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- PDB-8blv: The PDZ domains of human SDCBP with a bound SDC4 C-terminal peptide -

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Basic information

Entry
Database: PDB / ID: 8blv
TitleThe PDZ domains of human SDCBP with a bound SDC4 C-terminal peptide
Components
  • Syndecan-4
  • Syntenin-1
KeywordsSIGNALING PROTEIN / complex
Function / homology
Function and homology information


Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / regulation of fibroblast migration / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / interleukin-5 receptor complex / interleukin-5 receptor binding ...Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / regulation of fibroblast migration / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / HS-GAG degradation / inner ear receptor cell stereocilium organization / syndecan binding / Neurofascin interactions / presynapse assembly / neurexin family protein binding / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / costamere / frizzled binding / negative regulation of receptor internalization / protein targeting to membrane / Ephrin signaling / ureteric bud development / RIPK1-mediated regulated necrosis / Syndecan interactions / RSV-host interactions / positive regulation of transforming growth factor beta receptor signaling pathway / thrombospondin receptor activity / growth factor binding / positive regulation of focal adhesion assembly / Respiratory syncytial virus (RSV) attachment and entry / fibronectin binding / positive regulation of epithelial to mesenchymal transition / negative regulation of T cell proliferation / Retinoid metabolism and transport / positive regulation of phosphorylation / positive regulation of stress fiber assembly / cell adhesion molecule binding / protein sequestering activity / regulation of mitotic cell cycle / phosphatidylinositol-4,5-bisphosphate binding / ephrin receptor binding / lysosomal lumen / neural tube closure / Cell surface interactions at the vascular wall / protein kinase C binding / adherens junction / positive regulation of JNK cascade / ionotropic glutamate receptor binding / wound healing / Regulation of necroptotic cell death / Golgi lumen / azurophil granule lumen / extracellular vesicle / melanosome / cell migration / presynapse / actin cytoskeleton organization / positive regulation of cell growth / chemical synaptic transmission / nuclear membrane / Ras protein signal transduction / Attachment and Entry / cytoskeleton / blood microparticle / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein heterodimerization activity / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Syndecan / Syndecan, conserved site / Syndecans signature. / Syndecan/Neurexin domain / Syndecan domain / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...Syndecan / Syndecan, conserved site / Syndecans signature. / Syndecan/Neurexin domain / Syndecan domain / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Syntenin-1 / Syndecan-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Daniel-Mozo, M. / 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: The PDZ domains of human SDCBP with a bound SDC4 C-terminal peptide
Authors: Bradshaw, W.J. / Katis, V.L. / Daniel-Mozo, M. / Bountra, C. / von Delft, F. / Brennan, P.E.
History
DepositionNov 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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: Syndecan-4
D: Syndecan-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,22211
Polymers44,6864
Non-polymers5367
Water6,215345
1
A: Syntenin-1
C: Syndecan-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6596
Polymers22,3432
Non-polymers3164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Syntenin-1
D: Syndecan-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5635
Polymers22,3432
Non-polymers2203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.710, 67.462, 106.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A

Dom-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
1SERSER109 - 2856 - 182
2GLUGLU109 - 2976 - 194

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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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: 21430.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDCBP, MDA9, SYCL / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O00560
#2: Protein/peptide Syndecan-4 / SYND4 / Amphiglycan / Ryudocan core protein


Mass: 911.954 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P31431
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 200 mM sodium sulphate, 100 mM bis-tris-propane, 10% ethylene glycol, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→106.74 Å / Num. obs: 66371 / % possible obs: 100 % / Redundancy: 79.2 % / CC1/2: 0.999 / Rpim(I) all: 0.033 / Net I/σ(I): 15.2
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3237 / CC1/2: 0.658 / Rpim(I) all: 2.217

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1n99

1n99


Resolution: 1.5→57.027 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.172 / SU B: 2.476 / SU ML: 0.081 / Average fsc free: 0.9266 / Average fsc work: 0.9365 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.222 2006 3.031 %
Rwork0.1817 64184 -
all0.183 --
obs-66190 99.846 %
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: 32.561 Å2
Baniso -1Baniso -2Baniso -3
1-2.561 Å2-0 Å2-0 Å2
2--0.349 Å2-0 Å2
3----2.909 Å2
Refinement stepCycle: LAST / Resolution: 1.5→57.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2964 0 31 345 3340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0123136
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162986
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.6434237
X-RAY DIFFRACTIONr_angle_other_deg0.5821.5696983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7165409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.876520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71510591
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.83110136
X-RAY DIFFRACTIONr_chiral_restr0.090.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023533
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02588
X-RAY DIFFRACTIONr_nbd_refined0.2230.2563
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.22687
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21504
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21703
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.120.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1380.215
X-RAY DIFFRACTIONr_nbd_other0.1650.2111
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.180.225
X-RAY DIFFRACTIONr_mcbond_it3.8213.3091561
X-RAY DIFFRACTIONr_mcbond_other3.823.3091561
X-RAY DIFFRACTIONr_mcangle_it5.544.9291950
X-RAY DIFFRACTIONr_mcangle_other5.5394.9291951
X-RAY DIFFRACTIONr_scbond_it4.7553.8481575
X-RAY DIFFRACTIONr_scbond_other4.7543.8481576
X-RAY DIFFRACTIONr_scangle_it6.8355.5572272
X-RAY DIFFRACTIONr_scangle_other6.8345.5582273
X-RAY DIFFRACTIONr_lrange_it8.9755.6193541
X-RAY DIFFRACTIONr_lrange_other8.97151.2233445
X-RAY DIFFRACTIONr_ncsr_local_group_10.1270.055208
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.126520.05007
12AX-RAY DIFFRACTIONLocal ncs0.126520.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.5-1.5390.371250.4147080.40948420.8130.81599.81410.396
1.539-1.5810.431530.37645210.37846910.8010.84199.63760.35
1.581-1.6270.3591340.34244490.34346020.8620.8699.58710.314
1.627-1.6770.2961340.31643090.31544530.8960.89399.77540.287
1.677-1.7320.3481360.29342210.29443680.9010.91399.74820.258
1.732-1.7930.3051300.25440200.25641670.9260.94399.5920.214
1.793-1.860.2551300.22739060.22740410.9490.95999.87630.189
1.86-1.9360.2361190.20737690.20838940.9610.96899.84590.171
1.936-2.0220.2411150.18236420.18437590.960.97799.94680.154
2.022-2.1210.1951140.1734720.17135880.9740.98199.94430.148
2.121-2.2350.213980.15333260.15434250.9750.98699.97080.135
2.235-2.370.205990.15531400.15732400.9740.98599.96910.14
2.37-2.5340.264860.17229630.17430510.9630.98299.93440.157
2.534-2.7360.176740.16327810.16428550.9790.9831000.155
2.736-2.9970.238780.17125660.17326440.9640.9821000.166
2.997-3.3490.204700.16523390.16624090.9750.9841000.169
3.349-3.8650.183670.15720600.15821270.9820.9871000.169
3.865-4.7290.13540.12417760.12418300.9890.9911000.143
4.729-6.6650.247580.17313840.17514420.9690.9841000.202
6.665-57.0270.232320.1868320.1888640.9630.9761000.226

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