001042915 NP_001045980 NP_001049479
SP	O08623 Q13501 Q5RBA5 Q64337 B9DHA6 P05759 P0C016 P0C224 P0C8R3
TPG	DAA28341 DAA08405 DAA09244 DAA09283 DAA09489 DAA39608
PIR	G85036 JS0657 S28426 S42643 S49332
PRF	1101405A 1207189A 1515347A 1603402A 1604470A
TPD	FAA00316 FAA00317 FAA00318 FAA00319
TPE	CBF76581 CBF85986
AlphaFold	O08623 Q13501 Q5RBA5 Q64337 B9DHA6 P05759 P0C016 P0C224 P0C8R3

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks