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- PDB-1vii: THERMOSTABLE SUBDOMAIN FROM CHICKEN VILLIN HEADPIECE, NMR, MINIMI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1vii | ||||||
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Title | THERMOSTABLE SUBDOMAIN FROM CHICKEN VILLIN HEADPIECE, NMR, MINIMIZED AVERAGE STRUCTURE | ||||||
![]() | VILLIN | ||||||
![]() | ACTIN BINDING / 3 HELIX MOTIF / THERMOSTABLE SUBDOMAIN | ||||||
Function / homology | ![]() regulation of actin nucleation / cytoplasmic actin-based contraction involved in cell motility / lysophosphatidic acid binding / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / actin filament capping / actin filament depolymerization ...regulation of actin nucleation / cytoplasmic actin-based contraction involved in cell motility / lysophosphatidic acid binding / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / actin filament capping / actin filament depolymerization / barbed-end actin filament capping / actin polymerization or depolymerization / cellular response to hepatocyte growth factor stimulus / positive regulation of epithelial cell migration / actin filament bundle / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / microvillus / cellular response to epidermal growth factor stimulus / ruffle / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / filopodium / response to bacterium / epidermal growth factor receptor signaling pathway / actin filament binding / actin cytoskeleton / lamellipodium / regulation of cell shape / positive regulation of cell migration / calcium ion binding / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING | ||||||
![]() | Mcknight, C.J. | ||||||
![]() | ![]() Title: NMR structure of the 35-residue villin headpiece subdomain. Authors: McKnight, C.J. / Matsudaira, P.T. / Kim, P.S. #1: ![]() Title: A Thermostable 35-Residue Subdomain within Villin Headpiece Authors: Mcknight, C.J. / Doering, D.S. / Matsudaira, P.T. / Kim, P.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22.9 KB | Display | ![]() |
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PDB format | ![]() | 14.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 242.8 KB | Display | ![]() |
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Full document | ![]() | 242.5 KB | Display | |
Data in XML | ![]() | 2.7 KB | Display | |
Data in CIF | ![]() | 3.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 4195.901 Da / Num. of mol.: 1 / Fragment: THERMOSTABLE SUBDOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Sample conditions | pH: 3.7 / Temperature: 303 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AMX500 / Manufacturer: Bruker / Model: AMX500 / Field strength: 500 MHz |
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Processing
Software |
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NMR software |
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Refinement | Method: DISTANCE GEOMETRY SIMULATED ANNEALING / Software ordinal: 1 Details: THE X-PLOR (R6)1/6 NOE POTENTIAL WAS USED FOR NOE'S INVOLVING NON-STEREOSPECIFICALLY ASSIGNED METHYL, METHYLENE, AND AROMATIC PROTONS. NO ATTRACTIVE POTENTIALS WERE USED IN CALCULATING THE ...Details: THE X-PLOR (R6)1/6 NOE POTENTIAL WAS USED FOR NOE'S INVOLVING NON-STEREOSPECIFICALLY ASSIGNED METHYL, METHYLENE, AND AROMATIC PROTONS. NO ATTRACTIVE POTENTIALS WERE USED IN CALCULATING THE STRUCTURES. THE VAN DER WAALS CUTOFF USED FOR THE X-PLOR REPEL FUNCTION WAS 0.75 ANGSTROMS. AFTER DISTANCE GEOMETRY AND REGULARIZATION, EACH STRUCTURE WAS SUBJECTED TO ONE ROUND OF SIMULATED ANNEALING FROM 2000K TO 100K OVER 2000 STEPS. THIS IS THE AVERAGE OF 29 STRUCTURES MINIMIZED USING ONLY REPULSIVE POTENTIALS. | |||||||||
NMR ensemble | Conformer selection criteria: NO NOE VIOLATIONS > 0.4 ANGSTROMS, NO ANGLE VIOLATION > 5 DEG Conformers calculated total number: 100 / Conformers submitted total number: 1 |