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- PDB-1qzp: NMR structure of the human dematin headpiece domain -

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Basic information

Entry
Database: PDB / ID: 1qzp
TitleNMR structure of the human dematin headpiece domain
Componentsdematin
KeywordsPROTEIN BINDING / DEMATIN HEADPIECE / VILLIN HEADPIECE / ACTIN BINDING DOMAIN
Function / homology
Function and homology information


negative regulation of protein targeting to membrane / spectrin-associated cytoskeleton / negative regulation of peptidyl-tyrosine phosphorylation / negative regulation of substrate adhesion-dependent cell spreading / Miscellaneous transport and binding events / platelet dense tubular network membrane / negative regulation of focal adhesion assembly / cell projection membrane / regulation of filopodium assembly / actin filament capping ...negative regulation of protein targeting to membrane / spectrin-associated cytoskeleton / negative regulation of peptidyl-tyrosine phosphorylation / negative regulation of substrate adhesion-dependent cell spreading / Miscellaneous transport and binding events / platelet dense tubular network membrane / negative regulation of focal adhesion assembly / cell projection membrane / regulation of filopodium assembly / actin filament capping / positive regulation of fibroblast migration / regulation of lamellipodium assembly / negative regulation of cell-substrate adhesion / lamellipodium assembly / spectrin binding / positive regulation of wound healing / cortical cytoskeleton / negative regulation of peptidyl-threonine phosphorylation / negative regulation of peptidyl-serine phosphorylation / actin filament bundle assembly / : / positive regulation of blood coagulation / endomembrane system / erythrocyte development / cellular response to cAMP / cytoskeleton organization / cellular response to calcium ion / actin filament / regulation of actin cytoskeleton organization / : / actin filament binding / actin cytoskeleton / actin binding / regulation of cell shape / cytoplasmic vesicle / actin cytoskeleton organization / protein-containing complex assembly / postsynaptic density / signaling receptor binding / perinuclear region of cytoplasm / plasma membrane / cytosol
Similarity search - Function
Putative adherens-junction anchoring domain / Putative adherens-junction anchoring region of AbLIM / Villin Headpiece Domain; Chain A / Villin headpiece domain / Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Distance geometry, simulated annealing
Model type detailsminimized average
AuthorsFrank, B.S. / Vardar, D. / Chishti, A.H. / McKnight, C.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The NMR structure of dematin headpiece reveals a dynamic loop that is conformationally altered upon phosphorylation at a distal site
Authors: Frank, B.S. / Vardar, D. / Chishti, A.H. / McKnight, C.J.
History
DepositionSep 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE The DHP construct spans residues 316 to 383 of the 48 kDa form of human dematin. To ...SEQUENCE The DHP construct spans residues 316 to 383 of the 48 kDa form of human dematin. To facilitate the comparison with other headpiece domains, we use the numbering scheme from Vardar et al., 1999, J.Molec.Biol., 294, 1299-1310, such that the N-terminal proline of DHP is residue 9, and C-terminal phenylalanine is residue 76. The final residue (F76) is the natural C-terminal residue of dematin.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dematin


Theoretical massNumber of molelcules
Total (without water)7,9361
Polymers7,9361
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)13 / 50structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein dematin


Mass: 7936.326 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pD48 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: Q08495

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
121HNCA
131HN(CO)CA
141HNCO
151HN(CA)CO
1633D 15N-separated NOESY
1733D 15N-separated TOCSY
181(H)CCH-COSY
1932D NOESY
11032D TOCSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM DHP U-15N,13C10 mM phosphate, 0.5 mM TMSP, pH 6.0, 10% D2O, and 0.01% sodium azide
24 mM DHP U-15N10 mM phosphate, 0.5 mM TMSP, pH 6.0, 10% D2O, and 0.01% sodium azide
30.7 mM DHP 10% 13C, U-15N10 mM phosphate, 0.5 mM TMSP, pH 6.0, 10% D2O, and 0.01% sodium azide
Sample conditionsIonic strength: 10 mM phosphate / pH: 6.0 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brungerstructure solution
NMRPipesgi6xDelaglioprocessing
XwinNMR3.1Brukercollection
NMRView4.1.2Johnsondata analysis
MOLMOL2k.2Koradirefinement
RefinementMethod: Distance geometry, simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 1241 restraints: 1129 are NOE-derived distance constraints, 92 are dihedral angle restraints, and 20 are distance restraints from hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 13

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