+
Open data
-
Basic information
Entry | Database: PDB / ID: 7dtg | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of lamin B1 Ig-like domain from human | ||||||
![]() | Lamin-B1 | ||||||
![]() | NUCLEAR PROTEIN / Intermediate filament / nuclear lamin B1 / Ig-like domain | ||||||
Function / homology | ![]() structural constituent of nuclear lamina / Breakdown of the nuclear lamina / Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / nuclear envelope organization / nuclear pore localization / lamin filament / protein localization to nuclear envelope / nuclear lamina / Initiation of Nuclear Envelope (NE) Reformation ...structural constituent of nuclear lamina / Breakdown of the nuclear lamina / Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / nuclear envelope organization / nuclear pore localization / lamin filament / protein localization to nuclear envelope / nuclear lamina / Initiation of Nuclear Envelope (NE) Reformation / RHOF GTPase cycle / RHOD GTPase cycle / nuclear migration / nuclear inner membrane / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / phospholipase binding / heterochromatin formation / Meiotic synapsis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / structural constituent of cytoskeleton / nuclear matrix / sequence-specific double-stranded DNA binding / nuclear envelope / nuclear membrane / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ahn, J. / Lee, J. / Ha, N.-C. | ||||||
![]() | ![]() Title: Beta-strand-mediated dimeric formation of the Ig-like domains of human lamin A/C and B1. Authors: Ahn, J. / Lee, J. / Jeong, S. / Kang, S.M. / Park, B.J. / Ha, N.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 178.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 115.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 459.9 KB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7crgC ![]() 3umnS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
3 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 16346.178 Da / Num. of mol.: 6 / Fragment: Ig-like domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.75 % |
---|---|
Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, hanging drop / Details: magnesium nitrate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. obs: 17863 / % possible obs: 97.1 % / Redundancy: 7.4 % / Biso Wilson estimate: 25.16 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rpim(I) all: 0.025 / Rrim(I) all: 0.08 / Net I/σ(I): 17.95 |
Reflection shell | Resolution: 3.6→3.66 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 818 / CC1/2: 0.634 / CC star: 0.881 / Rpim(I) all: 0.15 / Rrim(I) all: 0.36 / % possible all: 91.1 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3UMN Resolution: 3.6→49.83 Å / SU ML: 0.4526 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 21.4258 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→49.83 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|