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- PDB-6r9h: Crystal structure of the PDZ tandem of syntenin in complex with f... -

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Basic information

Entry
Database: PDB / ID: 6r9h
TitleCrystal structure of the PDZ tandem of syntenin in complex with fragment C58
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 / presynapse assembly / neurexin family protein binding / 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 / presynapse assembly / neurexin family protein binding / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / frizzled binding / negative regulation of receptor internalization / protein targeting to membrane / Ephrin signaling / RIPK1-mediated regulated necrosis / positive regulation of transforming growth factor beta receptor signaling pathway / growth factor binding / positive regulation of epithelial to mesenchymal transition / positive regulation of phosphorylation / cell adhesion molecule binding / regulation of mitotic cell cycle / ionotropic glutamate receptor binding / phosphatidylinositol-4,5-bisphosphate 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 / chemical synaptic transmission / nuclear membrane / Ras protein signal transduction / blood microparticle / cytoskeleton / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein heterodimerization activity / focal adhesion / Neutrophil degranulation / positive regulation of cell population proliferation / protein-containing complex binding / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding / 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
ACETATE ION / Chem-JVK / PHOSPHATE ION / Syntenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFeracci, M. / Barral, K.
Funding support Belgium, France, 7items
OrganizationGrant numberCountry
KU LeuvenGOA/12/016 Belgium
French National Research AgencyAMIDEX project ANR-11-IDEX-0001-02 France
Belgian Foundation against CancerSTK-FAF-FA/2016/828 Belgium
Fondation ARCARC PDF20151203700 France
Fondation ARCPJA 2016204584 France
Research Foundation - FlandersFWO, G.0C57.18N Belgium
Other privateNational League Against Cancer France
CitationJournal: J Extracell Vesicles / Year: 2020
Title: Pharmacological inhibition of syntenin PDZ2 domain impairs breast cancer cell activities and exosome loadifing with syndecan and EpCAM cargo.
Authors: Leblanc, R. / Kashyap, R. / Barral, K. / Egea-Jimenez, A.L. / Kovalskyy, D. / Feracci, M. / Garcia, M. / Derviaux, C. / Betzi, S. / Ghossoub, R. / Platonov, M. / Roche, P. / Morelli, X. / ...Authors: Leblanc, R. / Kashyap, R. / Barral, K. / Egea-Jimenez, A.L. / Kovalskyy, D. / Feracci, M. / Garcia, M. / Derviaux, C. / Betzi, S. / Ghossoub, R. / Platonov, M. / Roche, P. / Morelli, X. / Hoffer, L. / Zimmermann, P.
History
DepositionApr 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)73,23513
Polymers72,0754
Non-polymers1,1619
Water4,720262
1
A: Syntenin-1
C: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9858
Polymers36,0372
Non-polymers9486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-25 kcal/mol
Surface area16160 Å2
MethodPISA
2
B: Syntenin-1
D: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2505
Polymers36,0372
Non-polymers2133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-12 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.937, 56.185, 100.874
Angle α, β, γ (deg.)82.59, 84.21, 78.59
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA111 - 2724 - 165
21ALAALABB111 - 2724 - 165
12PROPROAA111 - 2714 - 164
22PROPROCC111 - 2714 - 164
13PROPROAA111 - 2714 - 164
23PROPRODD111 - 2714 - 164
14PROPROBB111 - 2714 - 164
24PROPROCC111 - 2714 - 164
15PROPROBB111 - 2714 - 164
25PROPRODD111 - 2714 - 164
16ALAALACC111 - 2724 - 165
26ALAALADD111 - 2724 - 165

NCS ensembles :
ID
1
2
3
4
5
6

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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 K-12 (bacteria) / References: UniProt: O00560
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-JVK / (2~{S})-2-[2-(4-chlorophenyl)sulfanylethanoylamino]-3-methyl-butanoic acid


Mass: 301.789 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16ClNO3S
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM Sodium Acetate pH 4.6, 200mM Ammonium Acetate, 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→45.91 Å / Num. obs: 40550 / % possible obs: 97.37 % / Redundancy: 3.5 % / Biso Wilson estimate: 25.18 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08739 / Rpim(I) all: 0.05496 / Rrim(I) all: 0.1036 / Net I/σ(I): 7.57
Reflection shellResolution: 2.072→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 4087 / CC1/2: 0.761 / Rpim(I) all: 0.4229 / Rrim(I) all: 0.8104 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W9E

1w9e


Resolution: 2→45.91 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.858 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.196 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24622 4061 10 %RANDOM
Rwork0.2079 ---
obs0.21169 36490 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.873 Å2
Baniso -1Baniso -2Baniso -3
1-2.75 Å2-0.58 Å2-0.1 Å2
2---0.65 Å20.47 Å2
3----2.11 Å2
Refinement stepCycle: LAST / Resolution: 2→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4958 0 70 262 5290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135101
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174878
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.6396873
X-RAY DIFFRACTIONr_angle_other_deg1.2461.59211339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.115651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27723.417240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4915943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.4771528
X-RAY DIFFRACTIONr_chiral_restr0.0630.2711
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02971
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3583.1272613
X-RAY DIFFRACTIONr_mcbond_other2.3543.1272609
X-RAY DIFFRACTIONr_mcangle_it3.5354.683261
X-RAY DIFFRACTIONr_mcangle_other3.5344.683260
X-RAY DIFFRACTIONr_scbond_it3.3363.6472488
X-RAY DIFFRACTIONr_scbond_other3.3353.6472489
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0945.2823613
X-RAY DIFFRACTIONr_long_range_B_refined7.01237.8185430
X-RAY DIFFRACTIONr_long_range_B_other7.01237.8185431
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A45820.11
12B45820.11
21A45930.1
22C45930.1
31A45890.11
32D45890.11
41B45610.11
42C45610.11
51B45820.11
52D45820.11
61C46410.11
62D46410.11
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 298 -
Rwork0.309 2716 -
obs--96.66 %

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