[English] 日本語
Yorodumi
- PDB-7z21: BAF A12T bound to the lamin A/C Ig-fold domain -

+
Open data


ID or keywords:

Loading...

-
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 / Breakdown of the nuclear lamina / DNA double-strand break attachment to nuclear envelope / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / nuclear envelope organization / nuclear pore localization ...structural constituent of nuclear lamina / negative regulation of mesenchymal cell proliferation / negative regulation of protein ADP-ribosylation / establishment or maintenance of microtubule cytoskeleton polarity / Breakdown of the nuclear lamina / DNA double-strand break attachment to nuclear envelope / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / nuclear envelope organization / nuclear pore localization / Nuclear Envelope Breakdown / lamin filament / protein localization to nuclear envelope / mitotic nuclear membrane reassembly / XBP1(S) activates chaperone genes / nuclear lamina / Initiation of Nuclear Envelope (NE) Reformation / regulation of protein localization to nucleus / intermediate filament / regulation of telomere maintenance / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of type I interferon production / negative regulation of viral genome replication / nuclear migration / muscle organ development / negative regulation of cGAS/STING signaling pathway / 2-LTR circle formation / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Vpr-mediated nuclear import of PICs / negative regulation of release of cytochrome c from mitochondria / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / protein localization to nucleus / chromosome organization / condensed chromosome / Meiotic synapsis / negative regulation of innate immune response / regulation of cell migration / negative regulation of extrinsic apoptotic signaling pathway / regulation of protein stability / DNA integration / structural constituent of cytoskeleton / response to virus / nuclear matrix / protein import into nucleus / Signaling by BRAF and RAF1 fusions / cellular senescence / intracellular protein localization / nuclear envelope / site of double-strand break / heterochromatin formation / chromatin organization / response to oxidative stress / double-stranded DNA binding / nuclear membrane / cellular response to hypoxia / nuclear speck / negative regulation of cell population proliferation / positive regulation of gene expression / chromatin / perinuclear region of cytoplasm / structural molecule activity / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 ...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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more