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- PDB-1x8y: Human lamin coil 2B -

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Basic information

Entry
Database: PDB / ID: 1x8y
TitleHuman lamin coil 2B
ComponentsLamin A/C
KeywordsSTRUCTURAL PROTEIN / Intermediate filament protein
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 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 / DNA double-strand break attachment to nuclear envelope / Depolymerization of the Nuclear Lamina / 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 ...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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsStrelkov, S.V. / Schumacher, J. / Burkhard, P. / Aebi, U. / Herrmann, H.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of the human lamin A coil 2B dimer: implications for the head-to-tail association of nuclear lamins
Authors: Strelkov, S.V. / Schumacher, J. / Burkhard, P. / Aebi, U. / Herrmann, H.
History
DepositionAug 19, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lamin A/C


Theoretical massNumber of molelcules
Total (without water)10,1951
Polymers10,1951
Non-polymers00
Water45025
1
A: Lamin A/C

A: Lamin A/C


Theoretical massNumber of molelcules
Total (without water)20,3892
Polymers20,3892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area3560 Å2
ΔGint-42 kcal/mol
Surface area11110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.267, 89.267, 75.589
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological dimer is generated by the two-fold crystallographic axis

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Components

#1: Protein Lamin A/C / lamin fragment 2B / 70 kDa lamin


Mass: 10194.621 Da / Num. of mol.: 1 / Fragment: human lamin A fragment (residues 305-387)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02545
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 4.26 Å3/Da / Density % sol: 71.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.7M Na/K tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å
DetectorDetector: CCD / Date: Oct 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 9494 / Num. obs: 9456 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rsym value: 0.071 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 11 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.518 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.89 / SU B: 5.373 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.18
RfactorNum. reflection% reflectionSelection details
Rfree0.3046 453 4.8 %RANDOM
Rwork0.27446 ---
all0.27587 9494 --
obs0.27587 9456 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.079 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å21.21 Å20 Å2
2--2.42 Å20 Å2
3----3.62 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms594 0 0 25 619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021603
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.994800
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.248573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.287
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02443
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1810.2220
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.224
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7831.5369
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52586
X-RAY DIFFRACTIONr_scbond_it2.0813234
X-RAY DIFFRACTIONr_scangle_it3.7544.5214
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 20
Rwork0.32 670
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)
133.281130.2994-13.5527196.2802-8.339245.3967-0.07240.35052.10840.1858-0.1963-0.4524-1.21780.22520.26870.123-0.00060.00010.12120.00010.12284.155118.707216.86
21.0926-5.0837-0.120840.7452-0.30160.37780.0265-0.0353-0.1009-0.2894-0.02180.29150.03250.0583-0.00470.16-0.0274-0.03120.0833-0.01090.06580.69373.954621.185
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA313 - 32112 - 20
2X-RAY DIFFRACTION2AA322 - 38621 - 85

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