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- PDB-3rl7: Crystal structure of hDLG1-PDZ1 complexed with APC -

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Basic information

Entry
Database: PDB / ID: 3rl7
TitleCrystal structure of hDLG1-PDZ1 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


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 ...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 / guanylate kinase activity / negative regulation of p38MAPK cascade / membrane repolarization during ventricular cardiac muscle cell action potential / structural constituent of postsynaptic density / astral microtubule organization / embryonic skeletal system morphogenesis / NrCAM interactions / gamma-catenin binding / reproductive structure development / immunological synapse formation / lateral loop / myelin sheath abaxonal region / receptor localization to synapse / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / peristalsis / cell projection membrane / cortical microtubule organization / regulation of sodium ion transmembrane transport / positive regulation of protein localization to centrosome / smooth muscle tissue development / pattern specification process / Synaptic adhesion-like molecules / bicellular tight junction assembly / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of potassium ion transport / negative regulation of microtubule depolymerization / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / node of Ranvier / microtubule plus-end binding / regulation of ventricular cardiac muscle cell action potential / beta-catenin destruction complex / heart valve development / Trafficking of AMPA receptors / protein-containing complex localization / regulation of microtubule-based process / establishment or maintenance of epithelial cell apical/basal polarity / 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 / protein kinase regulator activity / Assembly and cell surface presentation of NMDA receptors / amyloid precursor protein metabolic process / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cell fate specification / endothelial cell proliferation / lens development in camera-type eye / Activation of Ca-permeable Kainate Receptor / endocardial cushion morphogenesis / regulation of myelination / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical actin cytoskeleton organization / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / establishment or maintenance of cell polarity / positive regulation of actin filament polymerization / dynein complex binding / mitotic spindle assembly checkpoint signaling / receptor clustering / Apoptotic cleavage of cellular proteins / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane neurotransmitter receptor levels / phosphoprotein phosphatase activity / mitotic cytokinesis / Long-term potentiation / immunological synapse / intercalated disc / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / bicellular tight junction / phosphatase binding / potassium channel regulator activity / negative regulation of T cell proliferation / T cell proliferation / cytoskeletal protein binding / ionotropic glutamate receptor binding / actin filament polymerization / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / regulation of membrane potential
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: 2.3 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
B: Disks large homolog 1
A: Disks large homolog 1
C: Disks large homolog 1
D: Disks large homolog 1
E: Disks large homolog 1
F: Disks large homolog 1
G: 11-mer peptide from Adenomatous polyposis coli protein
H: 11-mer peptide from Adenomatous polyposis coli protein
I: 11-mer peptide from Adenomatous polyposis coli protein
J: 11-mer peptide from Adenomatous polyposis coli protein
K: 11-mer peptide from Adenomatous polyposis coli protein
L: 11-mer peptide from Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)78,43612
Polymers78,43612
Non-polymers00
Water1,02757
1
A: Disks large homolog 1
G: 11-mer peptide from Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)13,0732
Polymers13,0732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disks large homolog 1
H: 11-mer peptide from Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)13,0732
Polymers13,0732
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Disks large homolog 1
J: 11-mer peptide from Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)13,0732
Polymers13,0732
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Disks large homolog 1
I: 11-mer peptide from Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)13,0732
Polymers13,0732
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Disks large homolog 1
K: 11-mer peptide from Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)13,0732
Polymers13,0732
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Disks large homolog 1
L: 11-mer peptide from Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)13,0732
Polymers13,0732
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.627, 105.627, 50.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 225 - 309 / Label seq-ID: 15 - 99

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB
3CC
4DD
5EE
6FF

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Components

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


Mass: 11865.397 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 220-317
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.: 6 / 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.: 57 / 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: 2.09 Å3/Da / Density % sol: 41.07 % / Mosaicity: 1.686 °
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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.262
11h+k,-k,-l20.239
11-h,-k,l30.261
11K, H, -L40.238
ReflectionResolution: 2.3→50.01 Å / Num. obs: 28225 / % possible obs: 99.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.099 / Χ2: 1.002 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.384.90.35328121.0041100
2.38-2.484.90.29728141.0011100
2.48-2.594.90.23428351.0061100
2.59-2.735.10.18728561.0091100
2.73-2.95.50.15128121.0031100
2.9-3.125.90.12128071.0011100
3.12-3.446.40.11428380.9991100
3.44-3.936.80.128171.0021100
3.93-4.956.90.07528161.0021100
4.95-506.90.06128181.001199.3

