BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 15592

Title: NMR structure of the ubiquitin associated (UBA) domain of p62 (SQSTM1) in complex with ubiquitin. RDC refined   PubMed: 18083707

Authors: Long, Jed; Layfield, Robert; Searle, Mark

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).

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

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

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

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

Data sets:
Data typeCount
13C chemical shifts227
15N chemical shifts53
1H chemical shifts339
residual dipolar couplings45

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1P62_UBA1
2ubiquitin2

Entities:

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

P62_UBA

1   GLYSERPROPROGLUALAASPPROARGLEU
2   ILEGLUSERLEUSERGLNMETLEUSERMET
3   GLYPHESERASPGLUGLYGLYTRPLEUTHR
4   ARGLEULEUGLNTHRLYSASNTYRASPILE
5   GLYALAALALEUASPTHRILEGLNTYRSER
6   LYSHIS

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

1   METGLNILEPHEVALLYSTHRLEUTHRGLY
2   LYSTHRILETHRLEUGLUVALGLUSERSER
3   ASPTHRILEASPASNVALLYSSERLYSILE
4   GLNASPLYSGLUGLYILEPROPROASPGLN
5   GLNARGLEUILEPHEALAGLYLYSGLNLEU
6   GLUASPGLYARGTHRLEUSERASPTYRASN
7   ILEGLNLYSGLUSERTHRLEUHISLEUVAL
8   LEUARGLEUARGGLYGLY

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HN(CA)COsample_2isotropicsample_conditions_1
2D 1H-15N HSQC-IPAPsample_3anisotropicsample_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
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