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- PDB-4yjl: Crystal structure of APC-ARM in complexed with Amer1-A2 -

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Basic information

Entry
Database: PDB / ID: 4yjl
TitleCrystal structure of APC-ARM in complexed with Amer1-A2
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 / 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: 2.1 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: Adenomatous polyposis coli protein
C: Adenomatous polyposis coli protein
D: Adenomatous polyposis coli protein
E: Adenomatous polyposis coli protein
F: Adenomatous polyposis coli protein
G: APC membrane recruitment protein 1
H: APC membrane recruitment protein 1
I: APC membrane recruitment protein 1
J: APC membrane recruitment protein 1
K: APC membrane recruitment protein 1
L: APC membrane recruitment protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,02949
Polymers244,73312
Non-polymers2,29737
Water43,1822397
1
A: Adenomatous polyposis coli protein
G: APC membrane recruitment protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,34711
Polymers40,7892
Non-polymers5599
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint8 kcal/mol
Surface area16710 Å2
MethodPISA
2
B: Adenomatous polyposis coli protein
K: APC membrane recruitment protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0997
Polymers40,7892
Non-polymers3105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-0 kcal/mol
Surface area16700 Å2
MethodPISA
3
C: Adenomatous polyposis coli protein
H: APC membrane recruitment protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0997
Polymers40,7892
Non-polymers3105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint9 kcal/mol
Surface area16630 Å2
MethodPISA
4
D: Adenomatous polyposis coli protein
I: APC membrane recruitment protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2239
Polymers40,7892
Non-polymers4347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint8 kcal/mol
Surface area17020 Å2
MethodPISA
5
E: Adenomatous polyposis coli protein
J: APC membrane recruitment protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2239
Polymers40,7892
Non-polymers4347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint4 kcal/mol
Surface area16870 Å2
MethodPISA
6
F: Adenomatous polyposis coli protein
L: APC membrane recruitment protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0376
Polymers40,7892
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-3 kcal/mol
Surface area17150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.592, 168.925, 170.272
Angle α, β, γ (deg.)60.29, 90.07, 90.05
Int Tables number1
Space group name H-MP1

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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.: 6 / 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: 1520.578 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 496-508 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5JTC6
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2397 / 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: 6.18 Å3/Da / Density % sol: 80.11 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.2M NACL, 10% PEG 8000

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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: Nov 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 335882 / % possible obs: 98.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 7.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.527 / % possible all: 97.3

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Processing

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

3nmw


Resolution: 2.1→49.34 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
RfactorNum. reflection% reflectionSelection details
Rfree0.225 16980 5.1 %RANDOM
Rwork0.207 ---
obs0.208 335766 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20.01 Å2-0.02 Å2
2--0.11 Å2-0.15 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16402 0 148 2397 18947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01916830
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9931.9522670
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.24652099
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64824.51745
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.456153032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7081596
X-RAY DIFFRACTIONr_chiral_restr0.0730.22578
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212349
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: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 1191 -
Rwork0.278 22779 -
obs--94.51 %

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