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- PDB-8aai: Crystal structure of the PDZ tandem of syntenin in complex with f... -

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Basic information

Entry
Database: PDB / ID: 8aai
TitleCrystal structure of the PDZ tandem of syntenin in complex with fragment E5
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 / Neurofascin interactions / neurexin family protein binding / 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 / Neurofascin interactions / neurexin family protein binding / presynapse assembly / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / negative regulation of receptor internalization / frizzled binding / Ephrin signaling / protein targeting to membrane / RIPK1-mediated regulated necrosis / growth factor binding / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of phosphorylation / positive regulation of epithelial to mesenchymal transition / cell adhesion molecule binding / ephrin receptor binding / phosphatidylinositol-4,5-bisphosphate binding / ionotropic glutamate receptor binding / protein sequestering activity / regulation of mitotic cell cycle / adherens junction / positive regulation of JNK cascade / Regulation of necroptotic cell death / azurophil granule lumen / melanosome / extracellular vesicle / presynapse / actin cytoskeleton organization / positive regulation of cell growth / nuclear membrane / blood microparticle / chemical synaptic transmission / Ras protein signal transduction / cytoskeleton / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein heterodimerization activity / 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 / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Chem-LKV / Syntenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Syntenin-1
D: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2928
Polymers72,0754
Non-polymers1,2174
Water3,387188
1
A: Syntenin-1
C: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6464
Polymers36,0372
Non-polymers6092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Syntenin-1
D: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6464
Polymers36,0372
Non-polymers6092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.114, 56.130, 102.867
Angle α, β, γ (deg.)82.710, 83.462, 77.033
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A

NCS domain segments:

Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 111 - 272 / Label seq-ID: 4 - 165

Dom-IDComponent-IDEns-ID
111
211
322
422
533
633
744
844
955
1055
1166
1266

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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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.: 4
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-LKV / (2~{S})-2-[[(2~{S})-3-methyl-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)butanoyl]amino]propanoic acid


Mass: 304.341 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H20N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting 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: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.76→27.63 Å / Num. obs: 15909 / % possible obs: 97.29 % / Redundancy: 5.27 % / Rmerge(I) obs: 0.1388 / Rpim(I) all: 0.08908 / Net I/σ(I): 5.27
Reflection shellResolution: 2.76→2.859 Å / Rmerge(I) obs: 0.4417 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 1613 / Rpim(I) all: 0.288 / % possible all: 96.74

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
xia2XIA2 0.5.337-g4c821dce-dials-1.6data reduction
DIALSDIALS 1.6.3-g2108d754-releasedata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N99

1n99


Resolution: 2.76→27.63 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.871 / SU B: 26.151 / SU ML: 0.507 / Cross valid method: FREE R-VALUE / ESU R Free: 0.528
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3171 782 4.942 %
Rwork0.2746 15041 -
all0.277 --
obs-15823 98.006 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 50.548 Å2
Baniso -1Baniso -2Baniso -3
1-7.622 Å2-1.163 Å2-0.676 Å2
2---2.241 Å22.756 Å2
3----5.081 Å2
Refinement stepCycle: LAST / Resolution: 2.76→27.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4928 0 88 188 5204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125092
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164830
X-RAY DIFFRACTIONr_angle_refined_deg0.7371.626870
X-RAY DIFFRACTIONr_angle_other_deg0.2941.58311271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.245646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.9861028
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27610937
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.57610209
X-RAY DIFFRACTIONr_chiral_restr0.0360.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025912
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02912
X-RAY DIFFRACTIONr_nbd_refined0.180.21079
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.24711
X-RAY DIFFRACTIONr_nbtor_refined0.1550.22538
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22852
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2166
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1710.227
X-RAY DIFFRACTIONr_nbd_other0.1590.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.25
X-RAY DIFFRACTIONr_mcbond_it1.4325.342593
X-RAY DIFFRACTIONr_mcbond_other1.4325.342593
X-RAY DIFFRACTIONr_mcangle_it2.5388.0053240
X-RAY DIFFRACTIONr_mcangle_other2.5388.0053240
X-RAY DIFFRACTIONr_scbond_it1.1425.4992499
X-RAY DIFFRACTIONr_scbond_other1.1415.52498
X-RAY DIFFRACTIONr_scangle_it2.078.1743630
X-RAY DIFFRACTIONr_scangle_other2.078.1743630
X-RAY DIFFRACTIONr_lrange_it5.77776.7215582
X-RAY DIFFRACTIONr_lrange_other5.74476.7885564
X-RAY DIFFRACTIONr_ncsr_local_group_10.1140.054440
X-RAY DIFFRACTIONr_ncsr_local_group_20.120.054494
X-RAY DIFFRACTIONr_ncsr_local_group_30.1170.054444
X-RAY DIFFRACTIONr_ncsr_local_group_40.1310.054453
X-RAY DIFFRACTIONr_ncsr_local_group_50.1230.054406
X-RAY DIFFRACTIONr_ncsr_local_group_60.110.054512
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.114240.05009
12AX-RAY DIFFRACTIONLocal ncs0.114240.05009
23AX-RAY DIFFRACTIONLocal ncs0.119610.0501
24AX-RAY DIFFRACTIONLocal ncs0.119610.0501
35AX-RAY DIFFRACTIONLocal ncs0.116620.0501
36AX-RAY DIFFRACTIONLocal ncs0.116620.0501
47AX-RAY DIFFRACTIONLocal ncs0.131270.05009
48AX-RAY DIFFRACTIONLocal ncs0.131270.05009
59AX-RAY DIFFRACTIONLocal ncs0.122770.0501
510AX-RAY DIFFRACTIONLocal ncs0.122770.0501
611AX-RAY DIFFRACTIONLocal ncs0.110480.0501
612AX-RAY DIFFRACTIONLocal ncs0.110480.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.8320.346720.371083X-RAY DIFFRACTION96.7337
2.832-2.9090.299640.341112X-RAY DIFFRACTION98.2456
2.909-2.9930.287490.2951048X-RAY DIFFRACTION97.5979
2.993-3.0850.319480.282995X-RAY DIFFRACTION98.2109
3.085-3.1860.294460.2861035X-RAY DIFFRACTION98.2727
3.186-3.2970.289450.275946X-RAY DIFFRACTION97.6355
3.297-3.4210.389440.243910X-RAY DIFFRACTION98.7578
3.421-3.560.27510.248915X-RAY DIFFRACTION96.6
3.56-3.7180.278530.227814X-RAY DIFFRACTION97.8555
3.718-3.8980.284350.225811X-RAY DIFFRACTION98.4866
3.898-4.1080.363530.245795X-RAY DIFFRACTION97.9215
4.108-4.3560.306250.224725X-RAY DIFFRACTION97.9112
4.356-4.6540.368410.259699X-RAY DIFFRACTION98.5353
4.654-5.0240.296450.229633X-RAY DIFFRACTION99.2679
5.024-5.4990.262340.27596X-RAY DIFFRACTION99.3691
5.499-6.140.301160.291553X-RAY DIFFRACTION98.4429
6.14-7.0750.577250.348482X-RAY DIFFRACTION97.6879
7.075-8.6290.259150.273392X-RAY DIFFRACTION98.5472
8.629-12.0530.352150.318311X-RAY DIFFRACTION97.8979
12.053-27.630.53660.457186X-RAY DIFFRACTION96.9697

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