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- PDB-2kbm: Ca-S100A1 interacting with TRTK12 -

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Basic information

Entry
Database: PDB / ID: 2kbm
TitleCa-S100A1 interacting with TRTK12
Components
  • F-actin-capping protein subunit alpha-2
  • Protein S100-A1
KeywordsMETAL BINDING PROTEIN / S100 / EF-hand / Protein-protein interaction / conformational change / CapZ / Acetylation / Actin capping / Actin-binding / Calcium / Cytoplasm / Metal-binding / Zinc
Function / homology
Function and homology information


COPI-independent Golgi-to-ER retrograde traffic / Advanced glycosylation endproduct receptor signaling / Factors involved in megakaryocyte development and platelet production / COPI-mediated anterograde transport / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / F-actin capping protein complex / MHC class II antigen presentation / barbed-end actin filament capping / M band / I band ...COPI-independent Golgi-to-ER retrograde traffic / Advanced glycosylation endproduct receptor signaling / Factors involved in megakaryocyte development and platelet production / COPI-mediated anterograde transport / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / F-actin capping protein complex / MHC class II antigen presentation / barbed-end actin filament capping / M band / I band / S100 protein binding / A band / regulation of heart contraction / cortical cytoskeleton / positive regulation of sprouting angiogenesis / brush border / sarcoplasmic reticulum / Z disc / calcium-dependent protein binding / actin filament binding / ATPase binding / actin cytoskeleton organization / calcium ion binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / mitochondrion / membrane / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Protein S100-A1 / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / S-100/ICaBP type calcium binding protein signature. ...Protein S100-A1 / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein S100-A1 / F-actin-capping protein subunit alpha-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing, DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 16
AuthorsWright, N.T. / Varney, K.M. / Cannon, B.R. / Morgan, M. / Weber, D.J.
CitationJournal: To be Published
Title: Solution structure of Ca-S100A1-TRTK12
Authors: Wright, N.T. / Morgan, M.T. / Cannon, B.R. / Varney, K.M. / Weber, D.J.
History
DepositionDec 2, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 8, 2018Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation
Category: database_PDB_caveat / pdbx_nmr_sample_details ...database_PDB_caveat / pdbx_nmr_sample_details / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _pdbx_nmr_sample_details.contents

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: F-actin-capping protein subunit alpha-2
Y: F-actin-capping protein subunit alpha-2
A: Protein S100-A1
B: Protein S100-A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9958
Polymers23,8354
Non-polymers1604
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4800 Å2
ΔGint-44 kcal/mol
Surface area11830 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide F-actin-capping protein subunit alpha-2 / CapZ alpha-2


Mass: 1477.728 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Capza2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3T1K5
#2: Protein Protein S100-A1 / / S100 calcium-binding protein A1 / S-100 protein alpha subunit / S-100 protein alpha chain


Mass: 10439.614 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: S100a1 / Production host: Escherichia coli (E. coli) / References: UniProt: P35467
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D C(CO)NH
1513D H(CCO)NH
1613D HNCO
1713D HNCA
1813D HNHA
1913D HN(CO)CA
1101IPAP-HSQC

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Sample preparation

DetailsContents: 10 % D2O-1, 10 mM CALCIUM ION-2, 10 mM DTT-3, 10 mM TRIS-4, 25 mM sodium chloride-5, 500 uM [U-100% 13C; U-100% 15N] entity_1-6, 1500 uM entity_3-7, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 %D2O-11
10 mMCALCIUM ION-21
10 mMDTT-31
10 mMTRIS-41
25 mMsodium chloride-51
500 uMentity_1-6[U-100% 13C; U-100% 15N]1
1500 uMentity_3-71
Sample conditionsIonic strength: 0.05 / pH: 7.2 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Bruker AvanceBrukerAvance6002

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Processing

NMR software
NameDeveloperClassification
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, DGSA-distance geometry simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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