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- PDB-5vfw: An engineered cyclic peptide alleviates symptoms of inflammation ... -

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Basic information

Entry
Database: PDB / ID: 5vfw
TitleAn engineered cyclic peptide alleviates symptoms of inflammation in a murine model of inflammatory bowel disease
ComponentsAnnexin A1
KeywordsPROTEIN BINDING / STRUCTURE FROM CYANA 3.97
Function / homology
Function and homology information


regulation of interleukin-1 production / myoblast migration involved in skeletal muscle regeneration / regulation of leukocyte migration / granulocyte chemotaxis / positive regulation of T-helper 1 cell differentiation / phospholipase A2 inhibitor activity / regulation of hormone secretion / positive regulation of vesicle fusion / neutrophil clearance / negative regulation of T-helper 2 cell differentiation ...regulation of interleukin-1 production / myoblast migration involved in skeletal muscle regeneration / regulation of leukocyte migration / granulocyte chemotaxis / positive regulation of T-helper 1 cell differentiation / phospholipase A2 inhibitor activity / regulation of hormone secretion / positive regulation of vesicle fusion / neutrophil clearance / negative regulation of T-helper 2 cell differentiation / positive regulation of neutrophil apoptotic process / negative regulation of interleukin-8 production / neutrophil activation / cadherin binding involved in cell-cell adhesion / peptide cross-linking / cornified envelope / neutrophil homeostasis / calcium-dependent phospholipid binding / Formyl peptide receptors bind formyl peptides and many other ligands / motile cilium / negative regulation of exocytosis / cellular response to glucocorticoid stimulus / vesicle membrane / alpha-beta T cell differentiation / arachidonate secretion / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of wound healing / phosphatidylserine binding / monocyte chemotaxis / phagocytic cup / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / lateral plasma membrane / Smooth Muscle Contraction / cellular response to vascular endothelial growth factor stimulus / positive regulation of G1/S transition of mitotic cell cycle / phagocytosis / positive regulation of T cell proliferation / keratinocyte differentiation / positive regulation of interleukin-2 production / adherens junction / sarcolemma / phospholipid binding / calcium-dependent protein binding / regulation of cell shape / regulation of inflammatory response / early endosome membrane / G alpha (i) signalling events / actin cytoskeleton organization / Interleukin-4 and Interleukin-13 signaling / basolateral plasma membrane / G alpha (q) signalling events / collagen-containing extracellular matrix / vesicle / adaptive immune response / cell surface receptor signaling pathway / endosome / inflammatory response / apical plasma membrane / innate immune response / signaling receptor binding / focal adhesion / lipid binding / calcium ion binding / negative regulation of apoptotic process / cell surface / signal transduction / extracellular space / extracellular exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Annexin A1 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDaly, N.L. / Cobos Caceres, C.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: An engineered cyclic peptide alleviates symptoms of inflammation in a murine model of inflammatory bowel disease.
Authors: Cobos Caceres, C. / Bansal, P.S. / Navarro, S. / Wilson, D. / Don, L. / Giacomin, P. / Loukas, A. / Daly, N.L.
History
DepositionApr 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 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: Annexin A1


Theoretical massNumber of molelcules
Total (without water)3,0491
Polymers3,0491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Annexin A1 / Annexin I / Annexin-1 / Calpactin II / Calpactin-2 / Chromobindin-9 / Lipocortin I / Phospholipase ...Annexin I / Annexin-1 / Calpactin II / Calpactin-2 / Chromobindin-9 / Lipocortin I / Phospholipase A2 inhibitory protein / p35


Mass: 3049.405 Da / Num. of mol.: 1 / Fragment: N terminal Annexin I (2-26) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04083

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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 TOCSY
121isotropic12D 1H-1H COSY
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-13C HSQC
151isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 0.2 mM Ac 2-26, 90% H2O/10% D2O / Label: Ac 2-26 / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.2 mM / Component: Ac 2-26 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 1 Not defined / Label: condition-1 / pH: 5 / Pressure: 1 atm / Temperature: 290 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CcpNMRCCPNchemical shift assignment
CcpNMRCCPNdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
TopSpinBruker Biospincollection
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 3
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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