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- PDB-3rl8: Crystal structure of hDLG1-PDZ2 complexed with APC -

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Basic information

Entry
Database: PDB / ID: 3rl8
TitleCrystal structure of hDLG1-PDZ2 complexed with APC
Components
  • 11-mer peptide from Adenomatous polyposis coli protein
  • Disks large homolog 1
KeywordsMEMBRANE PROTEIN/SIGNALING PROTEIN / PDZ-ligand complex / MEMBRANE PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / APC truncation mutants are not K63 polyubiquitinated / membrane raft organization / regulation of microtubule-based movement / establishment of centrosome localization / negative regulation of cell cycle G1/S phase transition ...L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / APC truncation mutants are not K63 polyubiquitinated / membrane raft organization / regulation of microtubule-based movement / establishment of centrosome localization / negative regulation of cell cycle G1/S phase transition / hard palate development / GMP kinase activity / structural constituent of postsynaptic density / membrane repolarization during ventricular cardiac muscle cell action potential / NrCAM interactions / astral microtubule organization / gamma-catenin binding / embryonic skeletal system morphogenesis / negative regulation of p38MAPK cascade / reproductive structure development / immunological synapse formation / regulation of attachment of spindle microtubules to kinetochore / lateral loop / receptor localization to synapse / myelin sheath abaxonal region / positive regulation of pseudopodium assembly / negative regulation of cyclin-dependent protein serine/threonine kinase activity / peristalsis / positive regulation of protein localization to centrosome / regulation of sodium ion transmembrane transport / smooth muscle tissue development / bicellular tight junction assembly / cortical microtubule organization / cell projection membrane / protein localization to synapse / pattern specification process / Synaptic adhesion-like molecules / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of microtubule depolymerization / catenin complex / beta-catenin destruction complex / regulation of ventricular cardiac muscle cell action potential / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / heart valve development / positive regulation of potassium ion transport / Trafficking of AMPA receptors / regulation of microtubule-based process / microtubule plus-end binding / 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 / node of Ranvier / amyloid precursor protein metabolic process / protein kinase regulator activity / endothelial cell proliferation / Wnt signalosome / Assembly and cell surface presentation of NMDA receptors / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cell fate specification / cortical actin cytoskeleton organization / lens development in camera-type eye / regulation of myelination / Activation of Ca-permeable Kainate Receptor / endocardial cushion morphogenesis / neurotransmitter receptor localization to postsynaptic specialization membrane / branching involved in ureteric bud morphogenesis / positive regulation of actin filament polymerization / negative regulation of G1/S transition of mitotic cell cycle / mitotic spindle assembly checkpoint signaling / Apoptotic cleavage of cellular proteins / receptor clustering / establishment or maintenance of cell polarity / dynein complex binding / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / mitotic cytokinesis / phosphoprotein phosphatase activity / Long-term potentiation / basement membrane / immunological synapse / intercalated disc / bicellular tight junction / lateral plasma membrane / regulation of postsynaptic membrane neurotransmitter receptor levels / potassium channel regulator activity / phosphatase binding / T cell proliferation / cytoskeletal protein binding / ionotropic glutamate receptor binding / negative regulation of T cell proliferation / actin filament polymerization / Ras activation upon Ca2+ influx through NMDA receptor / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / actin filament organization
Similarity search - Function
L27-1 / L27_1 / 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 ...L27-1 / L27_1 / 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 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Polyubiquitination (PEST) N-terminal domain of MAGUK / 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 / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / Armadillo/plakoglobin ARM repeat profile. / 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 / molecular replacement / Resolution: 2.2 Å
AuthorsZhang, Z. / Li, H. / Wu, G.
CitationJournal: Plos One / Year: 2011
Title: Molecular basis for the recognition of adenomatous polyposis coli by the Discs Large 1 protein.
Authors: Zhang, Z. / Li, H. / Chen, L. / Lu, X. / Zhang, J. / Xu, P. / Lin, K. / Wu, G.
History
DepositionApr 19, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Structure summary
Revision 1.2Nov 1, 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_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disks large homolog 1
B: Disks large homolog 1
C: Disks large homolog 1
D: Disks large homolog 1
E: Disks large homolog 1
F: 11-mer peptide from Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)58,5096
Polymers58,5096
Non-polymers00
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.806, 52.502, 87.426
Angle α, β, γ (deg.)90.000, 102.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 317 - 405 / Label seq-ID: 12 - 100

