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- PDB-6ysh: Lamin A 1-70 coil1A dimer stabilized by C-terminal capping -

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Basic information

Entry
Database: PDB / ID: 6ysh
TitleLamin A 1-70 coil1A dimer stabilized by C-terminal capping
Components(Prelamin-A/C,Microtubule-associated protein RP/EB family member 1) x 2
KeywordsNUCLEAR PROTEIN / intermediate filaments lamin coiled-coil
Function / homology
Function and homology information


negative regulation of mesenchymal cell proliferation / protein localization to astral microtubule / cortical microtubule cytoskeleton / DNA double-strand break attachment to nuclear envelope / mitotic spindle astral microtubule end / 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 ...negative regulation of mesenchymal cell proliferation / protein localization to astral microtubule / cortical microtubule cytoskeleton / DNA double-strand break attachment to nuclear envelope / mitotic spindle astral microtubule end / 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 microtubule / protein localization to nuclear envelope / lamin filament / nuclear lamina / microtubule plus-end / cell projection membrane / XBP1(S) activates chaperone genes / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / Initiation of Nuclear Envelope (NE) Reformation / non-motile cilium assembly / microtubule bundle formation / regulation of protein localization to nucleus / nuclear migration / regulation of telomere maintenance / protein localization to centrosome / intermediate filament / muscle organ development / negative regulation of cardiac muscle hypertrophy in response to stress / microtubule organizing center / negative regulation of microtubule polymerization / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / mitotic spindle pole / negative regulation of release of cytochrome c from mitochondria / microtubule polymerization / establishment of mitotic spindle orientation / protein localization to nucleus / spindle assembly / regulation of microtubule polymerization or depolymerization / spindle midzone / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / heterochromatin formation / Mitotic Prometaphase / regulation of cell migration / EML4 and NUDC in mitotic spindle formation / positive regulation of microtubule polymerization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Meiotic synapsis / AURKA Activation by TPX2 / ciliary basal body / RHO GTPases Activate Formins / negative regulation of extrinsic apoptotic signaling pathway / regulation of protein stability / protein localization / structural constituent of cytoskeleton / nuclear matrix / protein import into nucleus / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / cellular senescence / cell migration / Signaling by BRAF and RAF1 fusions / site of double-strand break / nuclear envelope / cellular response to hypoxia / nuclear membrane / microtubule / molecular adaptor activity / nuclear speck / cadherin binding / cell division / negative regulation of cell population proliferation / focal adhesion / centrosome / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / structural molecule activity / Golgi apparatus / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Intermediate filament protein, conserved site ...Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / 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 / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile.
Similarity search - Domain/homology
Prelamin-A/C / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsStalmans, G. / Lilina, A.V. / 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 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prelamin-A/C,Microtubule-associated protein RP/EB family member 1
B: Prelamin-A/C,Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)19,3882
Polymers19,3882
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-29 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.847, 108.847, 130.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Prelamin-A/C,Microtubule-associated protein RP/EB family member 1 / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 9836.950 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMNA, LMN1, MAPRE1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02545, UniProt: Q15691
#2: Protein Prelamin-A/C,Microtubule-associated protein RP/EB family member 1 / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 9550.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMNA, LMN1, MAPRE1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02545, UniProt: Q15691
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.91 Å3/Da / Density % sol: 68.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M NaH2PO4 H2O,0.1M KH2PO4,2.0M NaCl,0.1M Mes H20 pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97631 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97631 Å / Relative weight: 1
ReflectionResolution: 2.83→83.58 Å / Num. obs: 9665 / % possible obs: 99.9 % / Redundancy: 26.4 % / Biso Wilson estimate: 68.697 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.04 / Rrim(I) all: 0.205 / Net I/σ(I): 11.5
Reflection shellResolution: 2.83→2.88 Å / Redundancy: 27.2 % / Rmerge(I) obs: 2.51 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 482 / CC1/2: 0.868 / Rpim(I) all: 0.488 / Rrim(I) all: 2.558 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YF5

6yf5


Resolution: 2.83→83.58 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 48.452 / SU ML: 0.396 / Cross valid method: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28131 496 5.1 %RANDOM
Rwork0.23747 ---
obs0.23972 9158 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 110.135 Å2
Baniso -1Baniso -2Baniso -3
1--8.1 Å20 Å2-0 Å2
2---8.1 Å2-0 Å2
3---16.21 Å2
Refinement stepCycle: 1 / Resolution: 2.83→83.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 0 22 1382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0131371
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171294
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.651848
X-RAY DIFFRACTIONr_angle_other_deg1.5051.5832988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6875162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52622.277101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.70515265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.0331517
X-RAY DIFFRACTIONr_chiral_restr0.1060.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021542
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02289
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.6449.074654
X-RAY DIFFRACTIONr_mcbond_other8.6459.068653
X-RAY DIFFRACTIONr_mcangle_it12.41713.607814
X-RAY DIFFRACTIONr_mcangle_other12.4113.614815
X-RAY DIFFRACTIONr_scbond_it10.66210.572717
X-RAY DIFFRACTIONr_scbond_other10.67210.562715
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.82715.371034
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.83→2.904 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 39 -
Rwork0.422 639 -
obs--99.12 %
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)
14.5615-1.48790.18251.108-0.08130.0777-0.0063-0.10940.5139-0.08720.0594-0.2149-0.09660.0043-0.0530.1568-0.00570.1120.08570.01850.154121.50899.51-7.187
20.36530.3827-0.1130.4495-0.11520.0391-0.180.1024-0.1484-0.13270.1433-0.07910.0291-0.03890.03660.15840.04510.01820.15630.01430.251920.06711.3854-5.3879
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 107
2X-RAY DIFFRACTION2B26 - 106

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