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- PDB-7fsr: SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP... -

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Basic information

Entry
Database: PDB / ID: 7fsr
TitleSDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z54615640
ComponentsSyntenin-1
KeywordsSIGNALING PROTEIN / Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / Neurofascin interactions / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / negative regulation of receptor internalization / frizzled binding ...interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / Neurofascin interactions / 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 / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of phosphorylation / positive regulation of epithelial to mesenchymal transition / phosphatidylinositol-4,5-bisphosphate binding / protein sequestering activity / regulation of mitotic cell cycle / positive regulation of JNK cascade / adherens junction / Regulation of necroptotic cell death / azurophil granule lumen / melanosome / extracellular vesicle / 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 / synapse / Neutrophil degranulation / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
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
ALANINE / D-GLUTAMIC ACID / GLYCINE / Chem-YFN / Syntenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.29 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Bountra, C. / von Delft, F. / Brennan, P.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)5U54AG065187-03 United States
CitationJournal: To Be Published
Title: SDCBP PanDDA analysis group deposition
Authors: Bradshaw, W.J. / Katis, V.L. / Bountra, C. / von Delft, F. / Brennan, P.E.
History
DepositionJan 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)87,25921
Polymers85,7244
Non-polymers1,53617
Water4,432246
1
A: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4932
Polymers21,4311
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7024
Polymers21,4311
Non-polymers2713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6925
Polymers21,4311
Non-polymers2614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,37210
Polymers21,4311
Non-polymers9419
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.965, 49.493, 114.060
Angle α, β, γ (deg.)90.000, 95.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#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: 21430.881 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

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Non-polymers , 7 types, 263 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Chemical ChemComp-YFN / N-[(3S)-3-methyl-1,1-dioxo-1lambda~6~-thiolan-3-yl]cyclopropanecarboxamide


Mass: 217.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO3S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.65 Å3/Da / Density % sol: 53.66 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Morpheus amino acids, 100 mM Morpheus buffer system 1, 43% Morpheus precipitant mix 3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9179 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 2.29→113.56 Å / Num. obs: 40973 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.96 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.085 / Rrim(I) all: 0.159 / Net I/σ(I): 11.9 / Num. measured all: 141383 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.29-2.373.51.3711359739270.3420.8691.6281.297.7
8.85-113.563.10.04323947810.8890.0340.05661.599.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 8BLU

8blu


Resolution: 2.29→113.56 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / SU B: 31.454 / SU ML: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.582 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2765 1985 4.8 %RANDOM
Rwork0.2067 ---
obs0.2102 38950 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.56 Å2 / Biso mean: 58.501 Å2 / Biso min: 12.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å2-0 Å23.13 Å2
2---3.02 Å2-0 Å2
3---3.41 Å2
Refinement stepCycle: final / Resolution: 2.29→113.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5908 0 97 247 6252
Biso mean--63.58 51.55 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0149281
X-RAY DIFFRACTIONr_bond_other_d0.0020.0157873
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.64310813
X-RAY DIFFRACTIONr_angle_other_deg1.1931.59718259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.05451067
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0323.352364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.447151534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2391541
X-RAY DIFFRACTIONr_chiral_restr0.0640.21108
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029350
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021744
X-RAY DIFFRACTIONr_mcbond_it2.2534.8294750
X-RAY DIFFRACTIONr_mcbond_other2.2874.7774595
X-RAY DIFFRACTIONr_mcangle_it4.0067.0535173
LS refinement shellResolution: 2.29→2.345 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 135 -
Rwork0.397 2770 -
all-2905 -
obs--95.43 %
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)
11.9105-0.2115-0.58060.06610.23020.88460.1149-0.0407-0.2392-0.0435-0.0680.0181-0.1805-0.2063-0.04690.04340.03870.03780.17610.00810.1851-28.9263.091-45.107
20.65630.1575-0.06230.3206-0.46340.8269-0.00370.1871-0.18050.0515-0.0325-0.1396-0.08850.04880.03620.0129-0.02230.00210.1457-0.0190.2741-46.335-14.79-12.893
30.684-0.0211-0.29460.34150.75941.98840.1422-0.1241-0.1257-0.11920.0449-0.1223-0.24840.0928-0.18710.1022-0.06210.06630.1021-0.03430.1817-3.0042.255-50.821
40.3520.1942-0.11671.0103-0.51880.67390.06260.123-0.02950.1109-0.0180.1280.01080.0969-0.04460.03460.02220.02030.0879-0.01480.20599.265-13.999-5.329
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A108 - 298
2X-RAY DIFFRACTION2B106 - 298
3X-RAY DIFFRACTION3C106 - 298
4X-RAY DIFFRACTION4D108 - 298
5X-RAY DIFFRACTION4D301

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