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- PDB-2k89: Solution structure of a novel Ubiquitin-binding domain from Human... -

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Basic information

Entry
Database: PDB / ID: 2k89
TitleSolution structure of a novel Ubiquitin-binding domain from Human PLAA (PFUC, Gly76-Pro77 cis isomer)
ComponentsPhospholipase A-2-activating protein
KeywordsPROTEIN BINDING / Ubiquitin binding / WD repeat
Function / homology
Function and homology information


positive regulation of synaptic vesicle recycling / positive regulation of phospholipase A2 activity / negative regulation of protein K63-linked ubiquitination / ubiquitin recycling / phospholipase A2 activator activity / positive regulation of neuron migration / positive regulation of dendrite extension / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / prostaglandin metabolic process / phospholipid metabolic process ...positive regulation of synaptic vesicle recycling / positive regulation of phospholipase A2 activity / negative regulation of protein K63-linked ubiquitination / ubiquitin recycling / phospholipase A2 activator activity / positive regulation of neuron migration / positive regulation of dendrite extension / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / prostaglandin metabolic process / phospholipid metabolic process / ubiquitin binding / macroautophagy / nervous system development / proteasome-mediated ubiquitin-dependent protein catabolic process / cellular response to lipopolysaccharide / inflammatory response / synapse / signal transduction / extracellular exosome / nucleus / cytoplasm
Similarity search - Function
PFU (PLAA family ubiquitin binding), C-terminal domain / PUL domain / PLAA family ubiquitin binding domain / PFU domain superfamily / PUL domain / PFU (PLAA family ubiquitin binding) / PFU domain profile. / PUL domain profile. / Ubiquitin-like (UB roll) / Armadillo-like helical ...PFU (PLAA family ubiquitin binding), C-terminal domain / PUL domain / PLAA family ubiquitin binding domain / PFU domain superfamily / PUL domain / PFU (PLAA family ubiquitin binding) / PFU domain profile. / PUL domain profile. / Ubiquitin-like (UB roll) / Armadillo-like helical / Armadillo-type fold / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Phospholipase A-2-activating protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsFu, Q.S. / Zhou, C.J. / Gao, H.C. / Lin, D.H. / Hu, H.Y.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural Basis for Ubiquitin Recognition by a Novel Domain from Human Phospholipase A2-activating Protein.
Authors: Fu, Q.S. / Zhou, C.J. / Gao, H.C. / Jiang, Y.J. / Zhou, Z.R. / Hong, J. / Yao, W.M. / Song, A.X. / Lin, D.H. / Hu, H.Y.
History
DepositionSep 4, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A-2-activating protein


Theoretical massNumber of molelcules
Total (without water)9,0321
Polymers9,0321
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 20015 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Phospholipase A-2-activating protein / PLA2P / PLAP


Mass: 9032.011 Da / Num. of mol.: 1 / Fragment: UNP residues 386-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAA, PLAP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y263

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D H(CCO)NH
1613D HNHA
1713D 1H-15N NOESY
1823D (H)CCH-TOCSY
1923D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] PFUC_cis, 90% H2O, 10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] PFUC_cis, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPFUC_cis[U-99% 13C; U-99% 15N]1
1 mMPFUC_cis[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 50mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger, Adams, Clore, Gros, Nilges and Read / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures were calculated with aria/cns using torsion angle dynamics
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 15 structures for lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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