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- PDB-2rqu: Solution structure of the complex between the DDEF1 SH3 domain an... -

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Basic information

Entry
Database: PDB / ID: 2rqu
TitleSolution structure of the complex between the DDEF1 SH3 domain and the APC SAMP1 motif
Components
  • 19-mer from Adenomatous polyposis coli protein
  • DDEF1_SH3
KeywordsSIGNALING PROTEIN / SH3 domain / GAP / SAMP motif / Tumor suppressor / Cell junction / Disease mutation / Phosphoprotein / Wnt signaling pathway
Function / homology
Function and homology information


positive regulation of membrane tubulation / APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / negative regulation of dendritic spine development / VxPx cargo-targeting to cilium / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome ...positive regulation of membrane tubulation / APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / negative regulation of dendritic spine development / VxPx cargo-targeting to cilium / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome / pattern specification process / bicellular tight junction assembly / protein kinase regulator activity / negative regulation of microtubule depolymerization / negative regulation of cyclin-dependent protein serine/threonine kinase activity / protein localization to cilium / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / microtubule plus-end binding / beta-catenin destruction complex / regulation of microtubule-based process / heart valve development / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / catenin complex / podosome / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cell fate specification / regulation of postsynapse organization / endocardial cushion morphogenesis / dynein complex binding / negative regulation of G1/S transition of mitotic cell cycle / phosphatidylserine binding / mitotic spindle assembly checkpoint signaling / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / phosphatidylinositol-3,4,5-trisphosphate binding / mitotic cytokinesis / cilium assembly / bicellular tight junction / lateral plasma membrane / phosphatidylinositol-4,5-bisphosphate binding / GTPase activator activity / trans-Golgi network membrane / Deactivation of the beta-catenin transactivating complex / adherens junction / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / kinetochore / ruffle membrane / beta-catenin binding / Wnt signaling pathway / positive regulation of protein catabolic process / cell migration / Ovarian tumor domain proteases / lamellipodium / insulin receptor signaling pathway / nervous system development / positive regulation of cold-induced thermogenesis / microtubule binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / microtubule / dendritic spine / cell adhesion / positive regulation of cell migration / cadherin binding / positive regulation of apoptotic process / negative regulation of cell population proliferation / Golgi membrane / centrosome / glutamatergic synapse / DNA damage response / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ASAP1, BAR domain / ASAP1, SH3 domain / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / BAR domain of APPL family / Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP ...ASAP1, BAR domain / ASAP1, SH3 domain / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / BAR domain of APPL family / Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family / Adenomatous polyposis coli protein / Adenomatous polyposis coli, N-terminal dimerisation domain / APC, N-terminal coiled-coil domain superfamily / Adenomatous polyposis coli (APC) repeat / APC repeat / SAMP Motif / EB-1 Binding Domain / APC basic domain / APC 15 residue motif / Coiled-coil N-terminus of APC, dimerisation domain / Adenomatous polyposis coli (APC) repeat / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / BAR domain / ARFGAP/RecO-like zinc finger / AH/BAR domain superfamily / Variant SH3 domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / SH3 Domains / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Armadillo-like helical / PH-like domain superfamily / Armadillo-type fold / Roll / Mainly Beta
Similarity search - Domain/homology
Adenomatous polyposis coli protein / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsKaieda, S. / Matsui, C. / Mimori-Kiyosue, Y. / Ikegami, T.
CitationJournal: Biochemistry / Year: 2010
Title: Structural basis of the recognition of the SAMP motif of adenomatous polyposis coli by the Src-homology 3 domain.
Authors: Kaieda, S. / Matsui, C. / Mimori-Kiyosue, Y. / Ikegami, T.
History
DepositionDec 14, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DDEF1_SH3
B: 19-mer from Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)9,1172
Polymers9,1172
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DDEF1_SH3 / DDEF1_SH3 / 130 kDa phosphatidylinositol 4 / 5-biphosphate-dependent ARF1 GTPase-activating protein ...DDEF1_SH3 / 130 kDa phosphatidylinositol 4 / 5-biphosphate-dependent ARF1 GTPase-activating protein / PIP2-dependent ARF1 GAP / ADP-ribosylation factor-directed GTPase-activating protein 1 / ARF GTPase-activating protein 1 / Development and differentiation-enhancing factor 1 / Differentiation-enhancing factor 1 / DEF-1


Mass: 7066.801 Da / Num. of mol.: 1 / Fragment: UNP residues 1069-1129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ULH1
#2: Protein/peptide 19-mer from Adenomatous polyposis coli protein / Protein APC / Deleted in polyposis 2.5


Mass: 2050.511 Da / Num. of mol.: 1 / Fragment: UNP residues 1578-1596
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APC, DP2.5 / Production host: Escherichia coli (E. coli) / References: UniProt: P25054

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNCA
1323D HN(CA)CB
1423D CBCA(CO)NH
1523D HNCO
1623D HBHA(CO)NH
1733D MQ-(H)CCH-TOCSY
1833D (H)CCH-TOCSY
1913D 15N-edited NOESY
11033D aliphatic 13C-edited NOESY
11133D aromatic 13C-edited NOESY
11242D 1H-13C HSQC
11342D 1H-13C CT-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-15N] DDEF1 SH3-1, 0.5 mM [U-15N] APC SAMP1-2, 5 mM sodium phosphate-3, 5 mM [U-2H] DTT-4, 0.02 % sodium azide-5, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-13C; U-15N] DDEF1 SH3-6, 0.5 mM [U-13C; U-15N] APC SAMP1-7, 5 mM sodium phosphate-8, 5 mM [U-2H] DTT-9, 0.02 % sodium azide-10, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-13C; U-15N] DDEF1 SH3-11, 0.5 mM [U-13C; U-15N] APC SAMP1-12, 5 mM sodium phosphate-13, 5 mM [U-2H] DTT-14, 0.02 % sodium phosphate-15, 100% D2O100% D2O
40.5 mM [U-15% 13C; U-15N] DDEF1 SH3-16, 0.5 mM [U-15% 13C; U-15N] APC SAMP1-17, 5 mM sodium phosphate-18, 5 mM [U-2H] DTT-19, 0.02 % sodium azide-20, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMDDEF1 SH3-1[U-15N]1
0.5 mMAPC SAMP1-2[U-15N]1
5 mMsodium phosphate-31
5 mMDTT-4[U-2H]1
0.02 %sodium azide-51
0.5 mMDDEF1 SH3-6[U-13C; U-15N]2
0.5 mMAPC SAMP1-7[U-13C; U-15N]2
5 mMsodium phosphate-82
5 mMDTT-9[U-2H]2
0.02 %sodium azide-102
0.5 mMDDEF1 SH3-11[U-13C; U-15N]3
0.5 mMAPC SAMP1-12[U-13C; U-15N]3
5 mMsodium phosphate-133
5 mMDTT-14[U-2H]3
0.02 %sodium phosphate-153
0.5 mMDDEF1 SH3-16[U-15% 13C; U-15N]4
0.5 mMAPC SAMP1-17[U-15% 13C; U-15N]4
5 mMsodium phosphate-184
5 mMDTT-19[U-2H]4
0.02 %sodium azide-204
Sample conditionspH: 7.2 / Pressure: ambient / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
xwinnmr3.5Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SPARKY3.115Goddard and Knellerdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
ARIA2.2Rieping, Habeck, Bardiaux, Bernard, Malliavin, and Nilgesrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 1

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