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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: 2.3→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 1 / SU B: 16.83 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 1392 4.9 %RANDOM
Rwork0.1925 ---
obs0.1944 28155 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 106.68 Å2 / Biso mean: 38.498 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-14.62 Å20 Å20 Å2
2--14.62 Å20 Å2
3----29.25 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4295 0 0 57 4352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224318
X-RAY DIFFRACTIONr_angle_refined_deg0.971.9655808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7115548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35123.163196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.62715759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7951546
X-RAY DIFFRACTIONr_chiral_restr0.0660.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023189
Refine LS restraints NCS

Ens-ID: 1 / Number: 563 / Refine-ID: X-RAY DIFFRACTION / Type: MEDIUM POSITIONAL / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1B0.49
2A0.5
3C0.47
4D0.42
5E0.44
6F0.4
LS refinement shellResolution: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 100 -
Rwork0.231 1936 -
all-2036 -
obs--98.36 %
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)
12.5291-0.4846-0.30162.8960.29081.92340.0299-0.0750.10310.014-0.06050.0742-0.1888-0.17850.03060.02040.0161-0.01160.0221-0.00430.089639.9335-20.6765-4.7908
21.115-0.17680.14772.5338-0.53021.418-0.06540.10980.1254-0.0198-0.00650.1-0.247-0.07060.07190.06250.00240.00670.0198-0.00870.100850.254-14.035217.3585
31.36040.1804-0.74450.9317-0.67541.5987-0.00240.0260.1605-0.1055-0.0355-0.164-0.15450.23080.03790.1208-0.0179-0.02040.0901-0.01010.150812.22710.252417.5968
42.0541-0.16650.28622.0543-0.55081.49550.012-0.0558-0.13310.0905-0.0102-0.13130.03350.1382-0.00180.01740.02450.00660.084-0.02170.116913.4146-9.9981-4.4952
51.20620.65380.00440.3906-0.10690.68760.0782-0.10680.02920.0366-0.05450.0680.1049-0.1981-0.02360.16950.01970.01510.1849-0.0040.222338.703825.0949-5.1159
60.90630.0238-0.17091.81440.24571.4194-0.03840.1449-0.1292-0.0879-0.0072-0.03670.0584-0.01460.04560.0933-0.0191-0.01910.030.00110.170254.796213.916517.1066
70.9684-0.9454-0.18015.25140.97090.1977-0.7099-0.33470.06410.2620.73110.52950.03750.1517-0.02130.51340.1851-0.03240.16460.00320.432349.2039-4.424224.791
845.0916-20.0296-2.245411.70354.7685.1781-0.06460.5250.5925-0.2953-0.28090.0123-0.4323-0.08790.34550.12560.03260.00380.10590.07290.159132.3639-14.9696-13.2771
94.42411.3845-2.70640.4983-0.89811.7010.00930.4637-0.0304-0.13640.0014-0.04840.0996-0.1715-0.01070.32870.2890.06230.3267-0.04350.319821.6409-16.6215-12.6454
103.43036.2029-1.148418.14251.41062.14240.0530.00040.44920.18350.21870.54570.04430.1085-0.27170.1518-0.0255-0.0550.30160.01090.221519.865116.442525.6511
1137.134-3.842916.51570.4031-1.71627.3546-0.4566-0.51651.2392-0.0008-0.0013-0.0933-0.1277-0.22490.45790.46090.0265-0.17610.4134-0.00220.438731.26622.0446-13.1611
122.6724-1.153710.21730.5029-4.395739.12220.186-0.2053-0.0893-0.04350.02390.10491.2237-0.7424-0.20991.14780.11530.81980.12480.06140.950955.12795.384225.3685
130.1761-0.0794-0.02120.0464-0.00040.01310.03350.1115-0.0070.0115-0.0479-0.0047-0.0318-0.00950.01450.08150.0081-0.02450.08320.01330.074631.4371-2.71164.8052
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B219 - 310
2X-RAY DIFFRACTION2A220 - 309
3X-RAY DIFFRACTION3C220 - 310
4X-RAY DIFFRACTION4D219 - 310
5X-RAY DIFFRACTION5E220 - 310
6X-RAY DIFFRACTION6F219 - 309
7X-RAY DIFFRACTION7G2837 - 2843
8X-RAY DIFFRACTION8H2838 - 2842
9X-RAY DIFFRACTION9I2838 - 2842
10X-RAY DIFFRACTION10J2838 - 2843
11X-RAY DIFFRACTION11K2839 - 2843
12X-RAY DIFFRACTION12L2839 - 2842
13X-RAY DIFFRACTION13B1 - 54

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