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- PDB-7x5d: Crystal Structure of the K316C mutant of Human Lamin A/C Coil 2 (... -

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Basic information

Entry
Database: PDB / ID: 7x5d
TitleCrystal Structure of the K316C mutant of Human Lamin A/C Coil 2 (residues 244-340)
ComponentsLamin-A/C
KeywordsNUCLEAR PROTEIN / lamin / intermediate filament / nuclear
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 / AB INITIO PHASING / Resolution: 1.82 Å
AuthorsAhn, J. / Jo, I. / Ha, N.-C.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1A2C2085135 Korea, Republic Of
National Research Foundation (NRF, Korea)2021R1I1A1A01049976 Korea, Republic Of
CitationJournal: To Be Published
Title: Atomic structure of the antiparallel four-helix bundle interactions for the formation of lamin filament
Authors: Ahn, J. / Jo, I. / Ha, N.-C.
History
DepositionMar 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,5402
Polymers23,5402
Non-polymers00
Water2,234124
1
A: Lamin-A/C
B: Lamin-A/C

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


Theoretical massNumber of molelcules
Total (without water)47,0804
Polymers47,0804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area12020 Å2
ΔGint-77 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.788, 40.966, 140.714
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-412-

HOH

21B-413-

HOH

31B-423-

HOH

41B-454-

HOH

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Components

#1: Protein Lamin-A/C / 70 kDa lamin / Renal carcinoma antigen NY-REN-32


Mass: 11770.041 Da / Num. of mol.: 2 / Mutation: K316C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMNA, LMN1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02545
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.82 Å3/Da / Density % sol: 32.55 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: Tacsimate (pH 5.5), PEG 3350, methyl mercury acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20.1 Å / Num. obs: 15449 / % possible obs: 95.1 % / Redundancy: 9.5 % / Biso Wilson estimate: 16.67 Å2 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.02 / Rrim(I) all: 0.066 / Χ2: 0.966 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.836.80.3345410.9390.1170.3550.75568.4
1.83-1.867.10.335880.9640.1150.3510.75873.8
1.86-1.97.20.3516410.960.1220.3720.77783.5
1.9-1.946.90.3297300.9550.1160.3510.77188.3
1.94-1.987.40.2547330.9890.0880.2690.81294.2
1.98-2.037.90.2397720.9890.0810.2530.85197.8
2.03-2.088.30.2327840.9810.0780.2450.9398.7
2.08-2.138.60.2147940.9870.0720.2270.91298.5
2.13-2.28.80.1787890.9890.060.1890.9599.5
2.2-2.278.50.1698190.9920.0580.1791.0699.4
2.27-2.358.80.1367630.9950.0470.144199.9
2.35-2.449.50.1128210.9970.0380.1181.085100
2.44-2.5510.60.0958190.9980.0290.11.11699.8
2.55-2.6911.20.0948060.9980.0280.0981.12499.6
2.69-2.8611.10.0738030.9990.0220.0761.1100
2.86-3.0711.50.0638180.9990.0190.0661.05599.9
3.07-3.3811.80.0668360.9980.020.0691.12100
3.38-3.8712.10.0578270.9990.0170.061.08799.8
3.87-4.8610.70.0438520.9990.0140.0450.85299.6
4.86-20120.059130.9980.0170.0530.71599.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.82→20.1 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 31.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2792 695 4.99 %
Rwork0.2388 13229 -
obs0.2409 13924 86.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.19 Å2 / Biso mean: 36.0364 Å2 / Biso min: 3.29 Å2
Refinement stepCycle: final / Resolution: 1.82→20.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1559 0 0 124 1683
Biso mean---33.75 -
Num. residues----193
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.82-1.960.3302700.25741402147247
1.96-2.160.26741330.23852550268385
2.16-2.470.27831550.2333004315999
2.47-3.110.25941580.248930763234100
3.11-20.10.28771790.23333197337699
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)
10.6736-0.0911-0.13730.64470.4331.13770.220.0934-0.1092-0.0622-0.06750.11310.0349-0.1982-0.0041-0.0630.0496-0.12750.0315-0.06080.099712.972.964758.0176
2-0.2067-0.0935-0.1625-0.01710.55841.438-0.08150.1454-0.0917-0.216-0.0215-0.0728-0.4127-0.38880.20650.34490.0702-0.03780.20350.00390.110213.10422.96214.7034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 239 through 337 )A239 - 337
2X-RAY DIFFRACTION2chain 'B' and (resid 244 through 337 )B244 - 337

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