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- PDB-7p70: The PDZ-domain of SNTB1 complexed with the PDZ-binding motif of H... -

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Basic information

Entry
Database: PDB / ID: 7p70
TitleThe PDZ-domain of SNTB1 complexed with the PDZ-binding motif of HPV35-E6
Components
  • Beta-1-syntrophin,Annexin A2
  • Protein E6
KeywordsPEPTIDE BINDING PROTEIN / PDZ / complex
Function / homology
Function and homology information


: / AnxA2-p11 complex / membrane raft assembly / dystrophin-associated glycoprotein complex / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / 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 ...: / AnxA2-p11 complex / membrane raft assembly / dystrophin-associated glycoprotein complex / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / 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 / symbiont-mediated perturbation of host apoptosis / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / cornified envelope / vesicle budding from membrane / osteoclast development / plasma membrane protein complex / calcium-dependent phospholipid binding / negative regulation of receptor internalization / Dissolution of Fibrin Clot / S100 protein binding / collagen fibril organization / vesicle membrane / : / epithelial cell apoptotic process / phosphatidylserine binding / positive regulation of receptor recycling / positive regulation of exocytosis / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / cytoskeletal protein binding / fibrinolysis / muscle contraction / lipid droplet / phosphatidylinositol-4,5-bisphosphate binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cell-matrix adhesion / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / response to activity / PDZ domain binding / adherens junction / lung development / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / nuclear matrix / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / late endosome membrane / melanosome / actin binding / midbody / protease binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / angiogenesis / collagen-containing extracellular matrix / basolateral plasma membrane / vesicle / host cell cytoplasm / early endosome / cytoskeleton / calmodulin binding / endosome / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / lysosomal membrane / focal adhesion / DNA-templated transcription / : / calcium ion binding / synapse / Neutrophil degranulation / regulation of DNA-templated transcription / host cell nucleus / structural molecule activity / cell surface / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / identical protein binding / nucleus / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Syntrophin, split Pleckstrin homology (PH) domain / PH domain / : / Syntrophin / Syntrophin C-terminal PH domain / Annexin A2 / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / Annexin ...Syntrophin, split Pleckstrin homology (PH) domain / PH domain / : / Syntrophin / Syntrophin C-terminal PH domain / Annexin A2 / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / 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 / PH domain / PDZ domain / PH domain profile. / 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 / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Annexin A2 / Protein E6 / Beta-1-syntrophin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus 35
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGogl, G. / Cousido-Siah, A. / Trave, G.
CitationJournal: Nat Commun / Year: 2022
Title: Quantitative fragmentomics allow affinity mapping of interactomes.
Authors: Gogl, G. / Zambo, B. / Kostmann, C. / Cousido-Siah, A. / Morlet, B. / Durbesson, F. / Negroni, L. / Eberling, P. / Jane, P. / Nomine, Y. / Zeke, A. / Ostergaard, S. / Monsellier, E. / Vincentelli, R. / Trave, G.
History
DepositionJul 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 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
C: Protein E6
A: Beta-1-syntrophin,Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6219
Polymers48,2362
Non-polymers3857
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-49 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.800, 60.580, 140.640
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/peptide Protein E6


Mass: 1536.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: N-terminal biotin-ttds label / Source: (synth.) Human papillomavirus 35 / References: UniProt: P27228
#2: 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
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% polyethylene glycol 3350, 200 mM sodium malonate buffered at pH 7.0

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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→46 Å / Num. obs: 32358 / % possible obs: 99.5 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rrim(I) all: 0.153 / Net I/σ(I): 12.57
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 1.36 / Num. unique obs: 2327 / CC1/2: 0.503 / Rrim(I) all: 2.13

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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→45.897 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2087 1613 4.99 %
Rwork0.1826 30686 -
obs0.184 32299 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.63 Å2 / Biso mean: 46.0567 Å2 / Biso min: 17.57 Å2
Refinement stepCycle: final / Resolution: 2→45.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 17 253 3553
Biso mean--45.07 48.32 -
Num. residues----414
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0001-2.05890.33291300.2848248399
2.0589-2.12540.28761330.2502251299
2.1254-2.20130.2581320.2224251999
2.2013-2.28950.23351320.2171251299
2.2895-2.39360.25061320.20012534100
2.3936-2.51980.20671330.19182523100
2.5198-2.67770.24351330.19772523100
2.6777-2.88440.22721360.19592583100
2.8844-3.17460.23741340.18712543100
3.1746-3.63380.21661370.17512590100
3.6338-4.57760.15871370.14782623100
4.5776-45.8970.17941440.16892741100

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