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Basic information

Entry
Database: PDB / ID: 5iza
TitleProtein-protein interaction
Components
  • ACE-GLY-GLY-GLU-ALA-LEU-ALA-TRP-NH2
  • Adenomatous polyposis coli proteinFamilial adenomatous polyposis
KeywordsPROTEIN BINDING/INHIBITOR / APC / ASEF / Colon CANCER / Drug discovery / PROTEIN BINDING-INHIBITOR complex
Function / homology
Function and homology information


APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / 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 ...APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / 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 / 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 / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cell fate specification / endocardial cushion morphogenesis / dynein complex binding / negative regulation of G1/S transition of mitotic cell cycle / mitotic spindle assembly checkpoint signaling / regulation of cell differentiation / Apoptotic cleavage of cellular proteins / mitotic cytokinesis / bicellular tight junction / lateral plasma 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 / Wnt signaling pathway / beta-catenin binding / ruffle membrane / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule binding / protein-containing complex assembly / microtubule / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / negative regulation of cell population proliferation / centrosome / DNA damage response / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 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 / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Adenomatous polyposis coli protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsZhao, Y. / Jiang, H. / Yang, X. / Jiang, F. / Song, K. / Zhang, J.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Peptidomimetic inhibitors of APC-Asef interaction block colorectal cancer migration.
Authors: Jiang, H. / Deng, R. / Yang, X. / Shang, J. / Lu, S. / Zhao, Y. / Song, K. / Liu, X. / Zhang, Q. / Chen, Y. / Chinn, Y.E. / Wu, G. / Li, J. / Chen, G. / Yu, J. / Zhang, J.
History
DepositionMar 25, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 2019Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_Rsym_value / _reflns_shell.Rmerge_I_obs
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenomatous polyposis coli protein
B: ACE-GLY-GLY-GLU-ALA-LEU-ALA-TRP-NH2


Theoretical massNumber of molelcules
Total (without water)39,9952
Polymers39,9952
Non-polymers00
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-7 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.465, 66.436, 82.661
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Adenomatous polyposis coli protein / Familial adenomatous polyposis / Protein APC / Deleted in polyposis 2.5


Mass: 39268.246 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 407-751
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
#2: Protein/peptide ACE-GLY-GLY-GLU-ALA-LEU-ALA-TRP-NH2


Mass: 726.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M Ammonium sulfate, 0.1M Tris pH 8.0, 25% w/v PEG 4000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.5→51.78 Å / Num. obs: 46357 / % possible obs: 99.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.545 / Rsym value: 0.064 / Net I/σ(I): 21.27
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.86 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NMW
Resolution: 1.5→51.78 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.84 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15921 2319 5 %RANDOM
Rwork0.12064 ---
obs0.12252 43975 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.03 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2---0.06 Å20 Å2
3----1.06 Å2
Refinement stepCycle: 1 / Resolution: 1.5→51.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2694 0 0 343 3037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193023
X-RAY DIFFRACTIONr_bond_other_d0.0160.022934
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9534126
X-RAY DIFFRACTIONr_angle_other_deg1.81436767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.655405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80724.646127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64615566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9311517
X-RAY DIFFRACTIONr_chiral_restr0.0870.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023572
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02696
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9631.9841545
X-RAY DIFFRACTIONr_mcbond_other2.9331.9811543
X-RAY DIFFRACTIONr_mcangle_it3.7122.9781977
X-RAY DIFFRACTIONr_mcangle_other3.6762.9771977
X-RAY DIFFRACTIONr_scbond_it3.6542.5731478
X-RAY DIFFRACTIONr_scbond_other3.6532.5741479
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4743.8562150
X-RAY DIFFRACTIONr_long_range_B_refined5.24118.2343920
X-RAY DIFFRACTIONr_long_range_B_other4.69617.5343739
X-RAY DIFFRACTIONr_rigid_bond_restr7.12535955
X-RAY DIFFRACTIONr_sphericity_free45.633569
X-RAY DIFFRACTIONr_sphericity_bonded11.50356158
LS refinement shellResolution: 1.503→1.542 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 195 -
Rwork0.211 3015 -
obs--94.19 %

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