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- PDB-8x2q: The Crystal Structure of APC from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8x2q
TitleThe Crystal Structure of APC from Biortus.
ComponentsAdenomatous polyposis coli proteinFamilial adenomatous polyposis
KeywordsANTITUMOR PROTEIN / Wnt signaling pathway
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 / protein kinase regulator 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 / protein kinase regulator activity / negative regulation of microtubule depolymerization / negative regulation of cyclin-dependent protein serine/threonine kinase activity / 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 / regulation of microtubule-based process / heart valve development / 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 / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cell fate specification / endocardial cushion morphogenesis / dynein complex binding / negative regulation of G1/S transition of mitotic cell cycle / mitotic spindle assembly checkpoint signaling / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / mitotic cytokinesis / bicellular tight junction / lateral plasma membrane / Deactivation of the beta-catenin transactivating complex / adherens junction / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / kinetochore / ruffle membrane / beta-catenin binding / Wnt signaling pathway / positive regulation of protein catabolic process / cell migration / Ovarian tumor domain proteases / lamellipodium / insulin receptor signaling pathway / nervous system development / positive regulation of cold-induced thermogenesis / microtubule binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / 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 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 / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding ...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 / 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 / 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
Adenomatous polyposis coli protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Ju, C. / Bao, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of APC from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Ju, C. / Bao, C.
History
DepositionNov 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenomatous polyposis coli protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1394
Polymers14,9531
Non-polymers1863
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.645, 46.645, 114.035
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

21A-452-

HOH

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Components

#1: Protein Adenomatous polyposis coli protein / Familial adenomatous polyposis


Mass: 14952.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APC / Production host: Escherichia coli (E. coli) / References: UniProt: P25054
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: (PEG-G2) 0.2M NaAc pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40.4 Å / Num. obs: 10243 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 14
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.74 / Num. unique obs: 696

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.396 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.001 / SU ML: 0.116 / Cross valid method: FREE R-VALUE / ESU R: 0.17 / ESU R Free: 0.172
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2626 508 4.959 %
Rwork0.1979 9735 -
all0.201 --
obs-10243 99.718 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.211 Å2
Baniso -1Baniso -2Baniso -3
1--0.921 Å2-0.46 Å2-0 Å2
2---0.921 Å20 Å2
3---2.987 Å2
Refinement stepCycle: LAST / Resolution: 2→40.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms921 0 12 72 1005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.012944
X-RAY DIFFRACTIONr_bond_other_d0.0010.016940
X-RAY DIFFRACTIONr_angle_refined_deg1.0081.6731258
X-RAY DIFFRACTIONr_angle_other_deg0.3681.5752158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9825110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.535512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64310203
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.0261055
X-RAY DIFFRACTIONr_chiral_restr0.0590.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021129
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02225
X-RAY DIFFRACTIONr_nbd_refined0.2260.2202
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1620.2753
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2454
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0660.2515
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.250
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0890.213
X-RAY DIFFRACTIONr_nbd_other0.1030.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1060.217
X-RAY DIFFRACTIONr_mcbond_it3.9413.214437
X-RAY DIFFRACTIONr_mcbond_other3.9413.216437
X-RAY DIFFRACTIONr_mcangle_it5.0365.711545
X-RAY DIFFRACTIONr_mcangle_other5.0355.727546
X-RAY DIFFRACTIONr_scbond_it5.7543.892507
X-RAY DIFFRACTIONr_scbond_other5.7483.898508
X-RAY DIFFRACTIONr_scangle_it8.4436.86712
X-RAY DIFFRACTIONr_scangle_other8.4376.865713
X-RAY DIFFRACTIONr_lrange_it9.91438.2981110
X-RAY DIFFRACTIONr_lrange_other9.89635.8271096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.276500.228696X-RAY DIFFRACTION99.7326
2.052-2.1080.26280.209691X-RAY DIFFRACTION100
2.108-2.1690.187480.187636X-RAY DIFFRACTION100
2.169-2.2360.231360.182664X-RAY DIFFRACTION100
2.236-2.3090.234320.176626X-RAY DIFFRACTION100
2.309-2.3890.235400.189595X-RAY DIFFRACTION100
2.389-2.4790.207300.187593X-RAY DIFFRACTION99.8397
2.479-2.580.263340.182576X-RAY DIFFRACTION99.6732
2.58-2.6940.202190.202551X-RAY DIFFRACTION99.6503
2.694-2.8250.284180.214520X-RAY DIFFRACTION99.6296
2.825-2.9770.253360.205507X-RAY DIFFRACTION100
2.977-3.1570.208180.208476X-RAY DIFFRACTION100
3.157-3.3730.305310.21451X-RAY DIFFRACTION99.5868
3.373-3.6410.271120.179433X-RAY DIFFRACTION99.5526
3.641-3.9860.203120.177397X-RAY DIFFRACTION99.5134
3.986-4.4510.28210.154343X-RAY DIFFRACTION99.726
4.451-5.1290.276110.191337X-RAY DIFFRACTION99.1453
5.129-6.2570.47880.262276X-RAY DIFFRACTION99.3007
6.257-8.7440.31790.238232X-RAY DIFFRACTION99.177
Refinement TLS params.Method: refined / Origin x: 4.606 Å / Origin y: 8.907 Å / Origin z: 33.641 Å
111213212223313233
T0.0342 Å2-0.0158 Å20.0315 Å2-0.0759 Å2-0.0385 Å2--0.0995 Å2
L6.1456 °21.3384 °23.1659 °2-0.4507 °20.6502 °2--1.8682 °2
S-0.115 Å °0.3583 Å °-0.2667 Å °-0.0899 Å °0.133 Å °-0.137 Å °-0.0437 Å °0.2094 Å °-0.018 Å °
Refinement TLS groupSelection: ALL

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