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- PDB-7pc9: The PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of... -

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Basic information

Entry
Database: PDB / ID: 7pc9
TitleThe PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of HTLV1-TAX1
Components
  • Protein Tax-1
  • Synaptojanin-2-binding protein,Annexin A2
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 / negative regulation of sprouting angiogenesis / 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 / phospholipase A2 inhibitor activity / positive regulation of low-density lipoprotein particle clearance ...symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / negative regulation of sprouting angiogenesis / 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 / 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 / PCSK9-AnxA2 complex / regulation of Notch signaling pathway / cadherin binding involved in cell-cell adhesion / cornified envelope / Schmidt-Lanterman incisure / vesicle budding from membrane / plasma membrane protein complex / calcium-dependent phospholipid binding / osteoclast development / negative regulation of receptor internalization / Dissolution of Fibrin Clot / S100 protein binding / collagen fibril organization / vesicle membrane / negative regulation of endothelial cell migration / epithelial cell apoptotic process / phosphatidylserine binding / negative regulation of endothelial cell proliferation / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / regulation of endocytosis / positive regulation of receptor recycling / basement membrane / positive regulation of exocytosis / Smooth Muscle Contraction / regulation of neurogenesis / protein targeting / cytoskeletal protein binding / fibrinolysis / Rho protein signal transduction / phosphatidylinositol-4,5-bisphosphate binding / lipid droplet / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lung development / negative regulation of angiogenesis / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / response to activity / adherens junction / serine-type endopeptidase inhibitor activity / mRNA transcription by RNA polymerase II / sarcolemma / negative regulation of ERK1 and ERK2 cascade / SH3 domain binding / RNA polymerase II transcription regulator complex / nuclear matrix / calcium-dependent protein binding / azurophil granule lumen / late endosome membrane / melanosome / : / protease binding / midbody / angiogenesis / basolateral plasma membrane / vesicle / host cell cytoplasm / mitochondrial outer membrane / early endosome / endosome / lysosomal membrane / calcium ion binding / Neutrophil degranulation / positive regulation of DNA-templated transcription / host cell nucleus / cell surface / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular space / DNA binding / RNA binding / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
HTLV Tax / HTLV Tax / Annexin A2 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat ...HTLV Tax / HTLV Tax / Annexin A2 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / : / Annexin V; domain 1 / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Protein Tax-1 / Annexin A2 / Synaptojanin-2-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
HTLV-1 subtype A (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
B: Synaptojanin-2-binding protein,Annexin A2
A: Synaptojanin-2-binding protein,Annexin A2
C: Protein Tax-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,74513
Polymers95,3453
Non-polymers40110
Water6,539363
1
B: Synaptojanin-2-binding protein,Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2416
Polymers47,0401
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-49 kcal/mol
Surface area20160 Å2
MethodPISA
2
A: Synaptojanin-2-binding protein,Annexin A2
C: Protein Tax-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5057
Polymers48,3052
Non-polymers2005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-53 kcal/mol
Surface area20660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.990, 99.850, 173.340
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 Synaptojanin-2-binding protein,Annexin A2 / Mitochondrial outer membrane protein 25 / Annexin II / Annexin-2 / Calpactin I heavy chain / ...Mitochondrial outer membrane protein 25 / 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: 47040.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYNJ2BP, OMP25, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Production host: Escherichia coli (E. coli) / References: UniProt: P57105, 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.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.81 Å3/Da / Density % sol: 56.3 %
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: 2.4→49.327 Å / Num. obs: 41356 / % possible obs: 99.3 % / Redundancy: 13.46 % / CC1/2: 0.995 / Rrim(I) all: 0.316 / Net I/σ(I): 8.93
Reflection shellResolution: 2.4→2.46 Å / Mean I/σ(I) obs: 1.22 / Num. unique obs: 2991 / CC1/2: 0.449 / Rrim(I) all: 2.43

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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, 2JIK

5n7d

2jik


Resolution: 2.4→49.327 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 2067 5.01 %
Rwork0.2025 39223 -
obs0.2045 41290 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.46 Å2 / Biso mean: 53.8979 Å2 / Biso min: 20.82 Å2
Refinement stepCycle: final / Resolution: 2.4→49.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6472 0 10 363 6845
Biso mean--67.33 46.36 -
Num. residues----812
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.45580.32281350.28412561100
2.4558-2.51720.30191340.2807255598
2.5172-2.58530.38161360.27112580100
2.5853-2.66140.34411340.2655254799
2.6614-2.74730.31351360.2493258699
2.7473-2.84540.29811370.24542596100
2.8454-2.95940.31521350.2392257099
2.9594-3.0940.29341370.2263258599
3.094-3.25710.2781360.2189259799
3.2571-3.46110.27181380.2119261599
3.4611-3.72830.22851400.19992644100
3.7283-4.10330.20441370.1657261099
4.1033-4.69670.18441400.1542663100
4.6967-5.91570.20741430.18332696100
5.9157-49.3270.18291490.17422818100
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)
14.7809-0.5354-1.42095.59362.36936.61020.2502-0.04640.59550.699-0.1819-0.1216-0.05430.1001-0.07071.1192-0.14750.05291.13640.11911.351822.2829-5.2034-43.6615
20.5461-0.55680.361.6394-0.43821.35080.0790.3388-0.4498-0.2613-0.1366-0.19490.79060.43180.1240.77820.11860.05560.4944-0.04060.481.6155.4894-40.1548
31.31010.690.81031.03540.73971.4356-0.04670.04070.2133-0.185-0.01580.0475-0.177-0.00180.0520.28910.03470.00160.28840.0140.3409-0.106129.1457-15.0872
42.0384-0.30170.32352.75811.81863.3201-0.10980.17390.0625-0.35270.1165-0.0441-0.2920.0996-0.03140.45870.00690.04370.44630.00460.3319-4.3523-15.8117-30.5142
50.5708-0.0701-1.13131.84231.82893.76490.41970.42120.5748-0.31720.0041-0.4191-0.16120.5497-0.42150.52120.0360.05830.67630.0690.4672.4948-17.6286-29.5416
62.37460.1653-0.98371.8633-0.54913.3081-0.00480.5236-0.0484-0.3771-0.1495-0.00650.12580.35960.13670.3148-0.0175-0.00520.4574-0.03660.274527.9856-33.1837-32.6399
71.31620.4505-0.56380.9286-0.32981.6962-0.03010.137-0.0205-0.08180.0760.11820.1381-0.0466-0.05050.20860.0096-0.03010.2116-0.01870.264221.8167-34.3051-8.2642
82.0035-0.7179-4.5143.1341-0.82463.98390.1471.6884-0.0853-0.2118-0.2503-0.02090.27480.06460.09150.684-0.02710.01050.9041-0.03750.4843-0.0387-17.265-41.9713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 10 through 86 )B10 - 86
2X-RAY DIFFRACTION2chain 'B' and (resid 87 through 156 )B87 - 156
3X-RAY DIFFRACTION3chain 'B' and (resid 157 through 416 )B157 - 416
4X-RAY DIFFRACTION4chain 'A' and (resid 10 through 86 )A10 - 86
5X-RAY DIFFRACTION5chain 'A' and (resid 87 through 111 )A87 - 111
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 213 )A112 - 213
7X-RAY DIFFRACTION7chain 'A' and (resid 214 through 416 )A214 - 416
8X-RAY DIFFRACTION8chain 'C' and (resid 199 through 206 )C199 - 206

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