- PDB-6ysh: Lamin A 1-70 coil1A dimer stabilized by C-terminal capping -
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Basic information
Entry
Database: PDB / ID: 6ysh
Title
Lamin A 1-70 coil1A dimer stabilized by C-terminal capping
Components
(Prelamin-A/C,Microtubule-associated protein RP/EB family member 1) x 2
Keywords
NUCLEAR PROTEIN / intermediate filaments lamin coiled-coil
Function / homology
Function and homology information
structural constituent of nuclear lamina / negative regulation of mesenchymal cell proliferation / protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / 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 ...structural constituent of nuclear lamina / negative regulation of mesenchymal cell proliferation / protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / 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 / protein localization to microtubule / lamin filament / protein localization to nuclear envelope / nuclear lamina / microtubule plus-end / cell projection membrane / XBP1(S) activates chaperone genes / attachment of mitotic spindle microtubules to kinetochore / Initiation of Nuclear Envelope (NE) Reformation / non-motile cilium assembly / microtubule bundle formation / microtubule plus-end binding / regulation of protein localization to nucleus / nuclear migration / protein localization to centrosome / regulation of telomere maintenance / negative regulation of cardiac muscle hypertrophy in response to stress / muscle organ development / microtubule organizing center / intermediate filament / 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 polymerization / cytoplasmic microtubule / establishment of mitotic spindle orientation / protein localization to nucleus / regulation of microtubule polymerization or depolymerization / spindle assembly / spindle midzone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / heterochromatin formation / 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 / regulation of cell migration / positive regulation of microtubule polymerization / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / Meiotic synapsis / AURKA Activation by TPX2 / ciliary basal body / RHO GTPases Activate Formins / negative regulation of extrinsic apoptotic signaling pathway / regulation of protein stability / protein localization / structural constituent of cytoskeleton / nuclear matrix / Separation of Sister Chromatids / protein import into nucleus / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / cellular senescence / Signaling by BRAF and RAF1 fusions / cell migration / nuclear envelope / site of double-strand break / cellular response to hypoxia / nuclear membrane / microtubule / nuclear speck / cadherin binding / negative regulation of cell population proliferation / cell division / focal adhesion / centrosome / positive regulation of gene expression / protein kinase binding / structural molecule activity / perinuclear region of cytoplasm / Golgi apparatus / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function
Resolution: 2.83→83.58 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 48.452 / SU ML: 0.396 / Cross valid method: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.28131
496
5.1 %
RANDOM
Rwork
0.23747
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-
-
obs
0.23972
9158
99.81 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 110.135 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-8.1 Å2
0 Å2
-0 Å2
2-
-
-8.1 Å2
-0 Å2
3-
-
-
16.21 Å2
Refinement step
Cycle: 1 / Resolution: 2.83→83.58 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1360
0
0
22
1382
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.013
1371
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.017
1294
X-RAY DIFFRACTION
r_angle_refined_deg
1.909
1.65
1848
X-RAY DIFFRACTION
r_angle_other_deg
1.505
1.583
2988
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.687
5
162
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.526
22.277
101
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.705
15
265
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
25.033
15
17
X-RAY DIFFRACTION
r_chiral_restr
0.106
0.2
180
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
1542
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
289
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
8.644
9.074
654
X-RAY DIFFRACTION
r_mcbond_other
8.645
9.068
653
X-RAY DIFFRACTION
r_mcangle_it
12.417
13.607
814
X-RAY DIFFRACTION
r_mcangle_other
12.41
13.614
815
X-RAY DIFFRACTION
r_scbond_it
10.662
10.572
717
X-RAY DIFFRACTION
r_scbond_other
10.672
10.562
715
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_scangle_other
16.827
15.37
1034
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.83→2.904 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.419
39
-
Rwork
0.422
639
-
obs
-
-
99.12 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°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)
1
4.5615
-1.4879
0.1825
1.108
-0.0813
0.0777
-0.0063
-0.1094
0.5139
-0.0872
0.0594
-0.2149
-0.0966
0.0043
-0.053
0.1568
-0.0057
0.112
0.0857
0.0185
0.1541
21.5089
9.51
-7.187
2
0.3653
0.3827
-0.113
0.4495
-0.1152
0.0391
-0.18
0.1024
-0.1484
-0.1327
0.1433
-0.0791
0.0291
-0.0389
0.0366
0.1584
0.0451
0.0182
0.1563
0.0143
0.2519
20.067
11.3854
-5.3879
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
25 - 107
2
X-RAY DIFFRACTION
2
B
26 - 106
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