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- PDB-1ifr: Structure of Lamin A/C Globular Domain -

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Basic information

Entry
Database: PDB / ID: 1ifr
TitleStructure of Lamin A/C Globular Domain
ComponentsLamin A/CPre-Lamin A/C
KeywordsIMMUNE SYSTEM / immunoglobulin
Function / homology
Function and homology information


negative regulation of mesenchymal cell proliferation / DNA double-strand break attachment to nuclear envelope / establishment or maintenance of microtubule cytoskeleton polarity / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / Breakdown of the nuclear lamina / Nuclear Envelope Breakdown / nuclear envelope organization / nuclear pore localization / protein localization to nuclear envelope ...negative regulation of mesenchymal cell proliferation / DNA double-strand break attachment to nuclear envelope / establishment or maintenance of microtubule cytoskeleton polarity / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / Breakdown of the nuclear lamina / Nuclear Envelope Breakdown / nuclear envelope organization / nuclear pore localization / protein localization to nuclear envelope / lamin filament / nuclear lamina / XBP1(S) activates chaperone genes / Initiation of Nuclear Envelope (NE) Reformation / regulation of protein localization to nucleus / nuclear migration / regulation of telomere maintenance / muscle organ development / intermediate filament / negative regulation of cardiac muscle hypertrophy in response to stress / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / negative regulation of release of cytochrome c from mitochondria / protein localization to nucleus / heterochromatin formation / regulation of cell migration / Meiotic synapsis / negative regulation of extrinsic apoptotic signaling pathway / regulation of protein stability / protein localization / structural constituent of cytoskeleton / nuclear matrix / protein import into nucleus / cellular senescence / Signaling by BRAF and RAF1 fusions / site of double-strand break / nuclear envelope / cellular response to hypoxia / nuclear membrane / nuclear speck / negative regulation of cell population proliferation / structural molecule activity / positive regulation of gene expression / perinuclear region of cytoplasm / nucleoplasm / nucleus / identical protein binding / 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 / Intermediate filament (IF) rod domain profile. ...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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsDhe-Paganon, S. / Werner, E.D. / Shoelson, S.E.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structure of the globular tail of nuclear lamin.
Authors: Dhe-Paganon, S. / Werner, E.D. / Chi, Y.I. / Shoelson, S.E.
History
DepositionApr 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Lamin A/C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4782
Polymers13,3861
Non-polymers921
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.430, 52.550, 67.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lamin A/C / Pre-Lamin A/C


Mass: 13385.991 Da / Num. of mol.: 1 / Fragment: residues 436-552
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02545
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.75 Å3/Da / Density % sol: 29.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4000, ammonium acetate, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 %PEG40001reservoir
20.2 Mammonium acetate1reservoir
310 mMdithiothreitol1reservoir
40.1 MTris-HCl1reservoirpH8.5
520 mg/mlprotein1drop
65 mMTris-HCl1droppH8.0
70.1 M1dropNaCl
810 mMdithiothreitol1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.5418 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1

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Processing

SoftwareName: CNS / Classification: refinement
RefinementResolution: 1.4→50 Å /
RfactorNum. reflection
Rwork0.216 -
obs-18892
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms878 0 6 106 990
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.238 / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0056
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.41

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