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- PDB-2n7k: Unveiling the structural determinants of KIAA0323 binding prefere... -

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Basic information

Entry
Database: PDB / ID: 2n7k
TitleUnveiling the structural determinants of KIAA0323 binding preference for NEDD8
Components
  • NEDD8
  • Protein KHNYN
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


regulation of proteolysis / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / RNA endonuclease activity / Iron uptake and transport / protein modification process / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / protein tag activity ...regulation of proteolysis / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / RNA endonuclease activity / Iron uptake and transport / protein modification process / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / protein tag activity / UCH proteinases / protein localization / Cargo recognition for clathrin-mediated endocytosis / Neddylation / ubiquitin-dependent protein catabolic process / mRNA binding / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / proteolysis / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Ribonuclease Zc3h12a-like, NYN domain / : / Zc3h12a-like Ribonuclease NYN domain / Nedd8-like ubiquitin / K Homology domain, type 1 superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family ...Ribonuclease Zc3h12a-like, NYN domain / : / Zc3h12a-like Ribonuclease NYN domain / Nedd8-like ubiquitin / K Homology domain, type 1 superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Protein KHNYN / NEDD8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsSantonico, E. / Nepravishta, R. / Mattioni, A. / Valentini, E. / Mandaliti, W. / Procopio, R. / Iannuccelli, M. / Castagnoli, L. / Polo, S. / Paci, M. / Cesareni, G.
CitationJournal: To be Published
Title: Unveiling the structural determinants of KIAA0323 binding preference for NEDD8
Authors: Santonico, E. / Nepravishta, R. / Mattioni, A. / Valentini, E. / Mandaliti, W. / Procopio, R. / Iannuccelli, M. / Castagnoli, L. / Polo, S. / Paci, M. / Cesareni, G.
History
DepositionSep 14, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEDD8
B: Protein KHNYN


Theoretical massNumber of molelcules
Total (without water)15,3862
Polymers15,3862
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area804 Å2
ΔGint-9.4 kcal/mol
Surface area8661.7 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein NEDD8 / Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / ...Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / Ubiquitin-like protein Nedd8


Mass: 9086.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15843
#2: Protein Protein KHNYN / KH and NYN domain-containing protein


Mass: 6299.187 Da / Num. of mol.: 1 / Fragment: residues 627-678
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KHNYN, KIAA0323 / Production host: Escherichia coli (E. coli) / References: UniProt: O15037

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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 1H-15N NOESY
1313D 1H-15N TOCSY
1412D 1H-1H TOCSY
1513D 1H-15N TOCSY

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Sample preparation

DetailsContents: 0.15-1.5 mM [U-100% 15N] protein, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleUnits: mM / Component: entity_1-1 / Isotopic labeling: [U-100% 15N] / Conc. range: 0.15-1.5
Sample conditionsIonic strength: 0.02 / pH: 5.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 11

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