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- PDB-7d9n: Crystal structure of a non-canonic progeria mutation S143F at lam... -

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Basic information

Entry
Database: PDB / ID: 7d9n
TitleCrystal structure of a non-canonic progeria mutation S143F at lamin A/C and its structural implication to the premature aging
ComponentsLamin-A/C
KeywordsSTRUCTURAL PROTEIN / nuclear lamin A/C / lamin S143F / intermediate filament / HGPS
Function / homology
Function and homology information


structural constituent of nuclear lamina / negative regulation of mesenchymal cell proliferation / establishment or maintenance of microtubule cytoskeleton polarity / ventricular cardiac muscle cell development / Breakdown of the nuclear lamina / Depolymerization of the Nuclear Lamina / DNA double-strand break attachment to nuclear envelope / Nuclear Envelope Breakdown / nuclear envelope organization / nuclear pore localization ...structural constituent of nuclear lamina / negative regulation of mesenchymal cell proliferation / establishment or maintenance of microtubule cytoskeleton polarity / ventricular cardiac muscle cell development / Breakdown of the nuclear lamina / Depolymerization of the Nuclear Lamina / DNA double-strand break attachment to nuclear envelope / Nuclear Envelope Breakdown / nuclear envelope organization / 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 / regulation of telomere maintenance / negative regulation of cardiac muscle hypertrophy in response to stress / muscle organ development / intermediate filament / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / negative regulation of release of cytochrome c from mitochondria / protein localization to nucleus / heterochromatin formation / regulation of cell migration / Meiotic synapsis / negative regulation of extrinsic apoptotic signaling pathway / regulation of protein stability / protein localization / structural constituent of cytoskeleton / nuclear matrix / protein import into nucleus / cellular senescence / Signaling by BRAF and RAF1 fusions / 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 / structural molecule activity / perinuclear region of cytoplasm / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsAhn, J. / Jung, S. / Ha, N.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1A2C208513512 Korea, Republic Of
National Research Foundation (NRF, Korea)2020R1A4A101932211 Korea, Republic Of
CitationJournal: Commun Biol / Year: 2022
Title: Crystal structure of progeria mutant S143F lamin A/C reveals increased hydrophobicity driving nuclear deformation.
Authors: Ahn, J. / Jeong, S. / Kang, S.M. / Jo, I. / Park, B.J. / Ha, N.C.
History
DepositionOct 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lamin-A/C
B: Lamin-A/C


Theoretical massNumber of molelcules
Total (without water)47,3312
Polymers47,3312
Non-polymers00
Water00
1
A: Lamin-A/C
B: Lamin-A/C

A: Lamin-A/C
B: Lamin-A/C


Theoretical massNumber of molelcules
Total (without water)94,6624
Polymers94,6624
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area25060 Å2
ΔGint-213 kcal/mol
Surface area54950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.808, 123.808, 458.545
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 Lamin-A/C / 70 kDa lamin / Renal carcinoma antigen NY-REN-32


Mass: 23665.506 Da / Num. of mol.: 2 / Mutation: S143F
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
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

CrystalDensity Matthews: 5.88 Å3/Da / Density % sol: 79.1 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Tris-Hcl pH8 0.1 M Sodium citrate 18% PEG 400

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97942 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 16492 / % possible obs: 96.8 % / Redundancy: 10.4 % / CC1/2: 0.996 / Net I/σ(I): 24.09
Reflection shellResolution: 4→4.07 Å / Num. unique obs: 14820 / CC1/2: 0.699

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
DENZOdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JLB

6jlb


Resolution: 3.7→48.1 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 25.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3043 1648 9.99 %
Rwork0.2875 --
obs0.2892 16492 84.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.7→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 0 0 3271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033285
X-RAY DIFFRACTIONf_angle_d0.5634386
X-RAY DIFFRACTIONf_dihedral_angle_d3.998451
X-RAY DIFFRACTIONf_chiral_restr0.032502
X-RAY DIFFRACTIONf_plane_restr0.003579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.810.2761150.2948131X-RAY DIFFRACTION9
3.81-3.930.3223730.3093659X-RAY DIFFRACTION46
3.94-4.080.36841290.32491162X-RAY DIFFRACTION80
4.08-4.240.34421480.30611331X-RAY DIFFRACTION92
4.24-4.430.29951520.29651369X-RAY DIFFRACTION94
4.43-4.660.2871540.29621383X-RAY DIFFRACTION96
4.66-4.960.26631580.27531416X-RAY DIFFRACTION96
4.96-5.340.27711540.24851414X-RAY DIFFRACTION97
5.34-5.880.37981590.34661435X-RAY DIFFRACTION97
5.88-6.720.34661620.35851454X-RAY DIFFRACTION99
6.73-8.460.29231660.27451492X-RAY DIFFRACTION99
8.47-48.10.24291780.21581598X-RAY DIFFRACTION99
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)
10.1942-0.0589-0.47360.93090.02661.16790.06340.0303-0.0945-0.02880.0205-0.10230.08650.0918-0.01020.1760.014-0.09160.0528-0.00880.070295.854679.9241-51.9533
20.50130.4518-0.42890.6742-0.40970.42910.0685-0.09260.14740.0834-0.03740.1051-0.04940.0686-0.03140.3486-0.4792-0.02610.29510.00460.2067-11.72445.67489.2783
30.18860.2062-0.33140.15-0.22880.1799-0.0630.00670.12990.01670.12950.03180.0431-0.1155-0.03730.4132-0.47780.0880.36810.11210.246911.676124.4885-0.8723
40.0183-0.0119-0.0030.00770.0020.00050.00650.0510.1988-0.01320.03710.2697-0.1623-0.2216-0.04260.9112-0.069-0.0040.8799-0.00950.9191-89.7468-53.931464.6137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 229 )
3X-RAY DIFFRACTION3chain 'B' and (resid 30 through 224 )
4X-RAY DIFFRACTION4chain 'B' and (resid 225 through 230 )

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