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- PDB-1nj3: Structure and Ubiquitin Interactions of the Conserved NZF Domain ... -

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Basic information

Entry
Database: PDB / ID: 1nj3
TitleStructure and Ubiquitin Interactions of the Conserved NZF Domain of Npl4
ComponentsNPL4
KeywordsPROTEIN BINDING / NZF domain / Npl4 / rubredoxin knuckle / beta-ribbon / zinc-finger / ubiquitin
Function / homology
Function and homology information


Translesion Synthesis by POLH / UFD1-NPL4 complex / Neddylation / negative regulation of RIG-I signaling pathway / KEAP1-NFE2L2 pathway / VCP-NPL4-UFD1 AAA ATPase complex / retrograde protein transport, ER to cytosol / negative regulation of type I interferon production / Golgi organization / ERAD pathway ...Translesion Synthesis by POLH / UFD1-NPL4 complex / Neddylation / negative regulation of RIG-I signaling pathway / KEAP1-NFE2L2 pathway / VCP-NPL4-UFD1 AAA ATPase complex / retrograde protein transport, ER to cytosol / negative regulation of type I interferon production / Golgi organization / ERAD pathway / ubiquitin binding / ATPase binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / protein-containing complex binding / zinc ion binding / nucleus / cytosol
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 / Zinc finger domain / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily ...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 / Zinc finger domain / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / MPN domain / MPN domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Nuclear protein localization protein 4 homolog
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / Torsion Angle Dynamics, Simulated annealing
AuthorsWang, B. / Alam, S.L. / Meyer, H.H. / Payne, M. / Stemmler, T.L. / Davis, D.R. / Sundquist, W.I.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Structure and ubiquitin interactions of the conserved zinc finger domain of Npl4.
Authors: Wang, B. / Alam, S.L. / Meyer, H.H. / Payne, M. / Stemmler, T.L. / Davis, D.R. / Sundquist, W.I.
#1: Journal: Embo J. / Year: 2000
Title: A complex of mammalian ufd1 and nlp4 links the AAA-ATPase, p97, to ubiquitin and nuclear transport
Authors: Meyer, H.H. / Shorter, J.G. / Pappin, D. / Warren, G.
#2: Journal: Embo J. / Year: 2002
Title: Direct binding of ubiquitin conjugates by the mammalian p97 adapter complexes, p47 and ufd1-Npl4
Authors: Meyer, H.H. / Wang, Y. / Warren, G.
History
DepositionDec 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations
Category: pdbx_database_related / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_related.db_id
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NPL4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4422
Polymers3,3771
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide NPL4


Mass: 3376.865 Da / Num. of mol.: 1 / Fragment: NZF domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Npl4 / Plasmid: PGEX-4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9ES54
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CB
121HN(CA)CO
131H(CCO)NH-TOCSY
141(H)C(CO)NH-TOCSY
1513D 13C-separated NOESY
1613D 15N-separated NOESY

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Sample preparation

DetailsContents: 1mM Npl4 NZF domain, U-15N,13C; 20 mM sodium Phosphate, pH 5.5, 50mM NaCl, 5 mM BME,90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 70 mM / pH: 5.5 / Pressure: ambient / Temperature: 291 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian UNITYPLUSVarianUNITYPLUS5002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARRENrefinement
DYANA1.5Guntert, P., Mumenthaler, C., Wuthrich, K.refinement
Felix97processing
Sparky3.106data analysis
RefinementMethod: Torsion Angle Dynamics, Simulated annealing / Software ordinal: 1
Details: Inital structures from Torsion Angle Dynamics (DYANA) were regularized with a gentle annelaing protocol in CNS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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