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- PDB-2dzm: Solution Structure of the Ubiquitin-like Domain in Human FAS-asso... -

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Basic information

Entry
Database: PDB / ID: 2dzm
TitleSolution Structure of the Ubiquitin-like Domain in Human FAS-associated factor 1 (hFAF1)
ComponentsFAS-associated factor 1
KeywordsStructural Genomics Unknown Function / ubiquitin-like domain / FAS-associated factor 1 / hFAF1 / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / cytoplasmic sequestering of NF-kappaB / CD95 death-inducing signaling complex / protein kinase regulator activity / VCP-NPL4-UFD1 AAA ATPase complex / regulation of protein catabolic process / NF-kappaB binding / regulation of cell adhesion / ERAD pathway ...ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / cytoplasmic sequestering of NF-kappaB / CD95 death-inducing signaling complex / protein kinase regulator activity / VCP-NPL4-UFD1 AAA ATPase complex / regulation of protein catabolic process / NF-kappaB binding / regulation of cell adhesion / ERAD pathway / heat shock protein binding / positive regulation of DNA replication / ubiquitin binding / positive regulation of protein-containing complex assembly / positive regulation of protein catabolic process / nuclear envelope / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of apoptotic process / protein domain specific binding / ubiquitin protein ligase binding / protein kinase binding / apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / nucleoplasm / nucleus / cytosol
Similarity search - Function
FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / : / Fas-associated factor 1 / UAS / : / UAS / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain ...FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / : / Fas-associated factor 1 / UAS / : / UAS / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Thioredoxin-like superfamily / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
FAS-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsZhao, C. / Sato, M. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of the Ubiquitin-like Domain in Human FAS-associated factor 1 (hFAF1)
Authors: Zhao, C. / Sato, M. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S.
History
DepositionSep 29, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 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: FAS-associated factor 1


Theoretical massNumber of molelcules
Total (without water)10,9651
Polymers10,9651
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)20 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein FAS-associated factor 1 / Protein FAF1 / hFAF1


Mass: 10965.333 Da / Num. of mol.: 1 / Fragment: ubiquitin-like domain, residues 8-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: FAF1 / Plasmid: P060327-21 / References: UniProt: Q9UNN5

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 1.17mM ubiquitin-like domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9748Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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