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- PDB-3gef: Crystal structure of the R482W mutant of lamin A/C -

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Basic information

Entry
Database: PDB / ID: 3gef
TitleCrystal structure of the R482W mutant of lamin A/C
ComponentsLamin-A/C
KeywordsSTRUCTURAL PROTEIN / immunoglobulin fold / lamin / Cardiomyopathy / Charcot-Marie-Tooth disease / Disease mutation / Intermediate filament / Limb-girdle muscular dystrophy / Lipoprotein / Nucleus / Phosphoprotein / Prenylation
Function / homology
Function and homology information


negative regulation of mesenchymal cell proliferation / structural constituent of nuclear lamina / establishment or maintenance of microtubule cytoskeleton polarity / ventricular cardiac muscle cell development / Breakdown of the nuclear lamina / DNA double-strand break attachment to nuclear envelope / Depolymerization of the Nuclear Lamina / nuclear envelope organization / nuclear pore localization / Nuclear Envelope Breakdown ...negative regulation of mesenchymal cell proliferation / structural constituent of nuclear lamina / establishment or maintenance of microtubule cytoskeleton polarity / ventricular cardiac muscle cell development / Breakdown of the nuclear lamina / DNA double-strand break attachment to nuclear envelope / Depolymerization of the Nuclear Lamina / nuclear envelope organization / nuclear pore localization / Nuclear Envelope Breakdown / lamin filament / protein localization to nuclear envelope / XBP1(S) activates chaperone genes / nuclear lamina / Initiation of Nuclear Envelope (NE) Reformation / regulation of protein localization to nucleus / nuclear migration / regulation of telomere maintenance / negative regulation of cardiac muscle hypertrophy in response to stress / intermediate filament / muscle organ development / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / negative regulation of release of cytochrome c from mitochondria / protein localization to nucleus / Meiotic synapsis / regulation of cell migration / negative regulation of extrinsic apoptotic signaling pathway / regulation of protein stability / structural constituent of cytoskeleton / nuclear matrix / heterochromatin formation / protein import into nucleus / cellular senescence / Signaling by BRAF and RAF1 fusions / nuclear envelope / protein localization / site of double-strand break / nuclear membrane / cellular response to hypoxia / nuclear speck / negative regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / structural molecule activity / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMagracheva, E. / Kozlov, S. / Stuart, C. / Wlodawer, A. / Zdanov, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of the lamin A/C R482W mutant responsible for dominant familial partial lipodystrophy (FPLD).
Authors: Magracheva, E. / Kozlov, S. / Stewart, C.L. / Wlodawer, A. / Zdanov, A.
History
DepositionFeb 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 19, 2014Group: Non-polymer description
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lamin-A/C
B: Lamin-A/C
C: Lamin-A/C
D: Lamin-A/C


Theoretical massNumber of molelcules
Total (without water)52,3784
Polymers52,3784
Non-polymers00
Water5,765320
1
A: Lamin-A/C


Theoretical massNumber of molelcules
Total (without water)13,0951
Polymers13,0951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lamin-A/C


Theoretical massNumber of molelcules
Total (without water)13,0951
Polymers13,0951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lamin-A/C


Theoretical massNumber of molelcules
Total (without water)13,0951
Polymers13,0951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Lamin-A/C


Theoretical massNumber of molelcules
Total (without water)13,0951
Polymers13,0951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.195, 84.035, 98.750
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 / 70 kDa lamin / Renal carcinoma antigen NY-REN-32


Mass: 13094.613 Da / Num. of mol.: 4 / Fragment: Lamin A/C globular domain / Mutation: R482W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Lamin A/C 435-552, LMN1, LMNA / Plasmid: pET41a / Production host: Escherichia coli (E. coli) / References: UniProt: P02545
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.9M sodium citrate, 20mM DTT, 0.1M sodium cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.09 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.09 Å / Relative weight: 1
ReflectionResolution: 1.5→45 Å / Num. all: 83468 / Num. obs: 68652 / % possible obs: 82.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 31.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IFR

1ifr


Resolution: 1.5→45 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 6970 -RANDOM
Rwork0.2141 ---
all0.229 83468 --
obs-68652 82.2 %-
Displacement parametersBiso max: 90.33 Å2 / Biso mean: 33.028 Å2 / Biso min: 15.81 Å2
Baniso -1Baniso -2Baniso -3
1-3.891 Å20 Å20 Å2
2---11.434 Å20 Å2
3---7.543 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3672 0 0 320 3992
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg2

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