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- PDB-3v5b: Structure of Coil 2b of human lamin -

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Basic information

Entry
Database: PDB / ID: 3v5b
TitleStructure of Coil 2b of human lamin
ComponentsPrelamin-A/C
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


structural constituent of nuclear lamina / negative regulation of mesenchymal cell proliferation / establishment or maintenance of microtubule cytoskeleton polarity / ventricular cardiac muscle cell development / Breakdown of the nuclear lamina / Depolymerization of the Nuclear Lamina / DNA double-strand break attachment to nuclear envelope / Nuclear Envelope Breakdown / nuclear envelope organization / nuclear pore localization ...structural constituent of nuclear lamina / negative regulation of mesenchymal cell proliferation / establishment or maintenance of microtubule cytoskeleton polarity / ventricular cardiac muscle cell development / Breakdown of the nuclear lamina / Depolymerization of the Nuclear Lamina / DNA double-strand break attachment to nuclear envelope / Nuclear Envelope Breakdown / nuclear envelope organization / nuclear pore localization / lamin filament / protein localization to nuclear envelope / 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 / negative regulation of cardiac muscle hypertrophy in response to stress / muscle organ development / intermediate filament / 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 / nuclear envelope / site of double-strand break / cellular response to hypoxia / nuclear membrane / nuclear speck / negative regulation of cell population proliferation / positive regulation of gene expression / structural molecule activity / perinuclear region of cytoplasm / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
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 ...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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBollati, M. / Bolognesi, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2012
Title: Structures of the lamin A/C R335W and E347K mutants: Implications for dilated cardiolaminopathies.
Authors: Bollati, M. / Barbiroli, A. / Favalli, V. / Arbustini, E. / Charron, P. / Bolognesi, M.
History
DepositionDec 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Jun 20, 2018Group: Data collection / Category: diffrn_radiation
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_scattering_type
Revision 1.3Feb 28, 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

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Assembly

Deposited unit
A: Prelamin-A/C


Theoretical massNumber of molelcules
Total (without water)8,9051
Polymers8,9051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Prelamin-A/C

A: Prelamin-A/C


Theoretical massNumber of molelcules
Total (without water)17,8102
Polymers17,8102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area3820 Å2
ΔGint-37 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.020, 90.020, 74.722
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Prelamin-A/C / Lamin-A/C / 70 kDa lamin / Renal carcinoma antigen NY-REN-32


Mass: 8905.142 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMNA, LMN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02545

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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: 4.91 Å3/Da / Density % sol: 74.93 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 30% 2-methyl-2,4-pentanediol, 0.1 M Hepes pH 7.5, 0.5 M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9769 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2010
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9769 Å / Relative weight: 1
ReflectionResolution: 3→74.7 Å / Num. obs: 3889 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 106.77 Å2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
BUSTER2.11.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→19.49 Å / Cor.coef. Fo:Fc: 0.8857 / Cor.coef. Fo:Fc free: 0.8077 / SU R Cruickshank DPI: 0.568 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.326 475 12.4 %RANDOM
Rwork0.2804 ---
all0.2864 ---
obs0.2864 3830 99.4 %-
Displacement parametersBiso mean: 101.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.8781 Å20 Å20 Å2
2---0.8781 Å20 Å2
3---1.7562 Å2
Refine analyzeLuzzati coordinate error obs: 1.004 Å
Refinement stepCycle: LAST / Resolution: 3→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms619 0 0 0 619
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.009621HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.13824HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d260SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes0.006924HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0.01386HARMONIC5
X-RAY DIFFRACTIONt_it621HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion27.77
X-RAY DIFFRACTIONt_chiral_improper_torsion76SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact650SEMIHARMONIC4
LS refinement shellResolution: 3→3.35 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3697 122 11.66 %
Rwork0.3077 924 -
all0.3152 1046 -
obs--99.4 %

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