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- PDB-7ndy: Di-phosphorylated Barrier-to-Autointegration Factor (BAF) in comp... -

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Basic information

Entry
Database: PDB / ID: 7ndy
TitleDi-phosphorylated Barrier-to-Autointegration Factor (BAF) in complex with LEM domain of Emerin
Components
  • Barrier-to-autointegration factor, N-terminally processed
  • Emerin
KeywordsDNA BINDING PROTEIN / Phosphorylation Complex High Resolution
Function / homology
Function and homology information


TMEM240-body / nuclear membrane organization / negative regulation of protein ADP-ribosylation / Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / mitotic nuclear membrane reassembly / Initiation of Nuclear Envelope (NE) Reformation / RHOD GTPase cycle / nuclear outer membrane / regulation of canonical Wnt signaling pathway ...TMEM240-body / nuclear membrane organization / negative regulation of protein ADP-ribosylation / Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / mitotic nuclear membrane reassembly / Initiation of Nuclear Envelope (NE) Reformation / RHOD GTPase cycle / nuclear outer membrane / regulation of canonical Wnt signaling pathway / 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 / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of viral genome replication / negative regulation of cGAS/STING signaling pathway / 2-LTR circle formation / beta-tubulin binding / Vpr-mediated nuclear import of PICs / skeletal muscle cell differentiation / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / RHOG GTPase cycle / chromosome organization / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of fibroblast proliferation / condensed chromosome / RAC1 GTPase cycle / negative regulation of innate immune response / positive regulation of protein export from nucleus / muscle contraction / response to virus / negative regulation of canonical Wnt signaling pathway / cellular response to growth factor stimulus / DNA integration / spindle / chromatin organization / nuclear envelope / actin binding / double-stranded DNA binding / nuclear membrane / microtubule / response to oxidative stress / cadherin binding / chromatin / endoplasmic reticulum / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Emerin, LEM domain / Emerin / Barrier- to-autointegration factor, BAF / Barrier-to-autointegration factor, BAF superfamily / Barrier to autointegration factor / Barrier to autointegration factor / LEM domain / LEM domain / LEM domain profile. / in nuclear membrane-associated proteins / LEM/LEM-like domain superfamily
Similarity search - Domain/homology
Barrier-to-autointegration factor / Emerin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsMarcelot, A. / Le Du, M.H. / Hoffmann, G. / Zinn-Justin, S.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Di-phosphorylated BAF shows altered structural dynamics and binding to DNA, but interacts with its nuclear envelope partners.
Authors: Marcelot, A. / Petitalot, A. / Ropars, V. / Le Du, M.H. / Samson, C. / Dubois, S. / Hoffmann, G. / Miron, S. / Cuniasse, P. / Marquez, J.A. / Thai, R. / Theillet, F.X. / Zinn-Justin, S.
History
DepositionFeb 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 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
Item: _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
A: Barrier-to-autointegration factor, N-terminally processed
B: Barrier-to-autointegration factor, N-terminally processed
G: Emerin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6734
Polymers41,4343
Non-polymers2381
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, isothermal titration calorimetry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-4 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.05, 40.628, 43.224
Angle α, β, γ (deg.)69.51, 69.68, 85.03
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 10031.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BANF1, BAF, BCRG1 / Production host: Escherichia coli (E. coli) / References: UniProt: O75531
#2: Protein Emerin


Mass: 21372.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMD, EDMD, STA / Production host: Escherichia coli (E. coli) / References: UniProt: P50402
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Hepes Sodium salt 0.1 M pH 7.5 PEG 600 25% W/V

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.242→33.225 Å / Num. obs: 32449 / % possible obs: 84.8 % / Redundancy: 15 % / CC1/2: 0.989 / Net I/σ(I): 4.5
Reflection shellResolution: 1.242→1.411 Å / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1622 / CC1/2: 0.326 / Rpim(I) all: 0.527 / Rrim(I) all: 0.965

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ghd

6ghd


Resolution: 1.44→38.03 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.909 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.13 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.122
RfactorNum. reflection% reflectionSelection details
Rfree0.225 983 -RANDOM
Rwork0.1808 ---
obs0.1829 20430 57.2 %-
Displacement parametersBiso mean: 15.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.8125 Å2-1.4534 Å20.9865 Å2
2---0.6527 Å2-0.3211 Å2
3---2.4652 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.44→38.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 15 208 1972
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081840HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.872489HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d670SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes320HARMONIC5
X-RAY DIFFRACTIONt_it1840HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion219SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2077SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion14.58
LS refinement shellResolution: 1.44→1.56 Å
RfactorNum. reflection% reflection
Rfree0.2947 25 -
Rwork0.2196 --
obs0.2239 417 5.69 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4910.15720.29150.7886-0.15960.32160.03570.00870.0150.0087-0.0404-0.01180.015-0.01180.0047-0.0201-0.01720.0126-0.0247-0.0010.01692.3492-16.6061-16.5982
20.9691-0.19720.09550.59290.2290.45640.06240.00510.01360.0051-0.06210.00780.01360.0078-0.0003-0.0342-0.00820.0262-0.02910.00720.019410.01071.2639-28.8454
30.44060.00540.20211.73980.68112.2397-0.06770.0229-0.06220.02290.01860.0556-0.06220.05560.0491-0.020.0067-0.0149-0.02880.005-0.001818.1529-0.2069-7.0399
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ G|* }

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