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Basic information

Entry
Database: PDB / ID: 5iz8
TitleProtein-protein interaction
Components
  • ACE-ALA-GLY-GLU-ALA-LEU-ALA-ASP-NH2
  • Adenomatous polyposis coli protein
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 / 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
TRIETHYLENE GLYCOL / Adenomatous polyposis coli protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 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: RCSB / 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 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Adenomatous polyposis coli protein
C: ACE-ALA-GLY-GLU-ALA-LEU-ALA-ASP-NH2
D: ACE-ALA-GLY-GLU-ALA-LEU-ALA-ASP-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0265
Polymers79,8764
Non-polymers1501
Water1,910106
1
A: Adenomatous polyposis coli protein
C: ACE-ALA-GLY-GLU-ALA-LEU-ALA-ASP-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0883
Polymers39,9382
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-6 kcal/mol
Surface area16980 Å2
MethodPISA
2
B: Adenomatous polyposis coli protein
D: ACE-ALA-GLY-GLU-ALA-LEU-ALA-ASP-NH2


Theoretical massNumber of molelcules
Total (without water)39,9382
Polymers39,9382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-7 kcal/mol
Surface area16470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.073, 114.073, 308.295
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 401 - 723 / Label seq-ID: 4 - 326

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 39268.246 Da / Num. of mol.: 2 / 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-ALA-GLY-GLU-ALA-LEU-ALA-ASP-NH2


Mass: 669.705 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.62 Å3/Da / Density % sol: 66.07 %
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: 3.06→98.79 Å / Num. obs: 23462 / % possible obs: 99.9 % / Redundancy: 21.1 % / Net I/σ(I): 16.2
Reflection shellResolution: 3.06→3.27 Å / Redundancy: 21.5 % / Rmerge(I) obs: 0.815 / Mean I/σ(I) obs: 5.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-3000data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NMW

3nmw


Resolution: 3.06→98.79 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.878 / SU B: 16.419 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 1.756 / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25318 1124 4.8 %RANDOM
Rwork0.21307 ---
obs0.21504 22256 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.036 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20.5 Å20 Å2
2--1 Å2-0 Å2
3----3.23 Å2
Refinement stepCycle: LAST / Resolution: 3.06→98.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5261 0 10 106 5377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195348
X-RAY DIFFRACTIONr_bond_other_d0.0040.025186
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9527223
X-RAY DIFFRACTIONr_angle_other_deg1.136311918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.295674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.8324.957234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73215977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1441528
X-RAY DIFFRACTIONr_chiral_restr0.0740.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026051
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021189
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_it3.5375.9132717
X-RAY DIFFRACTIONr_mcbond_other3.5365.9122715
X-RAY DIFFRACTIONr_mcangle_it5.8698.8533388
X-RAY DIFFRACTIONr_mcangle_other5.878.8533388
X-RAY DIFFRACTIONr_scbond_it3.1066.2422631
X-RAY DIFFRACTIONr_scbond_other3.1066.2422631
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3069.2493836
X-RAY DIFFRACTIONr_long_range_B_refined8.80745.426139
X-RAY DIFFRACTIONr_long_range_B_other8.81745.4666127
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 38036 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.056→3.135 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 72 -
Rwork0.333 1605 -
obs--99.41 %

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