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE

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Components

#1: Protein
Disks large homolog 1 / Synapse-associated protein 97 / SAP-97 / SAP97 / hDlg


Mass: 11460.296 Da / Num. of mol.: 5 / Fragment: UNP RESIDUES 315-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLG1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12959
#2: Protein/peptide 11-mer peptide from Adenomatous polyposis coli protein / APC-C11


Mass: 1207.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P25054
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.6 Å3/Da / Density % sol: 52.65 % / Mosaicity: 0.279 °
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8M Na2HPO4, 0.9M KH2PO4, pH 7.5, vapor diffusion, hanging drop, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorDetector: CCD / Date: Nov 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.2→85.38 Å / Num. obs: 30730 / % possible obs: 99.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.088 / Χ2: 1.002 / Net I/σ(I): 17.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.2860.21630471.002199.9
2.28-2.3760.16430331.0021100
2.37-2.4860.13830550.9951100
2.48-2.6160.11830670.9991100
2.61-2.776.10.104306611100
2.77-2.996.10.08730441.0091100
2.99-3.2960.09131131.0111100
3.29-3.766.10.09330711.0021100
3.76-4.7460.07830911.0011100
4.74-505.80.07431431.002198.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZOK

1zok


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 11.851 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 1545 5 %RANDOM
Rwork0.2041 ---
obs0.2062 30711 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 160.64 Å2 / Biso mean: 38.8215 Å2 / Biso min: 11.77 Å2
Baniso -1Baniso -2Baniso -3
1--2.51 Å20 Å2-0.23 Å2
2--0.37 Å20 Å2
3---2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3507 0 0 286 3793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223576
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.9814819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.40626.905126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88515675
X-RAY DIFFRACTIONr_chiral_restr0.0930.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212552
X-RAY DIFFRACTIONr_mcbond_it0.4491.52312
X-RAY DIFFRACTIONr_mcangle_it0.84223714
X-RAY DIFFRACTIONr_scbond_it1.50831264
X-RAY DIFFRACTIONr_scangle_it2.5294.51103
Refine LS restraints NCS

Ens-ID: 1 / Number: 653 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.570.5
2BMEDIUM POSITIONAL0.550.5
3CMEDIUM POSITIONAL0.750.5
4DMEDIUM POSITIONAL0.450.5
5EMEDIUM POSITIONAL0.370.5
1AMEDIUM THERMAL12
2BMEDIUM THERMAL0.962
3CMEDIUM THERMAL0.792
4DMEDIUM THERMAL0.622
5EMEDIUM THERMAL0.522
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 126 -
Rwork0.224 2108 -
all-2234 -
obs--99.29 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.0496-0.6752-1.12113.2562-0.01781.617-0.02030.2372-0.1639-0.2210.06730.22340.28610.0381-0.0470.1693-0.0048-0.04870.026-0.01540.146220.48835.458142.0125
211.31711.44521.67664.48670.38771.2439-0.08820.32170.37770.06840.0426-0.2013-0.2369-0.05180.04570.11770.0181-0.00630.02060.0230.141852.05236.098941.1407
33.2474-0.03161.55582.648-0.03735.6620.0438-0.6426-0.13950.18810.00460.19830.1636-0.4782-0.04840.1804-0.01560.01850.25660.00650.122129.2418.795663.8628
412.05970.93632.20094.09041.54153.90690.0115-0.970.34140.1897-0.1347-0.1176-0.0119-0.03520.12320.15070.0221-0.00510.3888-0.04820.155444.042420.169279.7109
519.46181.2878-2.62991.59050.19154.6954-0.096-0.00810.7736-0.10650.23620.31580.10880.0045-0.14020.21440.01450.02040.4815-0.04610.31678.105720.722979.1349
646.3981-33.756317.25550.4297-0.248432.8998-0.6677-0.6898-1.1982.85351.5932-1.6131.47641.8893-0.92550.38830.0947-0.1830.27550.01410.398657.1838-4.069648.9956
71.33840.0411-0.1060.25110.02320.3011-0.0026-0.310.01050.0264-0.02710.0087-0.0142-0.02450.02970.33550.0127-0.01310.25450.0030.323532.576410.395355.869
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A316 - 409
2X-RAY DIFFRACTION2B316 - 405
3X-RAY DIFFRACTION3C316 - 410
4X-RAY DIFFRACTION4D316 - 409
5X-RAY DIFFRACTION5E316 - 405
6X-RAY DIFFRACTION6F2838 - 2843
7X-RAY DIFFRACTION7A3 - 286

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