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- PDB-6jlb: Crystal structure of lamin A/C fragment and assembly mechanisms o... -

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Basic information

Entry
Database: PDB / ID: 6jlb
TitleCrystal structure of lamin A/C fragment and assembly mechanisms of intermediate filaments
ComponentsLamin A/C
KeywordsSTRUCTURAL PROTEIN / Nuclear lamin / coiled-coil structure / intermediate filaments
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 / DNA double-strand break attachment to nuclear envelope / Depolymerization of the Nuclear Lamina / nuclear envelope organization / Nuclear Envelope Breakdown / 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 / 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 / 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 / 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 / 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 / SAD / Resolution: 3.205 Å
AuthorsAhn, J. / Jo, I. / Ha, N.C.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017R1A2B2003992 Korea, Republic Of
National Research Foundation (Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for lamin assembly at the molecular level.
Authors: Ahn, J. / Jo, I. / Kang, S.M. / Hong, S. / Kim, S. / Jeong, S. / Kim, Y.H. / Park, B.J. / Ha, N.C.
History
DepositionMar 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

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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
C: Lamin A/C
D: Lamin A/C


Theoretical massNumber of molelcules
Total (without water)140,2234
Polymers140,2234
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, Tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26750 Å2
ΔGint-224 kcal/mol
Surface area59980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.267, 84.997, 92.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Lamin A/C / Prelamin-A/C


Mass: 35055.629 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMNA, LMN1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P02545
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: 3.24 Å3/Da / Density % sol: 62.01 %
Description: The entry contains friedel pairs in F_plus/minus columns.
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl (pH 8.5), 0.9 M Lithium chloride, 7% (v/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 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: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 40335 / % possible obs: 93.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.043 / Rrim(I) all: 0.117 / Net I/σ(I): 11.5
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 3.1 / Rpim(I) all: 0.207 / % possible all: 80.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data scaling
PHASERphasing
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.205→46.191 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 25.17
Details: The entry contains friedel pairs in F_plus/minus columns.
RfactorNum. reflection% reflection
Rfree0.2605 3123 7.75 %
Rwork0.207 --
obs0.2112 40280 69.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.205→46.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7161 0 0 0 7161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027191
X-RAY DIFFRACTIONf_angle_d0.4539595
X-RAY DIFFRACTIONf_dihedral_angle_d9.3124635
X-RAY DIFFRACTIONf_chiral_restr0.0281083
X-RAY DIFFRACTIONf_plane_restr0.0021278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2054-3.25550.3306610.2829597X-RAY DIFFRACTION25
3.2555-3.30890.2849550.2765735X-RAY DIFFRACTION30
3.3089-3.36590.3133590.2557811X-RAY DIFFRACTION34
3.3659-3.42710.3533720.2658934X-RAY DIFFRACTION38
3.4271-3.4930.2896960.2524984X-RAY DIFFRACTION41
3.493-3.56430.2733940.24631118X-RAY DIFFRACTION45
3.5643-3.64170.2882960.24131204X-RAY DIFFRACTION51
3.6417-3.72640.27291020.2311403X-RAY DIFFRACTION57
3.7264-3.81960.31171270.2041564X-RAY DIFFRACTION64
3.8196-3.92280.2531460.20431682X-RAY DIFFRACTION70
3.9228-4.03810.27961680.19641825X-RAY DIFFRACTION75
4.0381-4.16840.25811450.19151935X-RAY DIFFRACTION80
4.1684-4.31730.23951660.18912010X-RAY DIFFRACTION83
4.3173-4.490.24111930.19192066X-RAY DIFFRACTION86
4.49-4.69420.23441630.19532138X-RAY DIFFRACTION87
4.6942-4.94140.27031910.1922162X-RAY DIFFRACTION90
4.9414-5.25060.24121940.1922293X-RAY DIFFRACTION94
5.2506-5.65530.33571910.23552327X-RAY DIFFRACTION96
5.6553-6.22320.27331940.2542306X-RAY DIFFRACTION96
6.2232-7.12090.31272030.23892340X-RAY DIFFRACTION96
7.1209-8.96080.23181930.17982367X-RAY DIFFRACTION98
8.9608-46.19630.20172140.17442356X-RAY DIFFRACTION98

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