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- PDB-7pc4: The PDZ domain of SNTB1 complexed with the PDZ-binding motif of H... -

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Basic information

Entry
Database: PDB / ID: 7pc4
TitleThe PDZ domain of SNTB1 complexed with the PDZ-binding motif of HTLV1-TAX1
Components
  • Beta-1-syntrophin,Annexin A2
  • Protein Tax-1
KeywordsPEPTIDE BINDING PROTEIN / PDZ / complex / crystallization chaperone
Function / homology
Function and homology information


symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / dystrophin-associated glycoprotein complex / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity ...symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / dystrophin-associated glycoprotein complex / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / myelin sheath adaxonal region / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / vesicle budding from membrane / cornified envelope / plasma membrane protein complex / calcium-dependent phospholipid binding / negative regulation of receptor internalization / collagen fibril organization / S100 protein binding / Dissolution of Fibrin Clot / virion binding / osteoclast development / positive regulation of low-density lipoprotein receptor activity / epithelial cell apoptotic process / positive regulation of receptor recycling / phosphatidylserine binding / positive regulation of exocytosis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / fibrinolysis / phosphatidylinositol-4,5-bisphosphate binding / cytoskeletal protein binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / cell-matrix adhesion / response to activity / muscle contraction / PDZ domain binding / adherens junction / lung development / calcium channel activity / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / nuclear matrix / SH3 domain binding / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / melanosome / late endosome membrane / actin binding / midbody / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / host cell cytoplasm / early endosome / cytoskeleton / calmodulin binding / endosome / lysosomal membrane / focal adhesion / synapse / calcium ion binding / host cell nucleus / Neutrophil degranulation / structural molecule activity / positive regulation of DNA-templated transcription / cell surface / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Syntrophin, split Pleckstrin homology (PH) domain / PH domain / Syntrophin / HTLV Tax / HTLV Tax / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin ...Syntrophin, split Pleckstrin homology (PH) domain / PH domain / Syntrophin / HTLV Tax / HTLV Tax / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / PH domain / PH domain profile. / PDZ domain / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Protein Tax-1 / Annexin A2 / Beta-1-syntrophin
Similarity search - Component
Biological speciesHomo sapiens (human)
HTLV-1 subtype A (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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Assembly

Deposited unit
A: Beta-1-syntrophin,Annexin A2
C: Protein Tax-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2889
Polymers47,9642
Non-polymers3257
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-40 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.270, 61.730, 145.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-1-syntrophin,Annexin A2 / 59 kDa dystrophin-associated protein A1 basic component 1 / DAPA1B / BSYN2 / Syntrophin-2 / Tax ...59 kDa dystrophin-associated protein A1 basic component 1 / DAPA1B / BSYN2 / Syntrophin-2 / Tax interaction protein 43 / TIP-43 / 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: 46699.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNTB1, SNT2B1, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Production host: Escherichia coli (E. coli) / References: UniProt: Q13884, 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
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 10% w/v PEG 8000, 8% v/v Ethylene glycol

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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: 2.3→47.035 Å / Num. obs: 22343 / % possible obs: 99.4 % / Redundancy: 13.15 % / CC1/2: 0.999 / Rrim(I) all: 0.112 / Net I/σ(I): 16.58
Reflection shellResolution: 2.3→2.36 Å / Mean I/σ(I) obs: 1.18 / Num. unique obs: 1644 / CC1/2: 0.636 / Rrim(I) all: 2.244

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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, 2VRF

5n7d

2vrf


Resolution: 2.3→47.035 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 1116 5.01 %
Rwork0.205 21172 -
obs0.2077 22288 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.64 Å2 / Biso mean: 71.862 Å2 / Biso min: 35.62 Å2
Refinement stepCycle: final / Resolution: 2.3→47.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3274 0 13 74 3361
Biso mean--75.45 60.33 -
Num. residues----413
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.40470.30231360.28257799
2.4047-2.53150.30491370.2676259699
2.5315-2.690.34971370.2724259799
2.69-2.89770.3541370.26022604100
2.8977-3.18930.29641400.2398264899
3.1893-3.65060.28681380.22422641100
3.6506-4.59880.23411420.17412682100
4.5988-47.0350.21351490.17422827100
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)
14.28481.54780.70754.28571.23064.06020.06390.4419-0.388-0.5618-0.42020.56060.1074-0.56170.28720.82930.0143-0.06720.7597-0.21970.8434-4.8701-6.90540.3818
21.99092.1980.92984.01983.02172.87850.4181-0.53230.07280.9175-0.4211-0.24690.3484-0.21090.12960.6969-0.0423-0.13810.6532-0.0140.5287-11.475-27.807-1.2121
30.59710.30520.62011.9657-0.7392.33970.06660.19150.002-0.0196-0.0852-0.29630.24820.63580.02870.41250.1089-0.06730.527-0.00620.4453-12.4446-32.956-28.1617
45.5485-1.956-2.74777.33953.14039.69260.05720.2986-0.6017-0.6804-0.48790.11340.817-0.23390.38270.85430.00010.07590.769-0.13371.11995.1217-10.1458-1.3251
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 109 through 182 )A109 - 182
2X-RAY DIFFRACTION2chain 'A' and (resid 183 through 240 )A183 - 240
3X-RAY DIFFRACTION3chain 'A' and (resid 241 through 515 )A241 - 515
4X-RAY DIFFRACTION4chain 'C' and (resid 193 through 198 )C193 - 198

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