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- PDB-7f6m: Crystal structure of APC complexed with a peptide inhibitor MAI-516 -

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Basic information

Entry
Database: PDB / ID: 7f6m
TitleCrystal structure of APC complexed with a peptide inhibitor MAI-516
Components
  • Adenomatous polyposis coli protein
  • MAI-516 inhibitor
KeywordsONCOPROTEIN / Protein-ptrotein interaction inhibitor
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 / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of protein localization to centrosome / bicellular tight junction assembly / pattern specification process ...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 / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of protein localization to centrosome / bicellular tight junction assembly / pattern specification process / negative regulation of microtubule depolymerization / catenin complex / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / heart valve development / regulation of microtubule-based process / microtubule plus-end binding / 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 / 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 / mitotic spindle assembly checkpoint signaling / Apoptotic cleavage of cellular proteins / dynein complex binding / mitotic cytokinesis / bicellular tight junction / lateral plasma membrane / adherens junction / Deactivation of the beta-catenin transactivating complex / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / Degradation of beta-catenin by the destruction complex / kinetochore / Wnt signaling pathway / ruffle membrane / positive regulation of protein catabolic process / Ovarian tumor domain proteases / insulin receptor signaling pathway / cell migration / nervous system development / lamellipodium / positive regulation of cold-induced thermogenesis / protein-containing complex assembly / microtubule binding / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / negative regulation of cell population proliferation / centrosome / ubiquitin protein ligase binding / DNA damage response / 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 / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Adenomatous polyposis coli protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSong, K. / Zhang, J.
CitationJournal: To Be Published
Title: Discovery of Efficient Adenomatous Polyposis Coli - Rho Guanine Nucleotide Exchange Factor 4 Inhibitors by Employing High Binding Affinity Tracer
Authors: Jie, Z. / Zhang, J.
History
DepositionJun 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenomatous polyposis coli protein
B: MAI-516 inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,90211
Polymers40,0372
Non-polymers8659
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-12 kcal/mol
Surface area17050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.751, 82.337, 49.743
Angle α, β, γ (deg.)90.000, 94.690, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 39137.047 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: Escherichia coli (E. coli) / References: UniProt: P25054
#2: Protein/peptide MAI-516 inhibitor


Mass: 899.921 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 106 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.24 Å3/Da / Density % sol: 45.03 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→59.95 Å / Num. obs: 13724 / % possible obs: 99.3 % / Redundancy: 7 % / CC1/2: 0.95 / Net I/σ(I): 9.83
Reflection shellResolution: 2.4→2.44 Å / Num. unique obs: 687 / CC1/2: 0.944

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
HKL-3000data collection
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IZ6

5iz6


Resolution: 2.4→59.95 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.892 / SU B: 12.199 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.691 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 721 5.3 %RANDOM
Rwork0.2078 ---
obs0.2105 13002 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.53 Å2 / Biso mean: 38.329 Å2 / Biso min: 20.07 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å2-0 Å2-0.43 Å2
2---4.03 Å2-0 Å2
3---5.53 Å2
Refinement stepCycle: final / Resolution: 2.4→59.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2709 0 55 97 2861
Biso mean--52.34 35.93 -
Num. residues----349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192801
X-RAY DIFFRACTIONr_bond_other_d0.0030.022711
X-RAY DIFFRACTIONr_angle_refined_deg1.0491.9663771
X-RAY DIFFRACTIONr_angle_other_deg0.88636230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3385346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29424.711121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22315502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4731515
X-RAY DIFFRACTIONr_chiral_restr0.0570.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023124
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02624
LS refinement shellResolution: 2.401→2.463 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 45 -
Rwork0.251 918 -
all-963 -
obs--94.88 %

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