[English] 日本語
Yorodumi
- PDB-8blv: The PDZ domains of human SDCBP with a bound SDC4 C-terminal peptide -

+
Open data


ID or keywords:

Loading...

-
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 / Glycosaminoglycan-protein linkage region biosynthesis / interleukin-5 receptor complex / HS-GAG biosynthesis / 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 / Glycosaminoglycan-protein linkage region biosynthesis / interleukin-5 receptor complex / HS-GAG biosynthesis / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / HS-GAG degradation / inner ear receptor cell stereocilium organization / syndecan binding / Neurofascin interactions / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / costamere / negative regulation of receptor internalization / frizzled binding / Ephrin signaling / protein targeting to membrane / ureteric bud development / RIPK1-mediated regulated necrosis / Syndecan interactions / thrombospondin receptor activity / positive regulation of transforming growth factor beta receptor signaling pathway / RSV-host interactions / Respiratory syncytial virus (RSV) attachment and entry / fibronectin binding / positive regulation of phosphorylation / positive regulation of focal adhesion assembly / positive regulation of epithelial to mesenchymal transition / Retinoid metabolism and transport / negative regulation of T cell proliferation / positive regulation of stress fiber assembly / phosphatidylinositol-4,5-bisphosphate binding / lysosomal lumen / protein sequestering activity / protein kinase C binding / regulation of mitotic cell cycle / Cell surface interactions at the vascular wall / neural tube closure / positive regulation of JNK cascade / adherens junction / wound healing / Regulation of necroptotic cell death / Golgi lumen / azurophil granule lumen / melanosome / cell migration / extracellular vesicle / actin cytoskeleton organization / positive regulation of cell growth / nuclear membrane / blood microparticle / chemical synaptic transmission / Ras protein signal transduction / Attachment and Entry / 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 / cell surface / 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
Syndecan / Syndecan, conserved site / Syndecans signature. / Syndecan/Neurexin domain / Syndecan domain / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / PDZ domain / Pdz3 Domain ...Syndecan / Syndecan, conserved site / Syndecans signature. / Syndecan/Neurexin domain / Syndecan domain / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more