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- PDB-1m5i: Crystal Structure of the coiled coil region 129-250 of the tumor ... -

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Basic information

Entry
Database: PDB / ID: 1m5i
TitleCrystal Structure of the coiled coil region 129-250 of the tumor suppressor gene product APC
ComponentsAPC protein
KeywordsANTITUMOR PROTEIN / coiled-coil
Function / homology
Function and homology information


APC truncation mutants are not K63 polyubiquitinated / negative regulation of cell cycle G1/S phase transition / 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 ...APC truncation mutants are not K63 polyubiquitinated / negative regulation of cell cycle G1/S phase transition / 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 / Disassembly of the destruction complex and recruitment of AXIN to the membrane / endocardial cushion morphogenesis / Apoptotic cleavage of cellular proteins / negative regulation of G1/S transition of mitotic cell cycle / mitotic spindle assembly checkpoint signaling / dynein complex binding / mitotic cytokinesis / lateral plasma membrane / bicellular tight junction / adherens junction / Deactivation of the beta-catenin transactivating complex / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / beta-catenin binding / kinetochore / ruffle membrane / Wnt signaling pathway / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / negative regulation of cell population proliferation / ubiquitin protein ligase binding / DNA damage response / centrosome / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Helix hairpin bin / 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 ...Helix hairpin bin / 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 / Armadillo-like helical / Helix Hairpins / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Adenomatous polyposis coli protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsTickenbrock, L. / Cramer, J. / Vetter, I.R. / Mueller, O.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: The coiled coil region (amino acids 129-250) of the tumor suppressor protein adenomatous polyposis coli (APC). Its structure and its interaction with chromosome maintenance region 1 (Crm-1).
Authors: Tickenbrock, L. / Cramer, J. / Vetter, I.R. / Muller, O.
History
DepositionJul 9, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APC protein


Theoretical massNumber of molelcules
Total (without water)14,9531
Polymers14,9531
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.047, 46.047, 113.299
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-559-

HOH

21A-560-

HOH

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Components

#1: Protein APC protein / Adenomatous polyposis coli protein


Mass: 14952.779 Da / Num. of mol.: 1 / Fragment: coiled-coil region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APC / Plasmid: pGEX-6P-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P25054
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 16% PEG 3350, 100mM potassium iodide, 10mM strontium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114-20 %PEG33501reservoir
2100 mMpotassium iodide1reservoir
310 mM1reservoirSrCl2
420-30 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 4, 2001 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→19.94 Å / Num. all: 10548 / Num. obs: 10548 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.067 / Net I/σ(I): 18.8
Reflection shellResolution: 2→2.1 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 7 / Num. unique all: 2317 / Rsym value: 0.216 / % possible all: 98.8
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 9685 / % possible obs: 98.6 % / Num. measured all: 65629 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 98.8 % / Mean I/σ(I) obs: 6.3

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
CNSrefinement
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.309 1033 -RANDOM
Rwork0.257 ---
all0.262 9794 --
obs0.262 9794 98.7 %-
Displacement parametersBiso mean: 42.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 0 56 939
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1
LS refinement shellResolution: 2→2.1 Å / Rfactor Rfree error: 0.027
RfactorNum. reflection% reflection
Rfree0.35 162 -
Rwork0.344 --
obs-1400 99 %
Refinement
*PLUS
Num. reflection obs: 10548 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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