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- PDB-6yjd: Lamin A coil2 dimer stabilized by N-terminal capping -

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Basic information

Entry
Database: PDB / ID: 6yjd
TitleLamin A coil2 dimer stabilized by N-terminal capping
ComponentsCapsid assembly scaffolding protein,Prelamin-A/C
KeywordsNUCLEAR PROTEIN / intermediate filaments / lamin / coiled-coil
Function / homology
Function and homology information


structural constituent of nuclear lamina / negative regulation of mesenchymal cell proliferation / viral scaffold / 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 organization / Nuclear Envelope Breakdown ...structural constituent of nuclear lamina / negative regulation of mesenchymal cell proliferation / viral scaffold / 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 organization / Nuclear Envelope Breakdown / nuclear pore localization / lamin filament / protein localization to nuclear envelope / nuclear lamina / XBP1(S) activates chaperone genes / Initiation of Nuclear Envelope (NE) Reformation / regulation of protein localization to nucleus / nuclear migration / negative regulation of cardiac muscle hypertrophy in response to stress / regulation of telomere maintenance / intermediate filament / muscle organ development / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / virion assembly / negative regulation of release of cytochrome c from mitochondria / protein localization to nucleus / regulation of cell migration / Meiotic synapsis / negative regulation of extrinsic apoptotic signaling pathway / regulation of protein stability / heterochromatin formation / structural constituent of cytoskeleton / nuclear matrix / protein import into nucleus / cellular senescence / Signaling by BRAF and RAF1 fusions / protein localization / nuclear envelope / site of double-strand break / cellular response to hypoxia / nuclear membrane / nuclear speck / negative regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / structural molecule activity / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / 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. ...Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / 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
NICKEL (II) ION / Prelamin-A/C / Capsid assembly scaffolding protein
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsLilina, A.V. / Stalmans, G. / Strelkov, S.V.
Funding support Belgium, 1items
OrganizationGrant numberCountry
KU LeuvenCELSA 18/044 Belgium
CitationJournal: Cells / Year: 2020
Title: Addressing the Molecular Mechanism of Longitudinal Lamin Assembly Using Chimeric Fusions.
Authors: Stalmans, G. / Lilina, A.V. / Vermeire, P.J. / Fiala, J. / Novak, P. / Strelkov, S.V.
History
DepositionApr 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid assembly scaffolding protein,Prelamin-A/C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2926
Polymers14,8951
Non-polymers3975
Water362
1
A: Capsid assembly scaffolding protein,Prelamin-A/C
hetero molecules

A: Capsid assembly scaffolding protein,Prelamin-A/C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,58412
Polymers29,7902
Non-polymers79410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_454-x+y-1,y,-z-1/21
Buried area6170 Å2
ΔGint-78 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.250, 117.250, 93.156
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Capsid assembly scaffolding protein,Prelamin-A/C / Gene product 7 / gp7 / Head morphogenesis protein / Protein p7 / Scaffold protein


Mass: 14894.788 Da / Num. of mol.: 1 / Mutation: F40C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus), (gene. exp.) Homo sapiens (human)
Gene: LMNA, LMN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13848, UniProt: P02545
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 6.21 Å3/Da / Density % sol: 80.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 35% (v/v) methanol, 0.2 M MgCl2 and 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.9→44.62 Å / Num. obs: 8792 / % possible obs: 98.28 % / Redundancy: 19.2 % / Biso Wilson estimate: 110.62 Å2 / CC1/2: 0.999 / Net I/σ(I): 20.27
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 0.99 / Num. unique obs: 847 / CC1/2: 0.934

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→44.62 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.899 / SU B: 14.152 / SU ML: 0.251 / Cross valid method: FREE R-VALUE / ESU R: 0.327 / ESU R Free: 0.298
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3042 841 9.567 %
Rwork0.2533 --
all0.258 --
obs-8791 99.75 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 115.019 Å2
Baniso -1Baniso -2Baniso -3
1-3.572 Å21.786 Å20 Å2
2--3.572 Å2-0 Å2
3----11.586 Å2
Refinement stepCycle: LAST / Resolution: 2.9→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms823 0 19 2 844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.013846
X-RAY DIFFRACTIONr_bond_other_d0.0010.017781
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.6511136
X-RAY DIFFRACTIONr_angle_other_deg1.3911.591808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.235103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96422.69252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.74115160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.216158
X-RAY DIFFRACTIONr_chiral_restr0.0840.2109
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02936
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02160
X-RAY DIFFRACTIONr_nbd_refined0.2330.2205
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.2621
X-RAY DIFFRACTIONr_nbtor_refined0.1550.2400
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2395
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.224
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1130.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1970.216
X-RAY DIFFRACTIONr_nbd_other0.330.261
X-RAY DIFFRACTIONr_nbtor_other0.020.21
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2170.28
X-RAY DIFFRACTIONr_mcbond_it9.86812.122417
X-RAY DIFFRACTIONr_mcbond_other9.83812.1414
X-RAY DIFFRACTIONr_mcangle_it12.2918.092517
X-RAY DIFFRACTIONr_mcangle_other12.27918.104518
X-RAY DIFFRACTIONr_scbond_it14.65413.305427
X-RAY DIFFRACTIONr_scbond_other14.6413.306428
X-RAY DIFFRACTIONr_scangle_it19.4219.484619
X-RAY DIFFRACTIONr_scangle_other19.40519.492620
X-RAY DIFFRACTIONr_lrange_it19.464143.836941
X-RAY DIFFRACTIONr_lrange_other19.466143.9942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.9750.376660.448550X-RAY DIFFRACTION99.0354
2.975-3.0570.362630.375560X-RAY DIFFRACTION100
3.057-3.1450.334540.326542X-RAY DIFFRACTION99.8325
3.145-3.2420.287480.315531X-RAY DIFFRACTION99.8276
3.242-3.3480.223540.243518X-RAY DIFFRACTION100
3.348-3.4660.218610.23488X-RAY DIFFRACTION99.8182
3.466-3.5960.201620.238467X-RAY DIFFRACTION100
3.596-3.7430.289470.219467X-RAY DIFFRACTION99.4197
3.743-3.9090.259540.212445X-RAY DIFFRACTION99.4024
3.909-4.10.296360.239430X-RAY DIFFRACTION100
4.1-4.3210.329400.24416X-RAY DIFFRACTION100
4.321-4.5820.277410.227393X-RAY DIFFRACTION100
4.582-4.8980.302330.228378X-RAY DIFFRACTION100
4.898-5.290.408310.295346X-RAY DIFFRACTION100
5.29-5.7930.349310.346329X-RAY DIFFRACTION100
5.793-6.4740.335340.289293X-RAY DIFFRACTION99.6951
6.474-7.470.239310.237261X-RAY DIFFRACTION100

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