+Open data
-Basic information
Entry | Database: PDB / ID: 6xf2 | ||||||
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Title | Nesprin-1G (aa2070-2200)-FHOD1(aa1-339) complex, H. sapiens | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / spectrin repeat / FH3 domain / armadillo repeat / scaffold protein / nuclear positioning / transmembrane / actin-associated / nuclear line | ||||||
Function / homology | Function and homology information 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 / muscle cell differentiation / negative regulation of mesenchymal cell apoptotic process / establishment of centrosome localization / bleb / 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 / muscle cell differentiation / negative regulation of mesenchymal cell apoptotic process / establishment of centrosome localization / bleb / lamin binding / cardiac muscle cell differentiation / regulation of stress fiber assembly / nuclear outer membrane / regulation of postsynaptic neurotransmitter receptor internalization / nuclear migration / nucleus organization / positive regulation of mesenchymal cell proliferation / cortical actin cytoskeleton organization / regulation of dendrite morphogenesis / dendritic spine head / Golgi organization / response to light stimulus / intercalated disc / positive regulation of stress fiber assembly / Meiotic synapsis / sarcomere / P-body / positive regulation of receptor-mediated endocytosis / : / actin filament binding / nuclear envelope / actin binding / midbody / postsynaptic membrane / spermatogenesis / 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 / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.11 Å | ||||||
Authors | Lim, S.M. / Schwartz, T.U. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xf2.cif.gz | 190.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xf2.ent.gz | 126.1 KB | Display | PDB format |
PDBx/mmJSON format | 6xf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/6xf2 ftp://data.pdbj.org/pub/pdb/validation_reports/xf/6xf2 | HTTPS FTP |
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-Related structure data
Related structure data | 6xf1SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) Homo sapiens (human) / Gene: SYNE1, C6orf98, KIAA0796, KIAA1262, KIAA1756, MYNE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NF91 #2: Protein | Mass: 35489.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FHOD1, FHOS, FHOS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y613 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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