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- PDB-2ain: Solution structure of the AF-6 PDZ domain complexed with the C-te... -

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Basic information

Entry
Database: PDB / ID: 2ain
TitleSolution structure of the AF-6 PDZ domain complexed with the C-terminal peptide from the Bcr protein
Components
  • 6-mer peptide from Breakpoint cluster region protein
  • Afadin
KeywordsCELL ADHESION/Transferase / AF-6 PDZ domain-Bcr complex / CELL ADHESION-Transferase COMPLEX
Function / homology
Function and homology information


negative regulation of respiratory burst / negative regulation of cellular extravasation / negative regulation of macrophage migration / neutrophil degranulation / negative regulation of blood vessel remodeling / establishment of protein localization to plasma membrane / negative regulation of neutrophil degranulation / positive regulation of cell-cell adhesion mediated by cadherin / macrophage migration / pore complex assembly ...negative regulation of respiratory burst / negative regulation of cellular extravasation / negative regulation of macrophage migration / neutrophil degranulation / negative regulation of blood vessel remodeling / establishment of protein localization to plasma membrane / negative regulation of neutrophil degranulation / positive regulation of cell-cell adhesion mediated by cadherin / macrophage migration / pore complex assembly / intracellular protein transmembrane transport / establishment of endothelial intestinal barrier / positive regulation of cell-cell adhesion / renal system process / bicellular tight junction assembly / cell-cell contact zone / cell-cell adhesion mediated by cadherin / regulation of vascular permeability / regulation of Rho protein signal transduction / focal adhesion assembly / activation of GTPase activity / Signaling by cytosolic FGFR1 fusion mutants / definitive hemopoiesis / Adherens junctions interactions / regulation of small GTPase mediated signal transduction / tight junction / inner ear morphogenesis / RHOB GTPase cycle / small GTPase-mediated signal transduction / pore complex / RHOC GTPase cycle / negative regulation of reactive oxygen species metabolic process / neuromuscular process controlling balance / CDC42 GTPase cycle / homeostasis of number of cells / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / phagocytosis / positive regulation of phagocytosis / keratinocyte differentiation / cell adhesion molecule binding / RAC1 GTPase cycle / Signaling by FGFR1 in disease / GTPase activator activity / negative regulation of cell migration / guanyl-nucleotide exchange factor activity / adherens junction / modulation of chemical synaptic transmission / brain development / Schaffer collateral - CA1 synapse / small GTPase binding / negative regulation of inflammatory response / actin filament binding / cell junction / cell-cell junction / cell-cell signaling / regulation of protein localization / actin cytoskeleton organization / cellular response to lipopolysaccharide / protein tyrosine kinase activity / dendritic spine / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / regulation of cell cycle / postsynaptic density / cell adhesion / nuclear speck / protein phosphorylation / cadherin binding / axon / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / glutamatergic synapse / signal transduction / protein-containing complex / extracellular exosome / nucleoplasm / ATP binding / membrane
Similarity search - Function
Bcr-Abl oncoprotein oligomerisation / Bcr-Abl oncoprotein oligomerisation domain superfamily / Abr/Bcr / Bcr-Abl oncoprotein oligomerisation domain / PH domain / : / Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Dilute domain ...Bcr-Abl oncoprotein oligomerisation / Bcr-Abl oncoprotein oligomerisation domain superfamily / Abr/Bcr / Bcr-Abl oncoprotein oligomerisation domain / PH domain / : / Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Ras-associating (RA) domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Forkhead associated domain / FHA domain / Forkhead-associated (FHA) domain / Rho GTPase activation protein / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / SMAD/FHA domain superfamily / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / PDZ domain / Pdz3 Domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / PDZ domain / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Breakpoint cluster region protein / Afadin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsChen, Q. / Wu, J. / Shi, Y.
CitationJournal: Protein Sci. / Year: 2007
Title: Solution structure and backbone dynamics of the AF-6 PDZ domain/Bcr peptide complex.
Authors: Chen, Q. / Niu, X. / Xu, Y. / Wu, J. / Shi, Y.
History
DepositionJul 30, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Afadin
B: 6-mer peptide from Breakpoint cluster region protein


Theoretical massNumber of molelcules
Total (without water)10,2612
Polymers10,2612
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 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Afadin / AF-6 protein


Mass: 9566.045 Da / Num. of mol.: 1 / Fragment: AF-6 PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b (+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P55196
#2: Protein/peptide 6-mer peptide from Breakpoint cluster region protein


Mass: 694.773 Da / Num. of mol.: 1 / Fragment: C-terminal peptide / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
References: UniProt: P11274, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131DQF-COSY
NMR detailsText: Intermolecular interactions were identified in a 13C/15N-filtered (F1), 13C-edited(F3) 3D NOESY spectrum

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Sample preparation

DetailsContents: 2.0mM 15N, 13C-labeled AF-6 PDZ domain, 50mM phosphate buffer (pH 5.9), 1mM EDTA, 10%(v/v) D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 5.9 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2F.Delaglioprocessing
Sparky3T.D.Goddard and D.G.Knellerdata analysis
CNS1.1A.T.Brungerstructure solution
CSI1David S. Wishartdata analysis
MOLMOL2K.2Koradidata analysis
CNS1.1refinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: The complex structure is solved using a total of 1606 experimental restraints that includes 1471 intramolecular NOEs, 61 intermolecular NOEs and 74 dihedral angles restraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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