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Open data
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Basic information
Entry | Database: PDB / ID: 1gk7 | ||||||
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Title | HUMAN VIMENTIN COIL 1A FRAGMENT (1A) | ||||||
![]() | VIMENTIN | ||||||
![]() | VIMENTIN / INTERMEDIATE FILAMENT / HEPTAD REPEAT | ||||||
Function / homology | ![]() lens fiber cell development / keratin filament binding / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / Striated Muscle Contraction / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / microtubule organizing center ...lens fiber cell development / keratin filament binding / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / Striated Muscle Contraction / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / microtubule organizing center / intermediate filament / cell leading edge / Bergmann glial cell differentiation / positive regulation of collagen biosynthetic process / Caspase-mediated cleavage of cytoskeletal proteins / regulation of mRNA stability / phagocytic vesicle / Late endosomal microautophagy / structural constituent of cytoskeleton / nuclear matrix / cellular response to type II interferon / Aggrephagy / Chaperone Mediated Autophagy / peroxisome / neuron projection development / double-stranded RNA binding / negative regulation of neuron projection development / scaffold protein binding / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / molecular adaptor activity / cytoskeleton / protein domain specific binding / axon / focal adhesion / positive regulation of gene expression / extracellular exosome / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Strelkov, S.V. / Herrmann, H. / Geisler, N. / Zimbelmann, R. / Aebi, U. / Burkhard, P. | ||||||
![]() | ![]() Title: Conserved Segments 1A and 2B of the Intermediate Filament Dimer: Their Atomic Structures and Role in Filament Assembly. Authors: Strelkov, S. / Herrmann, H. / Geisler, N. / Wedig, T. / Zimbelmann, R. / Aebi, U. / Burkhard, P. #1: Journal: J.Mol.Biol. / Year: 2001 Title: Divide-and-Conquer Crystallographic Approach Towards an Atomic Structure of Intermediate Filaments Authors: Strelkov, S.V. / Herrmann, H. / Geisler, N. / Lustig, A. / Ivaninskii, S. / Zimbelmann, R. / Burkhard, P. / Aebi, 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 | ![]() | 29.5 KB | Display | ![]() |
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PDB format | ![]() | 20.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.2 KB | Display | ![]() |
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Full document | ![]() | 433.7 KB | Display | |
Data in XML | ![]() | 4.4 KB | Display | |
Data in CIF | ![]() | 5.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gk4C ![]() 1gk6C ![]() 2ztaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein/peptide | Mass: 4654.214 Da / Num. of mol.: 1 / Fragment: 1A, RESIDUES 102-138 Source method: isolated from a genetically manipulated source Details: TWO EXTRA RESIDUES, GS, AT THE N-TERMINUS ARE RESULT OF THE CLONING PROCEDURE Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Sequence details | THE RESIDUE NUMBERING USED IN THE LITERATURE FOR VIMENTIN DIFFERS BY +1 FROM THE NUMBERING USED IN ...THE RESIDUE NUMBERING USED IN THE LITERATURE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 59 % / Description: THE SEARCH MODEL WAS A SINGLE CHAIN |
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Crystal grow | pH: 6.5 Details: 2.0M AMMONIUM ACETATE, 10%(V/V) DIOXANE, 0.1M MES/NA, PH6.5, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: IMAGE PLATE / Date: Apr 15, 1999 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 11440 / % possible obs: 99.7 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.9 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZTA Resolution: 1.4→49.39 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.967 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→49.39 Å
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Refine LS restraints |
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