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- PDB-2pjh: Strctural Model of the p97 N domain- npl4 UBD complex -

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Basic information

Entry
Database: PDB / ID: 2pjh
TitleStrctural Model of the p97 N domain- npl4 UBD complex
Components
  • Nuclear protein localization protein 4 homolog
  • Transitional endoplasmic reticulum ATPase
KeywordsTRANSPORT PROTEIN / p97 / Ufd1 / npl4 / AAA / Atpase / PROTEIN BINDING
Function / homology
Function and homology information


UFD1-NPL4 complex / negative regulation of RIG-I signaling pathway / RHOH GTPase cycle / HSF1 activation / Translesion Synthesis by POLH / Protein methylation / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ovarian tumor domain proteases / Hedgehog ligand biogenesis ...UFD1-NPL4 complex / negative regulation of RIG-I signaling pathway / RHOH GTPase cycle / HSF1 activation / Translesion Synthesis by POLH / Protein methylation / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ovarian tumor domain proteases / Hedgehog ligand biogenesis / KEAP1-NFE2L2 pathway / ABC-family proteins mediated transport / Neddylation / positive regulation of ubiquitin-dependent protein catabolic process / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / protein-DNA covalent cross-linking repair / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / aggresome assembly / NADH metabolic process / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / vesicle-fusing ATPase / cellular response to misfolded protein / stress granule disassembly / negative regulation of protein localization to chromatin / positive regulation of mitochondrial membrane potential / retrograde protein transport, ER to cytosol / K48-linked polyubiquitin modification-dependent protein binding / nuclear outer membrane-endoplasmic reticulum membrane network / negative regulation of type I interferon production / regulation of synapse organization / positive regulation of ATP biosynthetic process / ATPase complex / ubiquitin-specific protease binding / Golgi organization / MHC class I protein binding / polyubiquitin modification-dependent protein binding / autophagosome maturation / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / proteasomal protein catabolic process / interstrand cross-link repair / ATP metabolic process / negative regulation of smoothened signaling pathway / ERAD pathway / Neutrophil degranulation / proteasome complex / viral genome replication / lipid droplet / ubiquitin binding / macroautophagy / ADP binding / positive regulation of protein-containing complex assembly / autophagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of canonical Wnt signaling pathway / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / myelin sheath / site of double-strand break / cellular response to heat / ATPase binding / ubiquitin-dependent protein catabolic process / protein phosphatase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / protein domain specific binding / DNA repair / lipid binding / glutamatergic synapse / ubiquitin protein ligase binding / DNA damage response / synapse / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Nuclear pore localisation protein Npl4, ubiquitin-like domain / Nuclear pore localisation protein NPL4 / NPL4, zinc-binding putative / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / Nuclear protein localization protein 4 / NPL4 family / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 ...Nuclear pore localisation protein Npl4, ubiquitin-like domain / Nuclear pore localisation protein NPL4 / NPL4, zinc-binding putative / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / Nuclear protein localization protein 4 / NPL4 family / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Zinc finger domain / Barwin-like endoglucanases / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / : / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / MPN domain / MPN domain profile. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Nuclear protein localization protein 4 homolog / Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / HADDOCK -
AuthorsIsaacson, R. / Pye, V.E. / Simpson, S. / Meyer, H.H. / Zhang, X. / Freemont, P.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Detailed structural insights into the p97-Npl4-Ufd1 interface.
Authors: Isaacson, R.L. / Pye, V.E. / Simpson, P. / Meyer, H.H. / Zhang, X. / Freemont, P.S. / Matthews, S.
History
DepositionApr 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear protein localization protein 4 homolog
B: Transitional endoplasmic reticulum ATPase


Theoretical massNumber of molelcules
Total (without water)30,8922
Polymers30,8922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativelowest energy

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Components

#1: Protein Nuclear protein localization protein 4 homolog / Protein NPL4


Mass: 8912.345 Da / Num. of mol.: 1 / Fragment: N domain (Residues 1-80)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: p97 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): bl21 / References: UniProt: P60670
#2: Protein Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg2+ / - ATPase p97 subunit / Valosin-containing protein / VCP


Mass: 21979.191 Da / Num. of mol.: 1 / Fragment: UBD (Residues 21-213)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: npl4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01853

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: Data was not available to correct the large RMS deviations in SER B 73

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Sample preparation

Details
Solution-IDContentsSolvent system
115N labelled p97 N domain in complex with npl4 UBDh20/d20
215N labelled npl4 UBD in complex with p97 N domainh20/d20
Sample conditionsIonic strength: 125mM NaCl / pH: 7.5 / Pressure: Atomospheric atm / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
HADDOCK1.3Bonvinstructure solution
HADDOCK1.3Bonvinrefinement
RefinementMethod: HADDOCK - / Software ordinal: 1 / Details: chemical shift based docking
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers submitted total number: 1

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