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- PDB-4yk6: Crystal structure of APC-ARM in complexed with Amer1-A4 -

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Basic information

Entry
Database: PDB / ID: 4yk6
TitleCrystal structure of APC-ARM in complexed with Amer1-A4
Components
  • APC membrane recruitment protein 1
  • Adenomatous polyposis coli protein
KeywordsPROTEIN BINDING/CELL ADHESION / ARMADILLO-LIGAND COMPLEX / PROTEIN BINDING-CELL ADHESION COMPLEX
Function / homology
Function and homology information


mesenchymal cell differentiation involved in kidney development / APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / beta-catenin destruction complex binding / 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 ...mesenchymal cell differentiation involved in kidney development / APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / beta-catenin destruction complex binding / 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 / regulation of canonical Wnt signaling pathway / 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 / adipose tissue development / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of protein ubiquitination / adherens junction / Deactivation of the beta-catenin transactivating complex / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / bone development / Degradation of beta-catenin by the destruction complex / kinetochore / Wnt signaling pathway / ruffle membrane / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / Ovarian tumor domain proteases / positive regulation of canonical Wnt signaling pathway / insulin receptor signaling pathway / cell migration / nervous system development / lamellipodium / Neddylation / positive regulation of cold-induced thermogenesis / protein-containing complex assembly / microtubule binding / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / cell adhesion / nuclear body / positive regulation of cell migration / positive regulation of apoptotic process / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / 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
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: 1.7 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 4, 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
B: APC membrane recruitment protein 1
A: Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)40,4192
Polymers40,4192
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-8 kcal/mol
Surface area16530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.465, 71.152, 91.740
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/peptide APC membrane recruitment protein 1 / Amer1 / Protein FAM123B / Wilms tumor gene on the X chromosome protein


Mass: 1151.247 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 365-375 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5JTC6
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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 Å3/Da / Density % sol: 38.41 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.2M NACL, 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97884 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97884 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 36350 / % possible obs: 99.6 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.403 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.6.0117refinement
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NMW

3nmw


Resolution: 1.7→40.62 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.308 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1817 5 %RANDOM
Rwork0.197 ---
obs0.199 36198 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.34 Å20 Å20 Å2
2--2.47 Å20 Å2
3----4.81 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2705 0 0 174 2879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192781
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9553763
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3955357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71824.959121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97915514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6071515
X-RAY DIFFRACTIONr_chiral_restr0.10.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022054
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 128 -
Rwork0.219 2455 -
obs--98.36 %
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)
13.87443.0842.58069.566311.488818.4598-0.02170.157-0.1173-0.1082-0.11230.1651-0.2853-0.0620.1340.03640.01970.00880.07540.01550.039212.076514.918915.1302
20.53720.0040.86030.5741-0.37553.12050.0156-0.0045-0.03440.0719-0.02610.00480.0448-0.0110.01050.0159-0.00220.01060.0062-0.0020.03424.8748.812415.4623
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B365 - 375
2X-RAY DIFFRACTION2A403 - 741

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