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- PDB-5z8h: APC with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 5z8h
TitleAPC with an inhibitor
Components
  • Adenomatous polyposis coli protein
  • Peptide inhibitor
KeywordsPROTEIN BINDING/INHIBITOR / APC / inhibitor / 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 / negative regulation of cyclin-dependent protein serine/threonine kinase 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 / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of microtubule depolymerization / 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 / heart valve development / regulation of microtubule-based process / 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 / protein kinase regulator activity / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cell fate specification / endocardial cushion morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / dynein complex binding / mitotic spindle assembly checkpoint signaling / Apoptotic cleavage of cellular proteins / mitotic cytokinesis / lateral plasma membrane / bicellular tight junction / Deactivation of the beta-catenin transactivating complex / adherens junction / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / Wnt signaling pathway / kinetochore / beta-catenin binding / ruffle membrane / positive regulation of protein catabolic process / Ovarian tumor domain proteases / cell migration / insulin receptor signaling pathway / lamellipodium / positive regulation of cold-induced thermogenesis / nervous system development / microtubule binding / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / 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 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 ...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 / 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 / Coiled-coil N-terminus of APC, dimerisation domain / Adenomatous polyposis coli (APC) repeat / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Leucine-rich Repeat Variant / Armadillo/beta-catenin-like repeats / Armadillo / 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 / Resolution: 1.79 Å
AuthorsZhang, J. / Yang, X.Y. / Song, K.
CitationJournal: To Be Published
Title: APC with an inhibitor
Authors: Zhang, J. / Yang, X.Y. / Song, K.
History
DepositionJan 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9035
Polymers38,6272
Non-polymers2763
Water5,963331
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint4 kcal/mol
Surface area16060 Å2
Unit cell
Length a, b, c (Å)51.486, 63.328, 52.974
Angle α, β, γ (deg.)90.00, 95.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 37708.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APC, DP2.5 / Production host: Homo sapiens (human) / References: UniProt: P25054
#2: Protein/peptide Peptide inhibitor


Mass: 918.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium sulfate 0.1M Tris pH 8.0, 25% w/v PEG 3350

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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: Jul 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 30251 / % possible obs: 99.6 % / Redundancy: 6.7 % / Net I/σ(I): 20.2
Reflection shellResolution: 1.79→1.82 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.011 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.124 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21099 1616 5.1 %RANDOM
Rwork0.1544 ---
obs0.15733 30251 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.018 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å2-0 Å20.27 Å2
2---0.89 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: 1 / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2642 0 19 331 2992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192865
X-RAY DIFFRACTIONr_bond_other_d0.0050.022766
X-RAY DIFFRACTIONr_angle_refined_deg2.1231.963896
X-RAY DIFFRACTIONr_angle_other_deg1.60336359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.93324.683126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31615520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7151518
X-RAY DIFFRACTIONr_chiral_restr0.1410.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023345
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02660
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_it2.4532.2811448
X-RAY DIFFRACTIONr_mcbond_other2.4512.2791446
X-RAY DIFFRACTIONr_mcangle_it3.4523.3981837
X-RAY DIFFRACTIONr_mcangle_other3.4533.3981837
X-RAY DIFFRACTIONr_scbond_it4.0162.7871417
X-RAY DIFFRACTIONr_scbond_other4.0122.7871417
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6864.0262060
X-RAY DIFFRACTIONr_long_range_B_refined6.77219.9293675
X-RAY DIFFRACTIONr_long_range_B_other6.6419.3273501
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 114 -
Rwork0.2 2197 -
obs--98.38 %

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