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- PDB-2k6n: Solution Structure of Human Supervillin Headpiece, Minimized Average -

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Basic information

Entry
Database: PDB / ID: 2k6n
TitleSolution Structure of Human Supervillin Headpiece, Minimized Average
ComponentsSupervillin
KeywordsSTRUCTURAL PROTEIN / Supervillin / SVHP / HP / Headpiece / Villin / Archvillin / Actin capping / Actin-binding / Alternative splicing / Calcium / Cytoplasm / Cytoskeleton / Membrane / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


microtubule minus-end / actin filament severing / barbed-end actin filament capping / costamere / actin polymerization or depolymerization / podosome / positive regulation of cytokinesis / cleavage furrow / skeletal muscle tissue development / phosphatidylinositol-4,5-bisphosphate binding ...microtubule minus-end / actin filament severing / barbed-end actin filament capping / costamere / actin polymerization or depolymerization / podosome / positive regulation of cytokinesis / cleavage furrow / skeletal muscle tissue development / phosphatidylinositol-4,5-bisphosphate binding / cell projection / actin filament binding / actin cytoskeleton / midbody / focal adhesion / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Villin Headpiece Domain; Chain A / Villin headpiece domain / Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain ...Villin Headpiece Domain; Chain A / Villin headpiece domain / Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsBrown, J.W. / Didem, V. / McKnight, C.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: How to arm a supervillin: designing F-actin binding activity into supervillin headpiece.
Authors: Brown, J.W. / Vardar-Ulu, D. / McKnight, C.J.
History
DepositionJul 11, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 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: Supervillin


Theoretical massNumber of molelcules
Total (without water)7,7081
Polymers7,7081
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 / 100
RepresentativeModel #1lowest energy

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Components

#1: Protein Supervillin / Archvillin / p205/p250


Mass: 7708.040 Da / Num. of mol.: 1 / Fragment: UNP residues 2149-2214, HP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SVIL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95425

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1242D 1H-13C HSQC
1352D 1H-1H TOCSY
1452D 1H-1H COSY
1513D HNCO
1613D HNCA
1713D HN(CO)CA
1813D HN(CA)CO
1943D (H)CCH-TOCSY
11043D (H)CCH-COSY
11123D HNHA
11223D HNHB
11352D 1H-1H NOESY
11423D 1H-15N NOESY
11543D 1H-13C NOESY
11632D 1H-13C HSQC
11723D HMQC-J
NMR detailsText: DISTANCE RESTRAINTS WERE DETERMINED FROM A NOESY BUILDUP SERIES. MIXING TIMES OF 50, 75, 100, 125, 150 - 13C AND 15N NOE ASSIGNMENTS WERE BINED AS WEAK

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3-2.5 mM [U-13C; U-15N] Supervillin Headpiece, 4 mM DTT, 500 uM TMSP, 100 mM sodium chloride, 20 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
21.3-2.5 mM [U-15N] Supervillin Headpiece, 4 mM DTT, 500 uM TMSP, 100 mM sodium chloride, 20 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
31.3-2.5 mM [U-10% 13C] Supervillin Headpiece, 4 mM DTT, 500 uM TMSP, 100 mM sodium chloride, 20 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
41.3-2.5 mM [U-13C] Supervillin Headpiece, 4 mM DTT, 500 uM TMSP, 100 mM sodium chloride, 20 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
51.3-2.5 mM Supervillin Headpiece, 4 mM DTT, 500 uM TMSP, 100 mM sodium chloride, 20 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMSupervillin Headpiece[U-13C; U-15N]1
4 mMDTT1
500 uMTMSP1
100 mMsodium chloride1
20 mMsodium phosphate1
1.3 mMSupervillin Headpiece[U-15N]2
4 mMDTT2
500 uMTMSP2
100 mMsodium chloride2
20 mMsodium phosphate2
1.3 mMSupervillin Headpiece[U-10% 13C]3
4 mMDTT3
500 uMTMSP3
100 mMsodium chloride3
20 mMsodium phosphate3
1.3 mMSupervillin Headpiece[U-13C]4
4 mMDTT4
500 uMTMSP4
100 mMsodium chloride4
20 mMsodium phosphate4
1.3 mMSupervillin Headpiece5
4 mMDTT5
500 uMTMSP5
100 mMsodium chloride5
20 mMsodium phosphate5
Sample conditionspH: 7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGERrefinement
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MOLMOL2K.2Koradi, Billeter and Wuthrichstructural alignment
MOLMOL2K.2Koradi, Billeter and Wuthrichstructural visualization
XwinNMR3.1Bruker Biospincollection
TALOSCornilescu, Delaglio and Baxdata analysis
PREDITOR(PREDITOR) M. V. Berjanskii, S. Neal, D. S. Wishartdata analysis
NMRView7.0.16Johnson, One Moon Scientificpeak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers calculated total number: 100 / Conformers submitted total number: 1

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