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- PDB-6ghd: Structural analysis of the ternary complex between lamin A/C, BAF... -

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Basic information

Entry
Database: PDB / ID: 6ghd
TitleStructural analysis of the ternary complex between lamin A/C, BAF and emerin identifies an interface disrupted in autosomal recessive progeroid diseases
Components
  • Barrier-to-autointegration factor
  • Emerin
  • Prelamin-A/C
KeywordsPROTEIN BINDING / nuclear envelope / gene expression / ternary complex
Function / homology
Function and homology information


TMEM240-body / nuclear membrane organization / negative regulation of mesenchymal cell proliferation / DNA double-strand break attachment to nuclear envelope / negative regulation of protein ADP-ribosylation / establishment or maintenance of microtubule cytoskeleton polarity / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / Breakdown of the nuclear lamina / Nuclear Envelope Breakdown ...TMEM240-body / nuclear membrane organization / negative regulation of mesenchymal cell proliferation / DNA double-strand break attachment to nuclear envelope / negative regulation of protein ADP-ribosylation / establishment or maintenance of microtubule cytoskeleton polarity / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / Breakdown of the nuclear lamina / Nuclear Envelope Breakdown / nuclear envelope organization / nuclear pore localization / protein localization to nuclear envelope / lamin filament / nuclear lamina / mitotic nuclear membrane reassembly / XBP1(S) activates chaperone genes / Initiation of Nuclear Envelope (NE) Reformation / RHOD GTPase cycle / nuclear outer membrane / regulation of protein localization to nucleus / regulation of canonical Wnt signaling pathway / nuclear migration / regulation of telomere maintenance / muscle organ development / intermediate filament / nuclear inner membrane / negative regulation of cardiac muscle hypertrophy in response to stress / 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 cGAS/STING signaling pathway / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / negative regulation of viral genome replication / beta-tubulin binding / 2-LTR circle formation / 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 / RAC3 GTPase cycle / RAC2 GTPase cycle / heterochromatin formation / negative regulation of fibroblast proliferation / regulation of cell migration / condensed chromosome / RAC1 GTPase cycle / Meiotic synapsis / negative regulation of innate immune response / positive regulation of protein export from nucleus / muscle contraction / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of canonical Wnt signaling pathway / response to virus / regulation of protein stability / protein localization / structural constituent of cytoskeleton / spindle / cellular response to growth factor stimulus / nuclear matrix / DNA integration / protein import into nucleus / cellular senescence / Signaling by BRAF and RAF1 fusions / site of double-strand break / nuclear envelope / actin binding / chromatin organization / cellular response to hypoxia / double-stranded DNA binding / nuclear membrane / response to oxidative stress / microtubule / nuclear speck / cadherin binding / negative regulation of cell population proliferation / chromatin / structural molecule activity / positive regulation of gene expression / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
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: 2.1 Å
AuthorsSamson, C. / Petitalot, A. / Celli, F. / Herrada, I. / Ropars, V. / Ledu, M.H. / Nhiri, N. / Arteni, A.A. / Buendia, B. / ZinnJustin, S.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural analysis of the ternary complex between lamin A/C, BAF and emerin identifies an interface disrupted in autosomal recessive progeroid diseases.
Authors: Samson, C. / Petitalot, A. / Celli, F. / Herrada, I. / Ropars, V. / Le Du, M.H. / Nhiri, N. / Jacquet, E. / Arteni, A.A. / Buendia, B. / Zinn-Justin, S.
History
DepositionMay 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 17, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Emerin
D: Barrier-to-autointegration factor
B: Prelamin-A/C
E: Barrier-to-autointegration factor
A: Barrier-to-autointegration factor
C: Barrier-to-autointegration factor
F: Prelamin-A/C
H: Emerin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,15017
Polymers76,3208
Non-polymers8319
Water5,044280
1
G: Emerin
D: Barrier-to-autointegration factor
B: Prelamin-A/C
E: Barrier-to-autointegration factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6409
Polymers38,1604
Non-polymers4805
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Barrier-to-autointegration factor
C: Barrier-to-autointegration factor
F: Prelamin-A/C
H: Emerin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5108
Polymers38,1604
Non-polymers3504
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.770, 62.750, 64.340
Angle α, β, γ (deg.)66.440, 66.550, 88.050
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain G and (resid 2 through 10 or (resid 11...
21chain H
12(chain B and (resid 429 through 452 or resid 454 through 546))
22(chain F and (resid 429 through 452 or resid 454 through 546))
13(chain A and resid 3 through 89)
23chain C
33chain D
43(chain E and resid 3 through 89)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPTHRTHR(chain G and (resid 2 through 10 or (resid 11...GA2 - 102 - 10
121GLUGLUGLUGLU(chain G and (resid 2 through 10 or (resid 11...GA1111
131GLYGLYARGARG(chain G and (resid 2 through 10 or (resid 11...GA1 - 451 - 45
141GLYGLYARGARG(chain G and (resid 2 through 10 or (resid 11...GA1 - 451 - 45
151GLYGLYARGARG(chain G and (resid 2 through 10 or (resid 11...GA1 - 451 - 45
161GLYGLYARGARG(chain G and (resid 2 through 10 or (resid 11...GA1 - 451 - 45
211ASPASPGLNGLNchain HHH2 - 442 - 44
112SERSERVALVAL(chain B and (resid 429 through 452 or resid 454 through 546))BC429 - 4522 - 25
122LEULEUSERSER(chain B and (resid 429 through 452 or resid 454 through 546))BC454 - 54627 - 119
212SERSERVALVAL(chain F and (resid 429 through 452 or resid 454 through 546))FG429 - 4522 - 25
222LEULEUSERSER(chain F and (resid 429 through 452 or resid 454 through 546))FG454 - 54627 - 119
113THRTHRLEULEU(chain A and resid 3 through 89)AE3 - 892 - 88
213THRTHRLEULEUchain CCF3 - 892 - 88
313THRTHRLEULEUchain DDB3 - 892 - 88
413THRTHRLEULEU(chain E and resid 3 through 89)ED3 - 892 - 88

