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- PDB-7z21: BAF A12T bound to the lamin A/C Ig-fold domain -

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Basic information

Entry
Database: PDB / ID: 7z21
TitleBAF A12T bound to the lamin A/C Ig-fold domain
Components
  • Barrier-to-autointegration factor, N-terminally processed
  • Lamin-A/C
KeywordsPROTEIN BINDING / Complex / lamin A/C / BAF
Function / homology
Function and homology information


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 / DNA double-strand break attachment to nuclear envelope / Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / nuclear envelope 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 / 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 / mitotic nuclear membrane reassembly / 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 / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / negative regulation of type I interferon production / intermediate filament / 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 / negative regulation of release of cytochrome c from mitochondria / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / protein localization to nucleus / chromosome organization / heterochromatin formation / condensed chromosome / regulation of cell migration / Meiotic synapsis / negative regulation of innate immune response / negative regulation of extrinsic apoptotic signaling pathway / response to virus / regulation of protein stability / protein localization / structural constituent of cytoskeleton / nuclear matrix / DNA integration / protein import into nucleus / cellular senescence / Signaling by BRAF and RAF1 fusions / chromatin organization / nuclear envelope / site of double-strand break / cellular response to hypoxia / double-stranded DNA binding / nuclear membrane / response to oxidative stress / nuclear speck / negative regulation of cell population proliferation / positive regulation of gene expression / chromatin / structural molecule activity / perinuclear region of cytoplasm / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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. / Intermediate filament protein, conserved site / Intermediate filament protein ...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. / 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
Barrier-to-autointegration factor / Prelamin-A/C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.629 Å
AuthorsMarcelot, A. / Legrand, P. / Zinn-Justin, S.
Funding support France, European Union, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR- 10-INSB-05-01 France
H2020 Marie Curie Actions of the European Commission871037European Union
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: The BAF A12T mutation disrupts lamin A/C interaction, impairing robust repair of nuclear envelope ruptures in Nestor-Guillermo progeria syndrome cells.
Authors: Janssen, A. / Marcelot, A. / Breusegem, S. / Legrand, P. / Zinn-Justin, S. / Larrieu, D.
History
DepositionFeb 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Barrier-to-autointegration factor, N-terminally processed
B: Barrier-to-autointegration factor, N-terminally processed
C: Barrier-to-autointegration factor, N-terminally processed
D: Barrier-to-autointegration factor, N-terminally processed
E: Lamin-A/C
F: Lamin-A/C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,43110
Polymers74,2896
Non-polymers1424
Water12,538696
1
A: Barrier-to-autointegration factor, N-terminally processed
C: Barrier-to-autointegration factor, N-terminally processed
F: Lamin-A/C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2155
Polymers37,1453
Non-polymers712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Barrier-to-autointegration factor, N-terminally processed
D: Barrier-to-autointegration factor, N-terminally processed
E: Lamin-A/C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2155
Polymers37,1453
Non-polymers712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.11, 75.073, 65.034
Angle α, β, γ (deg.)90, 114.19, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Barrier-to-autointegration factor, N-terminally processed


Mass: 9901.208 Da / Num. of mol.: 4 / Mutation: A12T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BANF1, BAF, BCRG1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75531
#2: Protein Lamin-A/C / 70 kDa lamin / Renal carcinoma antigen NY-REN-32


Mass: 17342.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMNA, LMN1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02545
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 696 / 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: 1.89 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 3 M ammonium sulfate 0.1 M bicine pH 9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.63→46.54 Å / Num. obs: 68861 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 13.5 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.097 / Rrim(I) all: 0.172 / Net I/σ(I): 5.6
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 3 % / Rmerge(I) obs: 0.993 / Mean I/σ(I) obs: 1 / Num. unique obs: 5048 / CC1/2: 0.491 / Rpim(I) all: 0.68 / Rrim(I) all: 1.209 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSVERSION Jan 10, 2022 BUILT=20220110data reduction
autoPROC1.0.5 (20210716)data processing
STARANISO2.3.77data scaling
MOLREP11.7.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GHD

6ghd


Resolution: 1.629→14.9 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.869 / SU R Cruickshank DPI: 0.237 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.183 / SU Rfree Blow DPI: 0.158 / SU Rfree Cruickshank DPI: 0.153
RfactorNum. reflection% reflectionSelection details
Rfree0.3004 2931 -RANDOM
Rwork0.2684 ---
obs0.27 60425 87.5 %-
Displacement parametersBiso mean: 15.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.1694 Å20 Å2-0.031 Å2
2---0.288 Å20 Å2
3---0.1187 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 1.629→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4598 0 4 696 5298
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0079481HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9517160HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2864SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1540HARMONIC5
X-RAY DIFFRACTIONt_it9481HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion589SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies17HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact8193SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion13.7
LS refinement shellResolution: 1.63→1.68 Å
RfactorNum. reflection% reflection
Rfree0.282 68 -
Rwork0.3144 --
obs0.3125 1209 18.54 %

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