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- PDB-2k6m: Solution Structure of Human Supervillin Headpiece -

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Basic information

Entry
Database: PDB / ID: 2k6m
TitleSolution Structure of Human Supervillin Headpiece
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 / cytoplasm / cytosol
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
S: 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)22 / 100structures with the lowest energy
RepresentativeModel #1

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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
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H COSY
1513D HNCA
1613D HNCO
1713D HN(C 3D (H)CCH-TOCSY
1813D (H)CCH-COSY
1913D HNHA
11013D HNHB
11113D HN(CA)CO
11212D 1H-1H NOESY
11313D 1H-15N NOESY 3D 1H-13C NOESY
11413D HMQC-J
NMR detailsText: DISTANCE RESTRAINTS WERE DETERMINED FROM A NOESY BUILDUP SERIES. MIXING TIMES OF 50, 75, 100, 125 AND 150 US. EXTRA RESTRAINTS FROM 13C AND 15N-EDITTED NOESY BINED AS WEAK

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Sample preparation

DetailsContents: 1.3-2.5 MM [U-13C SUPERVILLIN HEADPIECE, 4 MM DTT, 100 MM SODIUM CHLORIDE, 500 UM TMSP, 20 MM SODIUM PHOSPHATE, 95% H2O/5% D2O; 1.3-2.5 MM [U-15N] SUPERVILLIN HEADPIECE, 20 MM SODIUM ...Contents: 1.3-2.5 MM [U-13C SUPERVILLIN HEADPIECE, 4 MM DTT, 100 MM SODIUM CHLORIDE, 500 UM TMSP, 20 MM SODIUM PHOSPHATE, 95% H2O/5% D2O; 1.3-2.5 MM [U-15N] SUPERVILLIN HEADPIECE, 20 MM SODIUM PHOSPHATE, 500 UM TMSP, 4 MM DTT, 100 MM SODIUM CHLORIDE, 95% H2O/5% D2O; 1.3-2.5 MM [U- 10% 13C] SUPERVILLIN HEADPIECE, 4 MM DTT, 500 UM TMSP, 100 MM SODIUM CHLORIDE, 20 MM SODIUM PHOSPHATE, 95% H2O/5% D2O; 1.3-2.5 MM SUPERVILLIN HEADPIECE, 4 MM DTT, 500 UM TMSP, 100 MM SODIUM CHLORIDE, 20 MM SODIUM PHOSPHATE, 95% H2O/5% D2O; 1.3-2.5 MM [U-13C] SUPERVILLIN HEADPIECE, 4 MM DTT, 100 MM SODIUM CHLORIDE, 20 MM SODIUM PHOSPHATE, 500 UM TMSP, 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMSupervillin Headpiece[U-13C; U-15N]1
4 mMDTT1
100 mMsodium chloride1
500 uMTMSP1
20 mMsodium phosphate1
1.3 mMSupervillin Headpiece[U-15N]2
20 mMsodium phosphate2
500 uMTMSP2
4 mMDTT2
100 mMsodium chloride2
1.3 mMSupervillin Headpiece[U-10% 13C]3
4 mMDTT3
500 uMTMSP3
100 mMsodium chloride3
20 mMsodium phosphate3
1.3 mMSupervillin Headpiece4
4 mMDTT4
500 uMTMSP4
100 mMsodium chloride4
20 mMsodium phosphate4
1.3 mMSupervillin Headpiece[U-13C]5
4 mMDTT5
100 mMsodium chloride5
20 mMsodium phosphate5
500 uMTMSP5
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
CNS1.1structure solution
NMRPipestructure solution
MOLMOL 2K.22K.2structure solution
XwinNMR3.1structure solution
TALOSstructure solution
PREDITORstructure solution
NMRView7.0.16structure solution
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 22

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