NCS ensembles :
ID
1
2
3

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Components

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Protein/peptide , 1 types, 2 molecules GH

#1: Protein/peptide Emerin /


Mass: 5324.915 Da / Num. of mol.: 2
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

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Protein , 2 types, 6 molecules DEACBF

#2: Protein
Barrier-to-autointegration factor / / Breakpoint cluster region protein 1


Mass: 9814.131 Da / Num. of mol.: 4
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
#3: Protein Prelamin-A/C


Mass: 13206.776 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 (E. coli) / References: UniProt: P02545

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Non-polymers , 3 types, 289 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 25% PEG3.350, 20mM Tris-BispH5.5, 30mM NaCl, 0.2M NH4SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9725 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 2.1→49.152 Å / Num. obs: 83934 / % possible obs: 95.67 % / Redundancy: 3.52 % / CC1/2: 0.992 / Rmerge(I) obs: 0.1173 / Rpim(I) all: 0.07375 / Rrim(I) all: 0.139 / Net I/σ(I): 5.9
Reflection shellResolution: 2.1→6.52 Å / Rmerge(I) obs: 0.7955 / CC1/2: 0.667 / Rpim(I) all: 0.5256 / Rrim(I) all: 0.9582

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Cootmodel building
MOLREPphasing
APEXdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BZF, 1IFR, 2ODC

