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- PDB-8aap: Crystal structure of the PDZ tandem of syntenin in complex with c... -

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Basic information

Entry
Database: PDB / ID: 8aap
TitleCrystal structure of the PDZ tandem of syntenin in complex with compound SYNTi
ComponentsSyntenin-1
KeywordsSIGNALING PROTEIN / signaling protein cell adhesion PDZ domain syntenin syndecan drug design
Function / homology
Function and homology information


interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / neurexin family protein binding / Neurofascin interactions / presynapse assembly / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion ...interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / neurexin family protein binding / Neurofascin interactions / presynapse assembly / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / negative regulation of receptor internalization / frizzled binding / protein targeting to membrane / Ephrin signaling / RIPK1-mediated regulated necrosis / growth factor binding / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of epithelial to mesenchymal transition / cell adhesion molecule binding / positive regulation of phosphorylation / phosphatidylinositol-4,5-bisphosphate binding / regulation of mitotic cell cycle / ionotropic glutamate receptor binding / protein sequestering activity / ephrin receptor binding / adherens junction / positive regulation of JNK cascade / Regulation of necroptotic cell death / azurophil granule lumen / extracellular vesicle / melanosome / presynapse / actin cytoskeleton organization / positive regulation of cell growth / nuclear membrane / chemical synaptic transmission / Ras protein signal transduction / blood microparticle / cytoskeleton / intracellular signal transduction / positive regulation of cell migration / protein heterodimerization activity / membrane raft / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / endoplasmic reticulum membrane / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Chem-LLV / Syntenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.174 Å
AuthorsFeracci, M. / Barral, K.
Funding support France, 1items
OrganizationGrant numberCountry
Other government France
CitationJournal: J.Med.Chem. / Year: 2023
Title: Discovery of a PDZ Domain Inhibitor Targeting the Syndecan/Syntenin Protein-Protein Interaction: A Semi-Automated "Hit Identification-to-Optimization" Approach.
Authors: Hoffer, L. / Garcia, M. / Leblanc, R. / Feracci, M. / Betzi, S. / Ben Yaala, K. / Daulat, A.M. / Zimmermann, P. / Roche, P. / Barral, K. / Morelli, X.
History
DepositionJul 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 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
A: Syntenin-1
B: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1724
Polymers36,0372
Non-polymers1,1352
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, HTRF
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-7 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.433, 56.822, 56.933
Angle α, β, γ (deg.)109.670, 104.390, 101.550
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Syntenin-1 / Melanoma differentiation-associated protein 9 / MDA-9 / Pro-TGF-alpha cytoplasmic domain- ...Melanoma differentiation-associated protein 9 / MDA-9 / Pro-TGF-alpha cytoplasmic domain-interacting protein 18 / TACIP18 / Scaffold protein Pbp1 / Syndecan-binding protein 1


Mass: 18018.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDCBP, MDA9, SYCL / Production host: Escherichia coli (E. coli) / References: UniProt: O00560
#2: Chemical ChemComp-LLV / (2S)-2-[[(2S)-2-(6-bromanyl-3-oxidanylidene-1H-isoindol-2-yl)-3-[4-(5-ethanoyl-2-fluoranyl-phenyl)phenyl]propanoyl]amino]propanoic acid


Mass: 567.403 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H24BrFN2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM sodium acetate 200mM ammonium acetate 20% PEG 3350
PH range: 4.4-4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980114 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980114 Å / Relative weight: 1
ReflectionResolution: 2.174→50.85 Å / Num. obs: 16420 / % possible obs: 95.59 % / Redundancy: 3.6 % / Biso Wilson estimate: 46.71 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.05743 / Rpim(I) all: 0.03557 / Net I/σ(I): 14.18
Reflection shellResolution: 2.408→2.494 Å / Rmerge(I) obs: 0.3519 / Num. unique obs: 1198 / CC1/2: 0.941 / Rpim(I) all: 0.2244

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (11-DEC-2020)refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N99

1n99


Resolution: 2.174→50.85 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.291 / SU Rfree Blow DPI: 0.219 / SU Rfree Cruickshank DPI: 0.227
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 --RANDOM
Rwork0.2037 ---
obs-16420 97.37 %-
Displacement parametersBiso max: 132.26 Å2 / Biso min: 32.08 Å2
Baniso -1Baniso -2Baniso -3
1--4.5581 Å21.1133 Å20.0857 Å2
2---2.786 Å2-4.1832 Å2
3---7.3441 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 2.174→50.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2467 0 74 76 2617
Biso mean--56.45 55.89 -
Num. residues----324
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d936SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes490HARMONIC5
X-RAY DIFFRACTIONt_it2578HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion356SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1870SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2578HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3480HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion18.74
LS refinement shellResolution: 2.174→2.252 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.5004 16 3.99 %
Rwork0.3352 385 -
obs--96.82 %
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)
10.37210.9718-0.58284.8009-2.88352.9999-0.0556-0.2103-0.04530.5294-0.125-0.1503-0.47640.00750.18050.17740.0569-0.079-0.0376-0.0048-0.17416.502415.7226-10.1013
20.1168-0.5264-0.06783.4297-1.97543.7049-0.13480.04940.1786-0.57660.0204-0.06640.75-0.26230.11440.2928-0.06850.0312-0.08270.008-0.229214.81055.8011-33.655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A112 - 273
2X-RAY DIFFRACTION2{ B|* }B111 - 272

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