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- PDB-2l3x: villin head piece domain of human ABLIM2 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2l3x
Titlevillin head piece domain of human ABLIM2
ComponentsABLIM2 protein
KeywordsPROTEIN BINDING / actin binding
Function / homology
Function and homology information


DCC mediated attractive signaling / lamellipodium assembly / cytoskeleton organization / actin filament binding / actin cytoskeleton / metal ion binding / cytoplasm
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 ...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 / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Actin-binding LIM protein 2 / Actin-binding LIM protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsfewest violations, model 1
AuthorsBruton, S. / Pfuhl, M.
CitationJournal: To be Published
Title: Solution NMR study of the actin binding domain of ABLIM2
Authors: Bruton, S. / Pfuhl, M.
History
DepositionSep 24, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABLIM2 protein


Theoretical massNumber of molelcules
Total (without water)8,2131
Polymers8,2131
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)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein ABLIM2 protein


Mass: 8212.551 Da / Num. of mol.: 1 / Fragment: Villin Head Piece Domain (unp residues 455-521)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABLIM2 / Plasmid: pLEICS-07 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (Invitrogen) / References: UniProt: Q08E71, UniProt: Q6H8Q1*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1233D CBCA(CO)NH
1333D HN(CA)CB
1433D HNCO
1533D HN(CA)CO
1623D 1H-15N NOESY
1733D HBHA(CO)NH
1812D NOESY
1943D 1H-13C NOESY
11043D (H)CCH-TOCSY
11142D 13C CT-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM VHD, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 0.02 % sodium azide, 100% D2O100% D2O
20.7 mM [U-99% 15N] VHD, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
30.7 mM [U-99% 13C; U-99% 15N] VHD, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
40.7 mM [U-99% 13C; U-99% 15N] VHD, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 0.02 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMVHD-11
20 mMsodium phosphate-21
50 mMsodium chloride-31
2 mMDTT-41
0.02 %sodium azide-51
0.7 mMVHD-6[U-99% 15N]2
20 mMsodium phosphate-72
50 mMsodium chloride-82
2 mMDTT-92
0.02 %sodium azide-102
0.7 mMVHD-11[U-99% 13C; U-99% 15N]3
20 mMsodium phosphate-123
50 mMsodium chloride-133
2 mMDTT-143
0.02 %sodium azide-153
0.7 mMVHD-16[U-99% 13C; U-99% 15N]4
20 mMsodium phosphate-174
50 mMsodium chloride-184
2 mMDTT-194
0.02 %sodium azide-204
Sample conditionsIonic strength: 90 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CCPN_Analysis2.1CCPN (Laue et al.)chemical shift assignment
CCPN_Analysis2.1CCPN (Laue et al.)peak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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