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- PDB-6rpr: LEM domain of Emerin mutant T43I in complex with BAF dimer and th... -

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Basic information

Entry
Database: PDB / ID: 6rpr
TitleLEM domain of Emerin mutant T43I in complex with BAF dimer and the Igfold of the lamin A/C
Components
  • LEM domain of emerin mutant T43I
  • Prelamin-A/C
  • barrier to autointegration factor (BAF)
KeywordsDNA BINDING PROTEIN / Nuclear membrane protein
Function / homology
Function and homology information


TMEM240-body / nuclear membrane organization / structural constituent of nuclear lamina / negative regulation of mesenchymal cell proliferation / negative regulation of protein ADP-ribosylation / 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 ...TMEM240-body / nuclear membrane organization / structural constituent of nuclear lamina / negative regulation of mesenchymal cell proliferation / negative regulation of protein ADP-ribosylation / 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 / mitotic nuclear membrane reassembly / nuclear lamina / XBP1(S) activates chaperone genes / Initiation of Nuclear Envelope (NE) Reformation / regulation of protein localization to nucleus / RHOD GTPase cycle / nuclear outer membrane / regulation of canonical Wnt signaling pathway / nuclear migration / regulation of telomere maintenance / negative regulation of cardiac muscle hypertrophy in response to stress / nuclear inner membrane / muscle organ development / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / negative regulation of type I interferon production / intermediate filament / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of viral genome replication / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / negative regulation of cGAS/STING signaling pathway / 2-LTR circle formation / beta-tubulin binding / negative regulation of release of cytochrome c from mitochondria / Vpr-mediated nuclear import of PICs / skeletal muscle cell differentiation / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / protein localization to nucleus / RHOG GTPase cycle / chromosome organization / RAC2 GTPase cycle / RAC3 GTPase cycle / heterochromatin formation / negative regulation of fibroblast proliferation / condensed chromosome / regulation of cell migration / Meiotic synapsis / RAC1 GTPase cycle / negative regulation of innate immune response / positive regulation of protein export from nucleus / muscle contraction / negative regulation of extrinsic apoptotic signaling pathway / response to virus / regulation of protein stability / negative regulation of canonical Wnt signaling pathway / protein localization / structural constituent of cytoskeleton / cellular response to growth factor stimulus / nuclear matrix / DNA integration / spindle / protein import into nucleus / cellular senescence / Signaling by BRAF and RAF1 fusions / chromatin organization / nuclear envelope / actin binding / site of double-strand break / cellular response to hypoxia / double-stranded DNA binding / nuclear membrane / microtubule / response to oxidative stress / nuclear speck / cadherin binding / negative regulation of cell population proliferation / positive regulation of gene expression / chromatin / structural molecule activity / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / DNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Emerin, LEM domain / Emerin / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #40 / Barrier-to-autointegration factor, BAF / Lamin Tail domain / Barrier- to-autointegration factor, BAF / Barrier-to-autointegration factor, BAF superfamily / Barrier to autointegration factor / Barrier to autointegration factor / Lamin tail domain superfamily ...Emerin, LEM domain / Emerin / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #40 / Barrier-to-autointegration factor, BAF / Lamin Tail domain / Barrier- to-autointegration factor, BAF / Barrier-to-autointegration factor, BAF superfamily / Barrier to autointegration factor / Barrier to autointegration factor / Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / LEM domain / LEM domain / LEM domain profile. / in nuclear membrane-associated proteins / LEM/LEM-like domain superfamily / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / 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 / DNA polymerase; domain 1 / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Barrier-to-autointegration factor / Prelamin-A/C / Emerin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsEssawy, N. / Samson, C.
Funding support France, 2items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural BiologyANR-10-INSB-05-01 France
European Communitys Seventh Framework Programme653706
CitationJournal: Cells / Year: 2019
Title: An Emerin LEM-Domain Mutation Impairs Cell Response to Mechanical Stress.
Authors: Essawy, N. / Samson, C. / Petitalot, A. / Moog, S. / Bigot, A. / Herrada, I. / Marcelot, A. / Arteni, A.A. / Coirault, C. / Zinn-Justin, S.
History
DepositionMay 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Prelamin-A/C
D: barrier to autointegration factor (BAF)
E: barrier to autointegration factor (BAF)
G: LEM domain of emerin mutant T43I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7837
Polymers37,4944
Non-polymers2883
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-42 kcal/mol
Surface area16110 Å2
Unit cell
Length a, b, c (Å)80.200, 81.490, 64.880
Angle α, β, γ (deg.)90.000, 121.370, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Prelamin-A/C


Mass: 12945.543 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
#2: Protein barrier to autointegration factor (BAF)


Mass: 9713.026 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O75531*PLUS
#3: Protein/peptide LEM domain of emerin mutant T43I


Mass: 5122.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P50402*PLUS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 18% PEG 3350, 100 mM Tris Bis pH 5.5, 0.1 M NH4SO4

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.26→40.74 Å / Num. obs: 16448 / % possible obs: 98.04 % / Redundancy: 4.5 % / Biso Wilson estimate: 55.09 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09554 / Rpim(I) all: 0.04968 / Rrim(I) all: 0.1061 / Net I/σ(I): 11.74
Reflection shellResolution: 2.26→2.34 Å / Num. unique obs: 16448

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GHD

6ghd


Resolution: 2.26→40 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.897 / SU R Cruickshank DPI: 0.314 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.302 / SU Rfree Blow DPI: 0.22 / SU Rfree Cruickshank DPI: 0.226
RfactorNum. reflection% reflectionSelection details
Rfree0.244 823 5 %RANDOM
Rwork0.196 ---
obs0.198 16448 98.1 %-
Displacement parametersBiso max: 159.53 Å2 / Biso mean: 47.15 Å2 / Biso min: 26.23 Å2
Baniso -1Baniso -2Baniso -3
1--2.2831 Å20 Å21.8072 Å2
2---3.9984 Å20 Å2
3---6.2815 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 2.26→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2639 0 15 83 2737
Biso mean--130.19 44.67 -
Num. residues----333
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d959SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes389HARMONIC5
X-RAY DIFFRACTIONt_it2703HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion328SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3032SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2703HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3642HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion18.99
LS refinement shellResolution: 2.26→2.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2853 142 5.01 %
Rwork0.2349 2694 -
all0.2375 2836 -
obs--94.32 %

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