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- PDB-1deb: CRYSTAL STRUCTURE OF THE N-TERMINAL COILED COIL DOMAIN FROM APC -

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Basic information

Entry
Database: PDB / ID: 1deb
TitleCRYSTAL STRUCTURE OF THE N-TERMINAL COILED COIL DOMAIN FROM APC
ComponentsADENOMATOUS POLYPOSIS COLI PROTEIN
KeywordsSTRUCTURAL PROTEIN / APC / COILED COIL / TUMOR SUPPRESSOR
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 / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of protein localization to centrosome / bicellular tight junction assembly / pattern specification process ...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 / 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 / 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 / adherens junction / Deactivation of the beta-catenin transactivating complex / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / Degradation of beta-catenin by the destruction complex / kinetochore / Wnt signaling pathway / ruffle membrane / positive regulation of protein catabolic process / Ovarian tumor domain proteases / insulin receptor signaling pathway / cell migration / nervous system development / lamellipodium / positive regulation of cold-induced thermogenesis / protein-containing complex assembly / microtubule binding / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / negative regulation of cell population proliferation / 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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #10 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #10 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Armadillo-like helical / Armadillo-type fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Adenomatous polyposis coli protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsDay, C.L. / Alber, T.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of the amino-terminal coiled-coil domain of the APC tumor suppressor.
Authors: Day, C.L. / Alber, T.
History
DepositionNov 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADENOMATOUS POLYPOSIS COLI PROTEIN
B: ADENOMATOUS POLYPOSIS COLI PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3163
Polymers12,2202
Non-polymers961
Water61334
1
A: ADENOMATOUS POLYPOSIS COLI PROTEIN


Theoretical massNumber of molelcules
Total (without water)6,1101
Polymers6,1101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADENOMATOUS POLYPOSIS COLI PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2062
Polymers6,1101
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: ADENOMATOUS POLYPOSIS COLI PROTEIN
B: ADENOMATOUS POLYPOSIS COLI PROTEIN
hetero molecules

A: ADENOMATOUS POLYPOSIS COLI PROTEIN
B: ADENOMATOUS POLYPOSIS COLI PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6316
Polymers24,4394
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area6270 Å2
ΔGint-72 kcal/mol
Surface area15400 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-29 kcal/mol
Surface area8560 Å2
MethodPISA
5
A: ADENOMATOUS POLYPOSIS COLI PROTEIN

A: ADENOMATOUS POLYPOSIS COLI PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,2202
Polymers12,2202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area2110 Å2
ΔGint-5 kcal/mol
Surface area8460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.86, 66.86, 127.47
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein ADENOMATOUS POLYPOSIS COLI PROTEIN / APC PROTEIN


Mass: 6109.825 Da / Num. of mol.: 2 / Fragment: N-TERMINAL COILED COIL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PAED4 / Production host: Escherichia coli (E. coli) / References: UniProt: P25054
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.37 Å3/Da / Density % sol: 63.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 15% PEG 4000, 0.1M AMMONIUM ACETATE, 0.1M NA ACETATE, pH 4.8, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlpeptide1drop
215 %(w/v)PEG40001reservoir
30.1 Mammonium sulfate1reservoir
40.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 76 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 18321 / % possible obs: 93.6 % / Redundancy: 2.8 % / Biso Wilson estimate: 34.63 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 5.3
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.164 / % possible all: 94
Reflection
*PLUS
Num. obs: 6743 / % possible obs: 96.4 % / Num. measured all: 18321 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 96.7 % / Rmerge(I) obs: 0.176

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNSrefinement
CCP4(TRUNCATE)data scaling
RefinementResolution: 2.4→20 Å / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.277 723 RANDOM 10%
Rwork0.234 --
obs0.234 6138 -
all-6138 -
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms844 0 5 34 883
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / σ(F): 1 / Num. reflection obs: 6148 / Rfactor obs: 0.2326 / Rfactor Rfree: 0.2746
Solvent computation
*PLUS
Displacement parameters
*PLUS

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