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- PDB-6snz: Crystal structure of lamin A coil1b tetramer -

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Basic information

Entry
Database: PDB / ID: 6snz
TitleCrystal structure of lamin A coil1b tetramer
ComponentsPrelamin-A/C
KeywordsNUCLEAR PROTEIN / intermediate filament / coiled coil / nuclear lamin
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 / DNA double-strand break attachment to nuclear envelope / Depolymerization of the Nuclear Lamina / 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 / DNA double-strand break attachment to nuclear envelope / Depolymerization of the Nuclear Lamina / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLilina, A.V. / Chernyatina, A.A. / Guzenko, D. / Strelkov, S.V.
Funding support Belgium, France, 2items
OrganizationGrant numberCountry
KU LeuvenCELSA18/044 Belgium
Synchrotron Light Research Institute20170756 France
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Lateral A11type tetramerization in lamins.
Authors: Lilina, A.V. / Chernyatina, A.A. / Guzenko, D. / Strelkov, S.V.
History
DepositionAug 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.2Jan 22, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prelamin-A/C
B: Prelamin-A/C
C: Prelamin-A/C
D: Prelamin-A/C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0876
Polymers72,9024
Non-polymers1842
Water2,036113
1
A: Prelamin-A/C
B: Prelamin-A/C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5433
Polymers36,4512
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-80 kcal/mol
Surface area22650 Å2
MethodPISA
2
C: Prelamin-A/C
D: Prelamin-A/C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5433
Polymers36,4512
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-76 kcal/mol
Surface area21090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.070, 37.470, 101.680
Angle α, β, γ (deg.)90.00, 94.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Prelamin-A/C


Mass: 18225.594 Da / Num. of mol.: 4
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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 8K 10%, Imodazole 0.1M, Calcium acetate 0.2M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.07169 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07169 Å / Relative weight: 1
ReflectionResolution: 2.6→35.15 Å / Num. obs: 20594 / % possible obs: 96.97 % / Redundancy: 6 % / Biso Wilson estimate: 50.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1318 / Rpim(I) all: 0.05835 / Rrim(I) all: 0.1446 / Net I/σ(I): 8.62
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.645 / Num. unique obs: 1810 / CC1/2: 0.644 / Rpim(I) all: 0.9139 / % possible all: 86.65

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CCFold generated model

Resolution: 2.6→35.15 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1221 6 %random
Rwork0.254 ---
obs-20594 96.97 %-
Displacement parametersBiso mean: 89 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4814 0 12 113 4939

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