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Open data
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Basic information
Entry | Database: PDB / ID: 6xf2 | ||||||
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Title | Nesprin-1G (aa2070-2200)-FHOD1(aa1-339) complex, H. sapiens | ||||||
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![]() | STRUCTURAL PROTEIN / spectrin repeat / FH3 domain / armadillo repeat / scaffold protein / nuclear positioning / transmembrane / actin-associated / nuclear line | ||||||
Function / homology | ![]() negative regulation of mini excitatory postsynaptic potential / regulation of nucleus organization / nuclear matrix anchoring at nuclear membrane / cytoskeleton-nuclear membrane anchor activity / meiotic nuclear membrane microtubule tethering complex / negative regulation of mesenchymal cell apoptotic process / establishment of centrosome localization / bleb / muscle cell differentiation / lamin binding ...negative regulation of mini excitatory postsynaptic potential / regulation of nucleus organization / nuclear matrix anchoring at nuclear membrane / cytoskeleton-nuclear membrane anchor activity / meiotic nuclear membrane microtubule tethering complex / negative regulation of mesenchymal cell apoptotic process / establishment of centrosome localization / bleb / muscle cell differentiation / lamin binding / cardiac muscle cell differentiation / regulation of stress fiber assembly / nuclear outer membrane / regulation of postsynaptic neurotransmitter receptor internalization / nuclear migration / positive regulation of mesenchymal cell proliferation / cortical actin cytoskeleton organization / regulation of dendrite morphogenesis / dendritic spine head / nucleus organization / Golgi organization / kinesin binding / intercalated disc / response to light stimulus / positive regulation of stress fiber assembly / cytoskeleton organization / Meiotic synapsis / sarcomere / P-body / positive regulation of receptor-mediated endocytosis / : / actin filament binding / nuclear envelope / actin binding / midbody / spermatogenesis / postsynaptic membrane / nuclear membrane / cytoskeleton / protein domain specific binding / signaling receptor binding / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lim, S.M. / Schwartz, T.U. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of FHOD1-Nesprin1/2 complexes reveal alternate binding modes for the FH3 domain of formins. Authors: Lim, S.M. / Cruz, V.E. / Antoku, S. / Gundersen, G.G. / Schwartz, T.U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190.5 KB | Display | ![]() |
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PDB format | ![]() | 126.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.6 KB | Display | ![]() |
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Full document | ![]() | 443.1 KB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 29.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xf1SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 15259.411 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 35489.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 65.27 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES/NaOH pH 7.0, 0.2 M sodium thiocyanate, 40% 5/4 pentaerythritol propoxylate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 7.1→60.58 Å / Num. obs: 2378 / % possible obs: 98.2 % / Redundancy: 6 % / Biso Wilson estimate: 464.08 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.063 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 7.1→7.35 Å / Num. unique obs: 232 / CC1/2: 0.63 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6XF1 Resolution: 7.11→60.58 Å / SU ML: 1.2952 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.3238 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 320.7 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 7.11→60.58 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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