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- PDB-6yf5: Lamin A 17-70 coil1A dimer stabilized by C-terminal capping -

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Basic information

Entry
Database: PDB / ID: 6yf5
TitleLamin A 17-70 coil1A dimer stabilized by C-terminal capping
ComponentsPrelamin-A/C,Microtubule-associated protein RP/EB family member 1
KeywordsNUCLEAR PROTEIN / intermediate filaments lamin coiled-coil
Function / homology
Function and homology information


negative regulation of mesenchymal cell proliferation / structural constituent of nuclear lamina / protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / ventricular cardiac muscle cell development / establishment or maintenance of microtubule cytoskeleton polarity / Breakdown of the nuclear lamina / DNA double-strand break attachment to nuclear envelope ...negative regulation of mesenchymal cell proliferation / structural constituent of nuclear lamina / protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / ventricular cardiac muscle cell development / establishment or maintenance of microtubule cytoskeleton polarity / Breakdown of the nuclear lamina / DNA double-strand break attachment to nuclear envelope / Depolymerization of the Nuclear Lamina / nuclear envelope organization / nuclear pore localization / Nuclear Envelope Breakdown / protein localization to microtubule / lamin filament / protein localization to nuclear envelope / microtubule plus-end / mitotic spindle microtubule / cell projection membrane / XBP1(S) activates chaperone genes / nuclear lamina / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / microtubule bundle formation / non-motile cilium assembly / Initiation of Nuclear Envelope (NE) Reformation / regulation of protein localization to nucleus / protein localization to centrosome / regulation of telomere maintenance / intermediate filament / negative regulation of cardiac muscle hypertrophy in response to stress / nuclear migration / muscle organ development / negative regulation of microtubule polymerization / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / mitotic spindle pole / negative regulation of release of cytochrome c from mitochondria / microtubule organizing center / microtubule polymerization / establishment of mitotic spindle orientation / protein localization to nucleus / regulation of microtubule polymerization or depolymerization / spindle midzone / cytoplasmic microtubule / spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of microtubule polymerization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Meiotic synapsis / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / regulation of cell migration / AURKA Activation by TPX2 / negative regulation of extrinsic apoptotic signaling pathway / RHO GTPases Activate Formins / regulation of protein stability / structural constituent of cytoskeleton / nuclear matrix / protein import into nucleus / Separation of Sister Chromatids / cellular senescence / The role of GTSE1 in G2/M progression after G2 checkpoint / Signaling by BRAF and RAF1 fusions / Regulation of PLK1 Activity at G2/M Transition / protein localization / nuclear envelope / heterochromatin formation / cell migration / site of double-strand break / nuclear membrane / cellular response to hypoxia / microtubule / nuclear speck / ciliary basal body / cadherin binding / negative regulation of cell population proliferation / cell division / focal adhesion / centrosome / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / structural molecule activity / Golgi apparatus / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / 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 / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Prelamin-A/C / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsLilina, A.V. / Stalmans, G. / Strelkov, S.V.
Funding support Belgium, 1items
OrganizationGrant numberCountry
KU LeuvenCELSA 18/044 Belgium
CitationJournal: Cells / Year: 2020
Title: Addressing the Molecular Mechanism of Longitudinal Lamin Assembly Using Chimeric Fusions.
Authors: Stalmans, G. / Lilina, A.V. / Vermeire, P.J. / Fiala, J. / Novak, P. / Strelkov, S.V.
History
DepositionMar 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prelamin-A/C,Microtubule-associated protein RP/EB family member 1
B: Prelamin-A/C,Microtubule-associated protein RP/EB family member 1
C: Prelamin-A/C,Microtubule-associated protein RP/EB family member 1
D: Prelamin-A/C,Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)42,4314
Polymers42,4314
Non-polymers00
Water1,54986
1
A: Prelamin-A/C,Microtubule-associated protein RP/EB family member 1
B: Prelamin-A/C,Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)21,2162
Polymers21,2162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-33 kcal/mol
Surface area11600 Å2
MethodPISA
2
C: Prelamin-A/C,Microtubule-associated protein RP/EB family member 1
D: Prelamin-A/C,Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)21,2162
Polymers21,2162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-32 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.374, 105.246, 119.773
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA24 - 1058 - 89
21THRTHRBB24 - 1058 - 89
12PROPROAA20 - 1054 - 89
22PROPROCC20 - 1054 - 89
13ARGARGAA25 - 1059 - 89
23ARGARGDD25 - 1059 - 89
14THRTHRBB24 - 1058 - 89
24THRTHRCC24 - 1058 - 89
15ARGARGBB25 - 1059 - 89
25ARGARGDD25 - 1059 - 89
16ARGARGCC25 - 1059 - 89
26ARGARGDD25 - 1059 - 89

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Prelamin-A/C,Microtubule-associated protein RP/EB family member 1 / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 10607.778 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMNA, LMN1, MAPRE1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02545, UniProt: Q15691
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.9
Details: 35.7% (w/v) 1,6-hexanediol, 5% (w/v) PEG 1K and 0.1 M trisodium citrate dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.83→52.05 Å / Num. obs: 31710 / % possible obs: 100 % / Redundancy: 10.22 % / Biso Wilson estimate: 22.16 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.73
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1.08 / Num. unique obs: 1487 / CC1/2: 0.54 / % possible all: 98.54

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XA3

4xa3


Resolution: 1.83→48.22 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.155 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 1566 5 %RANDOM
Rwork0.2245 ---
obs0.226 30047 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.93 Å2 / Biso mean: 32.806 Å2 / Biso min: 13.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0 Å2-0 Å2
2---1.67 Å20 Å2
3---2 Å2
Refinement stepCycle: final / Resolution: 1.83→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2786 0 0 86 2872
Biso mean---36.75 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132810
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172645
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.6543799
X-RAY DIFFRACTIONr_angle_other_deg1.3851.586111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4995337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.62222.245196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75715529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8271533
X-RAY DIFFRACTIONr_chiral_restr0.080.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02583
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A23940.15
12B23940.15
21A24600.15
22C24600.15
31A23970.14
32D23970.14
41B23770.14
42C23770.14
51B24360.13
52D24360.13
61C23440.16
62D23440.16
LS refinement shellResolution: 1.83→1.877 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 117 -
Rwork0.331 2140 -
all-2257 -
obs--99.96 %

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