2bzf

1ifr

2odc


Resolution: 2.1→49.152 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0.97 / Phase error: 29.81
RfactorNum. reflection% reflection
Rfree0.2468 4187 4.99 %
Rwork0.1917 --
obs0.1944 83934 95.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.07 Å2 / Biso mean: 43.7534 Å2 / Biso min: 17.71 Å2
Refinement stepCycle: final / Resolution: 2.1→49.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5339 0 44 280 5663
Biso mean--81.21 45.32 -
Num. residues----675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085490
X-RAY DIFFRACTIONf_angle_d0.9297397
X-RAY DIFFRACTIONf_chiral_restr0.054779
X-RAY DIFFRACTIONf_plane_restr0.006962
X-RAY DIFFRACTIONf_dihedral_angle_d16.9693262
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11G432X-RAY DIFFRACTION6.961TORSIONAL
12H432X-RAY DIFFRACTION6.961TORSIONAL
21B1102X-RAY DIFFRACTION6.961TORSIONAL
22F1102X-RAY DIFFRACTION6.961TORSIONAL
31A1703X-RAY DIFFRACTION6.961TORSIONAL
32C1703X-RAY DIFFRACTION6.961TORSIONAL
33D1703X-RAY DIFFRACTION6.961TORSIONAL
34E1703X-RAY DIFFRACTION6.961TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.12390.49081370.38092623276095
2.1239-2.14890.3761390.36882684282395
2.1489-2.17510.37161410.34222660280194
2.1751-2.20260.39341320.32162494262695
2.2026-2.23160.3671400.31352766290695
2.2316-2.26210.31081370.31632589272695
2.2621-2.29450.31251360.29822587272395
2.2945-2.32870.3361390.30642644278393
2.3287-2.36510.35891340.29682586272095
2.3651-2.40390.37021410.2952711285295
2.4039-2.44530.30861360.27312597273396
2.4453-2.48980.32411410.25832722286395
2.4898-2.53770.27561350.25792584271996
2.5377-2.58950.31221430.24712732287596
2.5895-2.64580.29741380.24982604274296
2.6458-2.70730.30231380.23012678281696
2.7073-2.7750.33531430.23022694283796
2.775-2.850.28451400.21042650279097
2.85-2.93390.26741430.18842687283096
2.9339-3.02860.23351420.17862698284097
3.0286-3.13680.25711460.18852695284197
3.1368-3.26240.23141390.18382658279797
3.2624-3.41080.20731440.16912711285597
3.4108-3.59060.21841390.15982631277096
3.5906-3.81550.2271430.1492673281696
3.8155-4.10990.2091370.13912631276894
4.1099-4.52330.15371380.12682651278996
4.5233-5.17720.19771420.12922689283196
5.1772-6.52030.20781410.15882721286299
6.5203-49.16540.16991430.14112697284097
Refinement TLS params.

Method: refined / 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)
17.33281.9550.15156.0372-0.84476.32380.3161-0.2213-0.63170.3268-0.1591-0.01050.9096-0.4144-0.11570.3432-0.0454-0.00820.20970.0030.2946-43.0664-54.3347-11.6602
25.23752.2401-0.86154.84510.68935.00680.1915-0.25980.16210.179-0.1480.1379-0.0814-0.1383-0.04140.2130.01550.02480.22920.01410.2015-36.0457-33.2013-3.0591
33.3483-0.02560.65922.63470.13714.9294-0.08790.10220.2152-0.129-0.0089-0.0119-0.52240.10750.09390.32260.0010.00170.2559-0.01760.2363-17.0914-13.7589-17.4312
43.79040.0898-0.78376.43090.26693.80060.14480.1115-0.1827-0.0929-0.1329-0.25490.18030.3354-0.00310.20340.0792-0.02950.27860.00810.2198-19.3008-44.3476-13.1617
56.38750.47930.01243.0872-1.46165.15940.1163-0.0019-0.2972-0.1644-0.2107-0.28620.32950.46670.05940.23640.06010.02740.23110.01250.240410.1239-14.521714.6154
64.23761.93010.00265.9738-1.25486.3343-0.11440.15440.1489-0.07740.1910.2312-0.1245-0.1629-0.06110.19260.02390.00950.2240.02850.1988-2.15962.14365.6773
72.78170.212-0.63112.7750.18194.0341-0.05010.02640.0128-0.08710.01620.10810.1011-0.25360.03930.19960.0172-0.010.25520.01490.2247-19.9791-18.455120.1501
85.5393.63590.23337.9790.96036.1946-0.18850.20990.0742-0.3640.1523-0.6616-0.61880.79250.05280.2597-0.0620.01630.33420.03920.276318.69899.320613.7761
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'G' and resid 1 through 45)G1 - 45
2X-RAY DIFFRACTION2(chain 'D' and resid 3 through 89)D3 - 89
3X-RAY DIFFRACTION3(chain 'B' and resid 428 through 546)B428 - 546
4X-RAY DIFFRACTION4(chain 'E' and resid 2 through 89)E2 - 89
5X-RAY DIFFRACTION5(chain 'A' and resid 2 through 89)A2 - 89
6X-RAY DIFFRACTION6(chain 'C' and resid 3 through 89)C3 - 89
7X-RAY DIFFRACTION7(chain 'F' and resid 429 through 546)F429 - 546
8X-RAY DIFFRACTION8(chain 'H' and resid 2 through 44)H2 - 44

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