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- PDB-2ms4: Cyclophilin a complexed with a fragment of crk-ii -

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Basic information

Entry
Database: PDB / ID: 2ms4
TitleCyclophilin a complexed with a fragment of crk-ii
Components
  • Peptide
  • Peptidyl-prolyl cis-trans isomerase A
KeywordsISOMERASE / CYCLOPHILIN A
Function / homology
Function and homology information


response to hepatocyte growth factor / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / postsynaptic specialization assembly / regulation of intracellular signal transduction / protein phosphorylated amino acid binding / regulation of T cell migration / regulation of dendrite development ...response to hepatocyte growth factor / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / postsynaptic specialization assembly / regulation of intracellular signal transduction / protein phosphorylated amino acid binding / regulation of T cell migration / regulation of dendrite development / response to peptide / positive regulation of skeletal muscle acetylcholine-gated channel clustering / response to yeast / negative regulation of wound healing / reelin-mediated signaling pathway / negative regulation of cell motility / negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / negative regulation of viral life cycle / ARMS-mediated activation / lipid droplet organization / MET receptor recycling / heparan sulfate binding / regulation of viral genome replication / virion binding / negative regulation of natural killer cell mediated cytotoxicity / leukocyte chemotaxis / protein localization to membrane / MET activates RAP1 and RAC1 / negative regulation of stress-activated MAPK cascade / endothelial cell activation / regulation of GTPase activity / Basigin interactions / cellular response to insulin-like growth factor stimulus / cyclosporin A binding / p130Cas linkage to MAPK signaling for integrins / enzyme-linked receptor protein signaling pathway / positive regulation of smooth muscle cell migration / Minus-strand DNA synthesis / Plus-strand DNA synthesis / establishment of cell polarity / Uncoating of the HIV Virion / protein peptidyl-prolyl isomerization / Early Phase of HIV Life Cycle / dendrite development / regulation of cell adhesion mediated by integrin / Integration of provirus / positive regulation of Rac protein signal transduction / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / Calcineurin activates NFAT / ephrin receptor signaling pathway / Binding and entry of HIV virion / regulation of signal transduction / positive regulation of viral genome replication / negative regulation of protein phosphorylation / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of protein kinase B activity / cellular response to transforming growth factor beta stimulus / cytoskeletal protein binding / signaling adaptor activity / insulin-like growth factor receptor binding / ephrin receptor binding / positive regulation of substrate adhesion-dependent cell spreading / phosphotyrosine residue binding / neutrophil chemotaxis / Downstream signal transduction / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cellular response to nitric oxide / SH2 domain binding / protein tyrosine kinase binding / peptidyl-prolyl cis-trans isomerase activity / hippocampus development / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / positive regulation of protein secretion / cell chemotaxis / peptidylprolyl isomerase / negative regulation of protein kinase activity / regulation of actin cytoskeleton organization / Regulation of signaling by CBL / FCGR3A-mediated phagocytosis / positive regulation of JNK cascade / Assembly Of The HIV Virion / neuron migration / cellular response to nerve growth factor stimulus / Budding and maturation of HIV virion / neuromuscular junction / response to hydrogen peroxide / lipid metabolic process / receptor tyrosine kinase binding / cerebral cortex development / neuron differentiation / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / kinase binding / platelet activation / platelet aggregation
Similarity search - Function
CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / : / Variant SH3 domain / Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. ...CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / : / Variant SH3 domain / Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Adapter molecule crk / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
Model detailslowest energy, model1
AuthorsJankowski, W. / Saleh, T. / Rossi, P. / Kalodimos, C.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Cyclophilin A promotes cell migration via the Abl-Crk signaling pathway.
Authors: Saleh, T. / Jankowski, W. / Sriram, G. / Rossi, P. / Shah, S. / Lee, K.B. / Cruz, L.A. / Rodriguez, A.J. / Birge, R.B. / Kalodimos, C.G.
History
DepositionJul 22, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Dec 30, 2015Group: Database references
Revision 1.3Feb 3, 2016Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase A
B: Peptide


Theoretical massNumber of molelcules
Total (without water)18,9922
Polymers18,9922
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A / Peptidyl-prolyl cis-trans ...PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A / Peptidyl-prolyl cis-trans isomerase A / N-terminally processed


Mass: 18036.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli (E. coli) / References: UniProt: P62937, peptidylprolyl isomerase
#2: Protein/peptide Peptide


Mass: 955.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P46108*PLUS

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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 aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCA
1513D HN(CA)CB
1613D HNCO
1713D HN(CO)CA
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY aliphatic
11113D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.8 mM [U-100% 13C; U-100% 15N] protein_1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.8 mM / Component: entity_1-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.1 / pH: 6.8 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger A.T. et.al.refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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