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- PDB-1ufg: Solution structure of immunoglobulin like domain of mouse nuclear... -

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Basic information

Entry
Database: PDB / ID: 1ufg
TitleSolution structure of immunoglobulin like domain of mouse nuclear lamin
ComponentsLamin A
KeywordsSTRUCTURAL PROTEIN / immunoglobulin like fold / nuclear lamin / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Breakdown of the nuclear lamina / : / : / Nuclear Envelope Breakdown / Depolymerization of the Nuclear Lamina / Initiation of Nuclear Envelope (NE) Reformation / negative regulation of mesenchymal cell proliferation / protein localization => GO:0008104 / establishment or maintenance of microtubule cytoskeleton polarity / ventricular cardiac muscle cell development ...Breakdown of the nuclear lamina / : / : / Nuclear Envelope Breakdown / Depolymerization of the Nuclear Lamina / Initiation of Nuclear Envelope (NE) Reformation / negative regulation of mesenchymal cell proliferation / protein localization => GO:0008104 / establishment or maintenance of microtubule cytoskeleton polarity / ventricular cardiac muscle cell development / nuclear envelope organization / lamin filament / negative regulation of adipose tissue development / protein phosphatase 1 binding / regulation of protein localization to nucleus / regulation of telomere maintenance / negative regulation of cardiac muscle hypertrophy in response to stress / muscle organ development / establishment of cell polarity / nucleus organization / negative regulation of release of cytochrome c from mitochondria / protein localization to nucleus / positive regulation of osteoblast differentiation / regulation of cell migration / negative regulation of extrinsic apoptotic signaling pathway / regulation of protein stability / nuclear matrix / protein import into nucleus / nuclear envelope / cellular response to hypoxia / nuclear membrane / nuclear body / negative regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Lamin Tail domain / : / Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain ...Lamin Tail domain / : / Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKobayashi, N. / Kigawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of immunoglobulin like domain of mouse nuclear lamin
Authors: Kobayashi, N. / Kigawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S.
History
DepositionMay 29, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 1.4Dec 27, 2023Group: 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: Lamin A


Theoretical massNumber of molelcules
Total (without water)16,2831
Polymers16,2831
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 Lamin A / nuclear lamin


Mass: 16282.997 Da / Num. of mol.: 1 / Fragment: C-terminal immunoglobulin like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 1200006N04 / Plasmid: P011206-07 / References: UniProt: P48678

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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
1323D 13C separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.88mM lamin U-15N, 13C, 20mM phosphate buffer NA, 100mM NaCl, 1mM d10-DTT, 0.02% NaN3, 10% D2O90% H2O/10% D2O
20.70mM lamin U-15N, 13C, 20mM phosphate buffer NA, 100mM NaCl, 1mM d10-DTT, 0.02% NaN3, 100% D2O100% D2O
Sample conditionsIonic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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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
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe2002045Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.816Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
CYANA1.0.7Guentert, P.refinement
RefinementMethod: torsion angle 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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