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- PDB-4yje: Crystal structure of APC-ARM in complexed with Amer1-A1 -

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Basic information

Entry
Database: PDB / ID: 4yje
TitleCrystal structure of APC-ARM in complexed with Amer1-A1
Components
  • APC membrane recruitment protein 1
  • Adenomatous polyposis coli protein
KeywordsCELL ADHESION/PROTEIN BINDING / ARMADILLO-LIGAND COMPLEX / CELL ADHESION-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


mesenchymal cell differentiation involved in kidney development / APC truncation mutants are not K63 polyubiquitinated / negative regulation of cell cycle G1/S phase transition / beta-catenin destruction complex binding / gamma-catenin binding / negative regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of microtubule-based movement / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome ...mesenchymal cell differentiation involved in kidney development / APC truncation mutants are not K63 polyubiquitinated / negative regulation of cell cycle G1/S phase transition / beta-catenin destruction complex binding / gamma-catenin binding / negative regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of microtubule-based movement / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / 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 / heart valve development / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / 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 / cell fate specification / regulation of canonical Wnt signaling pathway / Disassembly of the destruction complex and recruitment of AXIN to the membrane / endocardial cushion morphogenesis / mitotic spindle assembly checkpoint signaling / negative regulation of G1/S transition of mitotic cell cycle / Apoptotic cleavage of cellular proteins / dynein complex binding / mitotic cytokinesis / lateral plasma membrane / bicellular tight junction / adipose tissue development / positive regulation of protein ubiquitination / phosphatidylinositol-4,5-bisphosphate binding / Deactivation of the beta-catenin transactivating complex / adherens junction / Degradation of beta-catenin by the destruction complex / negative regulation of canonical Wnt signaling pathway / bone development / beta-catenin binding / kinetochore / ruffle membrane / Wnt signaling pathway / Ovarian tumor domain proteases / KEAP1-NFE2L2 pathway / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / insulin receptor signaling pathway / cell migration / nervous system development / Neddylation / lamellipodium / positive regulation of cold-induced thermogenesis / protein-containing complex assembly / microtubule binding / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / cell adhesion / nuclear body / positive regulation of cell migration / positive regulation of apoptotic process / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / centrosome / DNA damage response / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
APC membrane recruitment protein / APC membrane recruitment protein / 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 membrane recruitment protein / APC membrane recruitment protein / 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 / 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 / APC membrane recruitment protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhang, Z. / Xiao, Y. / Wu, G.
CitationJournal: Cell Discov / Year: 2015
Title: Structures of the APC-ARM domain in complexes with discrete Amer1/WTX fragments reveal that it uses a consensus mode to recognize its binding partners
Authors: Zhang, Z. / Akyildiz, S. / Xiao, Y. / Gai, Z. / An, Y. / Behrens, J. / Wu, G.
History
DepositionMar 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Structure summary
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

Downloads & links

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Assembly

Deposited unit
A: Adenomatous polyposis coli protein
B: APC membrane recruitment protein 1


Theoretical massNumber of molelcules
Total (without water)40,3872
Polymers40,3872
Non-polymers00
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-10 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.205, 68.204, 93.377
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 / Protein APC / Deleted in polyposis 2.5


Mass: 39268.246 Da / Num. of mol.: 1 / Fragment: ARM DOMAIN, UNP RESIDUES 407-751
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APC / Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25054
#2: Protein/peptide APC membrane recruitment protein 1 / Amer1 / Protein FAM123B / Wilms tumor gene on the X chromosome protein


Mass: 1119.247 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 325-335 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5JTC6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 12% PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 27310 / % possible obs: 99.9 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 16.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.366 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NMW

3nmw


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.873 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1368 5 %RANDOM
Rwork0.181 ---
obs0.183 27256 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2--1.49 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2662 0 0 265 2927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212702
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.011.9543652
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9575344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69624.87115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12815496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5031515
X-RAY DIFFRACTIONr_chiral_restr0.0720.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021976
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4471.51717
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.90322743
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6743985
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.744.5909
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 85 -
Rwork0.193 1862 -
obs--98.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.76235.6753-9.058510.4778-13.092934.49810.0270.2320.0443-0.68830.05010.21551.1639-0.0528-0.07710.07540.0077-0.01210.0301-0.03940.07-12.9569-13.61414.0845
20.8504-0.0821-1.15750.53980.23074.04130.0469-0.03320.03920.0633-0.0191-0.002-0.08610.0003-0.02780.0185-0.0011-0.0120.0084-0.00190.0857-5.6043-8.854316.2949
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B325 - 334
2X-RAY DIFFRACTION2A403 - 738

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