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- PDB-2yuj: Solution structure of human ubiquitin fusion degradation protein ... -

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Basic information

Entry
Database: PDB / ID: 2yuj
TitleSolution structure of human ubiquitin fusion degradation protein 1 homolog UFD1
ComponentsUbiquitin fusion degradation 1-like
KeywordsPROTEIN BINDING / ubiquitin-dependent proteolytic / degradation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


UFD1-NPL4 complex / negative regulation of RIG-I signaling pathway / VCP-NPL4-UFD1 AAA ATPase complex / cellular response to misfolded protein / K48-linked polyubiquitin modification-dependent protein binding / retrograde protein transport, ER to cytosol / negative regulation of type I interferon production / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / ERAD pathway ...UFD1-NPL4 complex / negative regulation of RIG-I signaling pathway / VCP-NPL4-UFD1 AAA ATPase complex / cellular response to misfolded protein / K48-linked polyubiquitin modification-dependent protein binding / retrograde protein transport, ER to cytosol / negative regulation of type I interferon production / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / ERAD pathway / skeletal system development / Translesion Synthesis by POLH / KEAP1-NFE2L2 pathway / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / cysteine-type deubiquitinase activity / Ub-specific processing proteases / nucleoplasm / nucleus / cytosol
Similarity search - Function
Ubiquitin fusion degradation protein UFD1, N-terminal domain / Ubiquitin fusion degradation protein Ufd1-like / Ufd1-like, Nn domain / : / : / Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 1 / Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 2 / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases ...Ubiquitin fusion degradation protein UFD1, N-terminal domain / Ubiquitin fusion degradation protein Ufd1-like / Ufd1-like, Nn domain / : / : / Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 1 / Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 2 / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ubiquitin recognition factor in ER-associated degradation protein 1 / Ubiquitin recognition factor in ER-associated degradation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsSaito, K. / Tomizawa, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of human ubiquitin fusion degradation protein 1 homolog UFD1
Authors: Saito, K. / Tomizawa, T. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / pdbx_nmr_software ...audit_author / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _audit_author.name / _pdbx_nmr_software.name ..._audit_author.name / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin fusion degradation 1-like


Theoretical massNumber of molelcules
Total (without water)21,2741
Polymers21,2741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11130 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin fusion degradation 1-like


Mass: 21274.270 Da / Num. of mol.: 1 / Fragment: UFD1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: AB1165_B04 / Plasmid: P061225-60 / References: UniProt: Q541A5, UniProt: Q92890*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1mM protein, 20mM d-Tris-HCl, 100mM NaCl, 1mM d-DTT, 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3brukercollection
NMRPipe2006delaglioprocessing
NMRView5johnsondata analysis
CNS1.1structure solution
CNS1.1refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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