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- PDB-4g69: Structure of the Human Discs Large 1 PDZ2 - Adenomatous Polyposis... -

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Basic information

Entry
Database: PDB / ID: 4g69
TitleStructure of the Human Discs Large 1 PDZ2 - Adenomatous Polyposis Coli Cytoskeletal Polarity Complex
Components
  • Adenomatous polyposis coli proteinFamilial adenomatous polyposis
  • Disks large homolog 1
KeywordsMEMBRANE PROTEIN/SIGNALING PROTEIN / PDZ / MAGUK / Polarity / Adenomatous Polyposis Coli / Tetramethylrhodamine / Adherens Junction / MEMBRANE PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / APC truncation mutants are not K63 polyubiquitinated / membrane raft organization / regulation of microtubule-based movement / hard palate development ...regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / APC truncation mutants are not K63 polyubiquitinated / membrane raft organization / regulation of microtubule-based movement / hard palate development / negative regulation of cell cycle G1/S phase transition / establishment of centrosome localization / cortical microtubule organization / negative regulation of p38MAPK cascade / guanylate kinase activity / NrCAM interactions / regulation of sodium ion transmembrane transport / embryonic skeletal system morphogenesis / astral microtubule organization / structural constituent of postsynaptic density / lateral loop / reproductive structure development / myelin sheath abaxonal region / immunological synapse formation / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / peristalsis / Synaptic adhesion-like molecules / cell projection membrane / positive regulation of protein localization to centrosome / smooth muscle tissue development / pattern specification process / bicellular tight junction assembly / protein kinase regulator activity / positive regulation of potassium ion transport / negative regulation of microtubule depolymerization / regulation of ventricular cardiac muscle cell action potential / negative regulation of cyclin-dependent protein serine/threonine kinase activity / amyloid precursor protein metabolic process / node of Ranvier / 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 / Trafficking of AMPA receptors / establishment or maintenance of epithelial cell apical/basal polarity / heart valve development / protein-containing complex localization / 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 / Assembly and cell surface presentation of NMDA receptors / endothelial cell proliferation / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / neurotransmitter receptor localization to postsynaptic specialization membrane / cell fate specification / lens development in camera-type eye / regulation of myelination / Activation of Ca-permeable Kainate Receptor / cortical actin cytoskeleton organization / endocardial cushion morphogenesis / establishment or maintenance of cell polarity / branching involved in ureteric bud morphogenesis / dynein complex binding / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of actin filament polymerization / receptor clustering / mitotic spindle assembly checkpoint signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / phosphoprotein phosphatase activity / Long-term potentiation / mitotic cytokinesis / immunological synapse / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / bicellular tight junction / intercalated disc / potassium channel regulator activity / lateral plasma membrane / phosphatase binding / T cell proliferation / negative regulation of T cell proliferation / actin filament polymerization / Ras activation upon Ca2+ influx through NMDA receptor / regulation of membrane potential / cytoskeletal protein binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / synaptic membrane / actin filament organization
Similarity search - Function
L27-1 / L27_1 / 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 ...L27-1 / L27_1 / 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 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / Polyubiquitination (PEST) N-terminal domain of MAGUK / L27 domain superfamily / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Armadillo/plakoglobin ARM repeat profile. / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / PDZ domain / Pdz3 Domain / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Armadillo-like helical / Armadillo-type fold / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Adenomatous polyposis coli protein / Disks large homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSlep, K.C.
CitationJournal: Plos One / Year: 2012
Title: Structure of the Human Discs Large 1 PDZ2- Adenomatous Polyposis Coli Cytoskeletal Polarity Complex: Insight into Peptide Engagement and PDZ Clustering.
Authors: Slep, K.C.
History
DepositionJul 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disks large homolog 1
B: Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)11,8082
Polymers11,8082
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-4 kcal/mol
Surface area6190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.109, 51.184, 71.756
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 Disks large homolog 1 / Synapse-associated protein 97 / SAP-97 / SAP97 / hDlg


Mass: 10600.230 Da / Num. of mol.: 1 / Fragment: PDZ2, UNP residues 310-407
Source method: isolated from a genetically manipulated source
Details: GST N-terminal fusion, GST cleaved via Thrombin treatment
Source: (gene. exp.) Homo sapiens (human) / Gene: DLG1 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q12959
#2: Protein/peptide Adenomatous polyposis coli protein / Familial adenomatous polyposis / Protein APC / Deleted in polyposis 2.5


Mass: 1207.338 Da / Num. of mol.: 1 / Fragment: APC C-terminal peptide, UNP residues 2833-2843 / Source method: obtained synthetically
Details: Adenomatous Polyposis Coli (APC) C-terminal 11 residues synthesized with N-terminal Tetramethyl rhodamine tag
Source: (synth.) Homo sapiens (human) / References: UniProt: P25054
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: Protein solution: 1.4 mM Dlg1 PDZ2, 1.7 mM APC, 100 mM NaCl, 25 mM Tris pH 7.0, 0.1% B-ME Well: 200 mM sodium acetate, 100 mM sodium cacodylate pH 6.25, 28% PEG 8000 Drop = 1:1 protein:well ...Details: Protein solution: 1.4 mM Dlg1 PDZ2, 1.7 mM APC, 100 mM NaCl, 25 mM Tris pH 7.0, 0.1% B-ME Well: 200 mM sodium acetate, 100 mM sodium cacodylate pH 6.25, 28% PEG 8000 Drop = 1:1 protein:well solution , VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 8, 2007
RadiationMonochromator: collected at 1.127 A / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2→70 Å / Num. all: 7000 / Num. obs: 6846 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rsym value: 0.07 / Net I/σ(I): 20.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 590 / Rsym value: 0.22 / % possible all: 82.9

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FE5

2fe5


Resolution: 2→29.379 Å / SU ML: 0.17 / σ(F): 0.1 / Phase error: 15.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1833 688 10.05 %10%
Rwork0.1711 ---
all0.1723 7000 --
obs0.1723 6846 95.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.336 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.8885 Å20 Å20 Å2
2--0.33 Å2-0 Å2
3---2.5586 Å2
Refinement stepCycle: LAST / Resolution: 2→29.379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms769 0 0 106 875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007779
X-RAY DIFFRACTIONf_angle_d0.981051
X-RAY DIFFRACTIONf_dihedral_angle_d12.794288
X-RAY DIFFRACTIONf_chiral_restr0.063127
X-RAY DIFFRACTIONf_plane_restr0.004132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9977-2.15190.18721160.1641067X-RAY DIFFRACTION85
2.1519-2.36830.20351390.16511208X-RAY DIFFRACTION96
2.3683-2.71080.19131390.17821255X-RAY DIFFRACTION97
2.7108-3.41460.18211430.17631277X-RAY DIFFRACTION98
3.4146-29.38230.16781510.16761351X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -4.1675 Å / Origin y: -4.9337 Å / Origin z: 14.8774 Å
111213212223313233
T0.0144 Å2-0.0003 Å20.0033 Å2-0.0142 Å2-0.0293 Å2--0.0138 Å2
L0.4398 °20.0187 °20.2044 °2-0.3595 °2-0.2575 °2--0.2922 °2
S0.008 Å °0.0054 Å °-0.0127 Å °-0.0022 Å °-0.0015 Å °-0.0104 Å °0.003 Å °-0.0302 Å °0.0062 Å °
Refinement TLS groupSelection details: all

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