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- PDB-7pc3: The second PDZ domain of DLG1 complexed with the PDZ-binding moti... -

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Basic information

Entry
Database: PDB / ID: 7pc3
TitleThe second PDZ domain of DLG1 complexed with the PDZ-binding motif of HTLV1-TAX1
Components
  • Disks large homolog 1,Annexin A2
  • Protein Tax-1
KeywordsPEPTIDE BINDING PROTEIN / PDZ / complex / crystallization chaperone
Function / homology
Function and homology information


L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / symbiont-mediated perturbation of host exit from mitosis / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / AnxA2-p11 complex / membrane raft assembly / symbiont-mediated activation of host NF-kappaB cascade ...L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / symbiont-mediated perturbation of host exit from mitosis / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / AnxA2-p11 complex / membrane raft assembly / symbiont-mediated activation of host NF-kappaB cascade / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / membrane raft organization / phospholipase A2 inhibitor activity / positive regulation of low-density lipoprotein particle clearance / positive regulation of vesicle fusion / myelin sheath adaxonal region / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / establishment of centrosome localization / myelin sheath abaxonal region / GMP kinase activity / structural constituent of postsynaptic density / PCSK9-AnxA2 complex / NrCAM interactions / embryonic skeletal system morphogenesis / astral microtubule organization / reproductive structure development / immunological synapse formation / membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of p38MAPK cascade / peristalsis / receptor localization to synapse / lateral loop / cadherin binding involved in cell-cell adhesion / smooth muscle tissue development / cell projection membrane / cornified envelope / bicellular tight junction assembly / cortical microtubule organization / Schmidt-Lanterman incisure / regulation of sodium ion transmembrane transport / Synaptic adhesion-like molecules / protein localization to synapse / vesicle budding from membrane / establishment or maintenance of epithelial cell apical/basal polarity / plasma membrane protein complex / positive regulation of potassium ion transport / regulation of ventricular cardiac muscle cell action potential / Trafficking of AMPA receptors / calcium-dependent phospholipid binding / hard palate development / osteoclast development / negative regulation of receptor internalization / protein-containing complex localization / node of Ranvier / Dissolution of Fibrin Clot / amyloid precursor protein metabolic process / S100 protein binding / collagen fibril organization / endothelial cell proliferation / Assembly and cell surface presentation of NMDA receptors / vesicle membrane / lens development in camera-type eye / cortical actin cytoskeleton organization / epithelial cell apoptotic process / regulation of myelination / Activation of Ca-permeable Kainate Receptor / branching involved in ureteric bud morphogenesis / phosphatidylserine binding / neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of G1/S transition of mitotic cell cycle / receptor clustering / positive regulation of actin filament polymerization / establishment or maintenance of cell polarity / Negative regulation of NMDA receptor-mediated neuronal transmission / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of receptor recycling / phosphoprotein phosphatase activity / basement membrane / positive regulation of exocytosis / Long-term potentiation / intercalated disc / lateral plasma membrane / immunological synapse / Smooth Muscle Contraction / regulation of neurogenesis / bicellular tight junction / potassium channel regulator activity / phosphatase binding / T cell proliferation / regulation of postsynaptic membrane neurotransmitter receptor levels / cytoskeletal protein binding / fibrinolysis / negative regulation of T cell proliferation / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / lipid droplet
Similarity search - Function
HTLV Tax / HTLV Tax / L27-1 / L27_1 / Annexin A2 / 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 ...HTLV Tax / HTLV Tax / L27-1 / L27_1 / Annexin A2 / 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 / Annexin / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / : / Annexin V; domain 1 / 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. / 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 / Roll / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Protein Tax-1 / Annexin A2 / Disks large homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
HTLV-1 subtype A (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCousido-Siah, A. / Trave, G. / Gogl, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: A scalable strategy to solve structures of PDZ domains and their complexes.
Authors: Cousido-Siah, A. / Carneiro, L. / Kostmann, C. / Ecsedi, P. / Nyitray, L. / Trave, G. / Gogl, G.
History
DepositionAug 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disks large homolog 1,Annexin A2
C: Protein Tax-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,86011
Polymers48,2352
Non-polymers6259
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-51 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.670, 61.320, 143.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein Disks large homolog 1,Annexin A2 / Synapse-associated protein 97 / SAP-97 / SAP97 / hDlg / Annexin II / Annexin-2 / Calpactin I heavy ...Synapse-associated protein 97 / SAP-97 / SAP97 / hDlg / Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy chain / Chromobindin-8 / Lipocortin II / Placental anticoagulant protein IV / PAP-IV / Protein I / p36


Mass: 46970.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLG1, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Production host: Escherichia coli (E. coli) / References: UniProt: Q12959, UniProt: P07355
#2: Protein/peptide Protein Tax-1 / Protein X-LOR / Protein PX / Trans-activating transcriptional regulatory protein of HTLV-1


Mass: 1264.363 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: N-terminal biotin-ttds (trioxatridecan-succinamic acid) label
Source: (synth.) HTLV-1 subtype A (virus) / References: UniProt: P03409

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Non-polymers , 4 types, 406 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate, 0.1 M bis-Tris pH 5.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→46.553 Å / Num. obs: 36311 / % possible obs: 99.2 % / Redundancy: 13.37 % / CC1/2: 0.998 / Rrim(I) all: 0.178 / Net I/σ(I): 12.58
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 1.79 / Num. unique obs: 2616 / CC1/2: 0.645 / Rrim(I) all: 1.605 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N7D, 2X7Z

5n7d

2x7z


Resolution: 1.95→46.553 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 1812 5 %
Rwork0.1711 34443 -
obs0.1726 36255 99.21 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.94 Å2 / Biso mean: 30.8243 Å2 / Biso min: 11.76 Å2
Refinement stepCycle: final / Resolution: 1.95→46.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3270 0 33 397 3700
Biso mean--44.41 40.38 -
Num. residues----412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-2.00280.3011360.2502257698
2.0028-2.06170.24931370.216261198
2.0617-2.12820.23821350.2026258699
2.1282-2.20430.21291360.1864259099
2.2043-2.29260.23311370.1797260699
2.2926-2.39690.20111380.1696262399
2.3969-2.52320.20141390.1734263699
2.5232-2.68130.2011390.1763263399
2.6813-2.88830.17931390.17482648100
2.8883-3.17890.19911410.1672670100
3.1789-3.63880.19321410.1592687100
3.6388-4.58380.16761440.13372720100
4.5838-46.5530.20791500.18422857100
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)
12.78211.8520.6423.7280.1263.1301-0.14470.21630.1641-0.32950.13880.2791-0.1167-0.0745-0.00160.1650.0227-0.02490.2211-0.00110.212.9696-19.96829.9948
20.95480.1884-0.24650.728-0.20061.41790.02190.0368-0.0548-0.1252-0.0471-0.09190.01520.110.02770.12990.01840.00390.1129-0.01050.160217.40367.101229.784
34.45724.50884.42474.57014.51387.2922-0.16850.80590.1563-0.21040.648-0.9129-0.45941.3815-0.47030.4289-0.08790.02670.6396-0.00350.481725.117-19.416110.0649
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 314 through 417 )A314 - 417
2X-RAY DIFFRACTION2chain 'A' and (resid 418 through 725 )A418 - 725
3X-RAY DIFFRACTION3chain 'C' and (resid 200 through 206 )C200 - 206

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