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- PDB-7crg: Beta-strand-mediated dimeric formation of the extended Ig-like do... -

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Basic information

Entry
Database: PDB / ID: 7crg
TitleBeta-strand-mediated dimeric formation of the extended Ig-like domains of human lamin A/C
ComponentsPrelamin-A/C
KeywordsNUCLEAR PROTEIN / lamin A/C / Ig-like domain / dimer
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: 1.8 Å
AuthorsAhn, J. / Ha, N.C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Beta-strand-mediated dimeric formation of the Ig-like domains of human lamin A/C and B1.
Authors: Ahn, J. / Lee, J. / Jeong, S. / Kang, S.M. / Park, B.J. / Ha, N.C.
History
DepositionAug 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2Nov 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.3Nov 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: Prelamin-A/C
B: Prelamin-A/C
C: Prelamin-A/C


Theoretical massNumber of molelcules
Total (without water)51,1533
Polymers51,1533
Non-polymers00
Water5,423301
1
A: Prelamin-A/C
C: Prelamin-A/C


Theoretical massNumber of molelcules
Total (without water)34,1022
Polymers34,1022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint1 kcal/mol
Surface area14030 Å2
MethodPISA
2
B: Prelamin-A/C

B: Prelamin-A/C


Theoretical massNumber of molelcules
Total (without water)34,1022
Polymers34,1022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/31
Buried area1290 Å2
ΔGint0 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.648, 92.648, 205.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-688-

HOH

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Components

#1: Protein Prelamin-A/C


Mass: 17050.943 Da / Num. of mol.: 3
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.61 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium Chloride, 0.05 M HEPES pH 7.5, 35%(v/v) Pentaerythritol Propoxylate (5/4PO/OH)

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 47954 / % possible obs: 98.1 % / Redundancy: 24.5 % / CC1/2: 0.995 / Net I/σ(I): 34.2
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 47954 / Rpim(I) all: 0.073

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data scaling
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IFR

1ifr


Resolution: 1.8→39.38 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.86 / Phase error: 19.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 2373 4.95 %
Rwork0.1931 --
obs0.1942 47954 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→39.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3063 0 0 301 3364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073138
X-RAY DIFFRACTIONf_angle_d0.8234250
X-RAY DIFFRACTIONf_dihedral_angle_d6.088429
X-RAY DIFFRACTIONf_chiral_restr0.059468
X-RAY DIFFRACTIONf_plane_restr0.005558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.29121160.23682358X-RAY DIFFRACTION88
1.84-1.880.27981370.2232481X-RAY DIFFRACTION92
1.88-1.920.23281400.21582547X-RAY DIFFRACTION95
1.92-1.970.22961290.20722617X-RAY DIFFRACTION97
1.97-2.020.26371240.20112666X-RAY DIFFRACTION98
2.02-2.080.26491540.20912601X-RAY DIFFRACTION98
2.08-2.150.23081350.2022693X-RAY DIFFRACTION99
2.15-2.230.21791250.19112665X-RAY DIFFRACTION98
2.23-2.320.23851430.19872702X-RAY DIFFRACTION99
2.32-2.420.26061530.20472665X-RAY DIFFRACTION99
2.42-2.550.22011530.20792694X-RAY DIFFRACTION99
2.55-2.710.23061310.20112732X-RAY DIFFRACTION99
2.71-2.920.25291490.21842730X-RAY DIFFRACTION99
2.92-3.210.20511330.21742778X-RAY DIFFRACTION100
3.21-3.670.22721430.17992785X-RAY DIFFRACTION100
3.68-4.630.15181450.1582855X-RAY DIFFRACTION100
4.63-39.380.16411630.16563012X-RAY DIFFRACTION99

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