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- PDB-8eb1: Chim2 - Intragenic antimicrobial peptide -

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Basic information

Entry
Database: PDB / ID: 8eb1
TitleChim2 - Intragenic antimicrobial peptide
ComponentsUnconventional myosin-Ih, Transcription activator BRG1 intragenic antimicrobial chimeric peptide
KeywordsANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


microfilament motor activity => GO:0000146 / positive regulation of glucose mediated signaling pathway / bBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / npBAF complex / negative regulation of androgen receptor signaling pathway / Tat protein binding / nBAF complex / GBAF complex / neural retina development ...microfilament motor activity => GO:0000146 / positive regulation of glucose mediated signaling pathway / bBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / npBAF complex / negative regulation of androgen receptor signaling pathway / Tat protein binding / nBAF complex / GBAF complex / neural retina development / regulation of G0 to G1 transition / EGR2 and SOX10-mediated initiation of Schwann cell myelination / nucleosome disassembly / regulation of nucleotide-excision repair / vesicle transport along actin filament / RSC-type complex / RNA polymerase I preinitiation complex assembly / positive regulation by host of viral transcription / myosin complex / regulation of mitotic metaphase/anaphase transition / ATP-dependent chromatin remodeler activity / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear androgen receptor binding / microfilament motor activity / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / microvillus / positive regulation of Wnt signaling pathway / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / Chromatin modifying enzymes / DNA polymerase binding / transcription initiation-coupled chromatin remodeling / Interleukin-7 signaling / helicase activity / transcription coregulator binding / positive regulation of cell differentiation / actin filament organization / Formation of the beta-catenin:TCF transactivating complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lysine-acetylated histone binding / negative regulation of cell growth / kinetochore / fibrillar center / RMTs methylate histone arginines / positive regulation of DNA-binding transcription factor activity / nuclear matrix / positive regulation of miRNA transcription / transcription corepressor activity / actin filament binding / p53 binding / actin cytoskeleton / nervous system development / positive regulation of cold-induced thermogenesis / vesicle / transcription coactivator activity / hydrolase activity / chromatin remodeling / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular space / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
SWI/SNF complex subunit BRG1 / Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / domain in helicases and associated with SANT domains ...SWI/SNF complex subunit BRG1 / Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transcription activator BRG1 / Unconventional myosin-Ih
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Authorsde Freitas, T.V. / Oliveira, A.L. / Santos, M.A. / Brand, G.D.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Other governmentFAP-DF: 0193.001566/2017 Brazil
Other governmentFAP-DF: 0193.000866/2015 Brazil
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Release of immunomodulatory peptides at bacterial membrane interfaces as a novel strategy to fight microorganisms.
Authors: Viana de Freitas, T. / Karmakar, U. / Vasconcelos, A.G. / Santos, M.A. / Oliveira do Vale Lira, B. / Costa, S.R. / Barbosa, E.A. / Cardozo-Fh, J. / Correa, R. / Ribeiro, D.J.S. / Prates, M.V. ...Authors: Viana de Freitas, T. / Karmakar, U. / Vasconcelos, A.G. / Santos, M.A. / Oliveira do Vale Lira, B. / Costa, S.R. / Barbosa, E.A. / Cardozo-Fh, J. / Correa, R. / Ribeiro, D.J.S. / Prates, M.V. / Magalhaes, K.G. / Soller Ramada, M.H. / Roberto de Souza Almeida Leite, J. / Bloch Jr., C. / Lima de Oliveira, A. / Vendrell, M. / Brand, G.D.
History
DepositionAug 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 12, 2023Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Unconventional myosin-Ih, Transcription activator BRG1 intragenic antimicrobial chimeric peptide


Theoretical massNumber of molelcules
Total (without water)2,9501
Polymers2,9501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Unconventional myosin-Ih, Transcription activator BRG1 intragenic antimicrobial chimeric peptide / Myosin-1H / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth ...Myosin-1H / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and transcription activator / Protein BRG-1 / Protein brahma homolog 1 / SNF2-beta / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4


Mass: 2949.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q8N1T3, UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 1.28 mM peptide, 32 mM D-98% Dodecylphosphorylcholine-d38, 10 mM PBS, 90% H2O/10% D2O
Label: Chim2 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.28 mMpeptidenatural abundance1
32 mMDodecylphosphorylcholine-d38D-98%1
10 mMPBSnatural abundance1
Sample conditionsIonic strength: PBS 10 mM mM / Label: condition_1 / pH: 7.4 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.1 / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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