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- PDB-1vii: THERMOSTABLE SUBDOMAIN FROM CHICKEN VILLIN HEADPIECE, NMR, MINIMI... -

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Basic information

Entry
Database: PDB / ID: 1vii
TitleTHERMOSTABLE SUBDOMAIN FROM CHICKEN VILLIN HEADPIECE, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsVILLIN
KeywordsACTIN BINDING / 3 HELIX MOTIF / THERMOSTABLE SUBDOMAIN
Function / homology
Function and homology information


regulation of actin nucleation / lysophosphatidic acid binding / cytoplasmic actin-based contraction involved in cell motility / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / actin filament capping / barbed-end actin filament capping ...regulation of actin nucleation / lysophosphatidic acid binding / cytoplasmic actin-based contraction involved in cell motility / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / actin filament capping / barbed-end actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cellular response to hepatocyte growth factor stimulus / actin filament bundle / microvillus / positive regulation of epithelial cell migration / ruffle / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / cellular response to epidermal growth factor stimulus / response to bacterium / filopodium / epidermal growth factor receptor signaling pathway / actin filament binding / regulation of cell shape / lamellipodium / actin cytoskeleton / positive regulation of cell migration / calcium ion binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / Gelsolin-like domain superfamily / Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING
AuthorsMcknight, C.J.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: NMR structure of the 35-residue villin headpiece subdomain.
Authors: McKnight, C.J. / Matsudaira, P.T. / Kim, P.S.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: A Thermostable 35-Residue Subdomain within Villin Headpiece
Authors: Mcknight, C.J. / Doering, D.S. / Matsudaira, P.T. / Kim, P.S.
History
DepositionJan 15, 1997Processing site: BNL
Revision 1.0Aug 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VILLIN


Theoretical massNumber of molelcules
Total (without water)4,1961
Polymers4,1961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100NO NOE VIOLATIONS > 0.4 ANGSTROMS, NO ANGLE VIOLATION > 5 DEG
Representative

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Components

#1: Protein/peptide VILLIN / HP-36 / R42-76


Mass: 4195.901 Da / Num. of mol.: 1 / Fragment: THERMOSTABLE SUBDOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Tissue: EPITHELIUM / Cell: EPITHELIAL / Cellular location: MICROVILLI / Organ: INTESTINE / Plasmid: PVHP42-76B / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02640

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121CLEANTOCSY
131DQFCOSY
141HSQC
151ECOSY
161HMQCJ

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Sample preparation

Sample conditionspH: 3.7 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX500 / Manufacturer: Bruker / Model: AMX500 / Field strength: 500 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: 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 ensembleConformer selection criteria: NO NOE VIOLATIONS > 0.4 ANGSTROMS, NO ANGLE VIOLATION > 5 DEG
Conformers calculated total number: 100 / Conformers submitted total number: 1

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