[English] 日本語
Yorodumi
- PDB-8hu2: Rattus Syntenin-1 PDZ domain with inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hu2
TitleRattus Syntenin-1 PDZ domain with inhibitor
ComponentsSyntenin-1
KeywordsSIGNALING PROTEIN/INHIBITOR / Inhibitor / Complex / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


RIPK1-mediated regulated necrosis / Neurofascin interactions / Regulation of necroptotic cell death / Ephrin signaling / interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / neurexin family protein binding / presynapse assembly / syndecan binding ...RIPK1-mediated regulated necrosis / Neurofascin interactions / Regulation of necroptotic cell death / Ephrin signaling / interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / neurexin family protein binding / presynapse assembly / syndecan binding / positive regulation of exosomal secretion / negative regulation of receptor internalization / frizzled binding / Neutrophil degranulation / growth factor binding / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of phosphorylation / positive regulation of epithelial to mesenchymal transition / ephrin receptor binding / cell adhesion molecule binding / phosphatidylinositol-4,5-bisphosphate binding / ionotropic glutamate receptor binding / protein sequestering activity / regulation of mitotic cell cycle / adherens junction / melanosome / presynapse / positive regulation of cell growth / Ras protein signal transduction / cytoskeleton / positive regulation of cell migration / membrane raft / protein heterodimerization activity / focal adhesion / positive regulation of cell population proliferation / endoplasmic reticulum membrane / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / 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
Chem-M8R / Syntenin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHeo, Y. / Lee, J. / Yun, J.H. / Lee, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of STNPDZ with inhibitor at 1.60 Angstroms resolution.
Authors: Heo, Y. / Lee, J. / Yun, J.H. / Lee, W.
History
DepositionDec 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9422
Polymers17,5361
Non-polymers4051
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The calculated molecular weight of the syntenin-1 PDZ domain by gel filtration is almost similar to the molecular weight of the syntenin-1 PDZ domain monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.098, 71.098, 73.072
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-571-

HOH

-
Components

#1: Protein Syntenin-1 / Syndecan-binding protein 1


Mass: 17536.158 Da / Num. of mol.: 1 / Fragment: PDZ domain / Mutation: None
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sdcbp / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9JI92
#2: Chemical ChemComp-M8R / (2~{S})-2-(9~{H}-fluoren-9-ylmethoxycarbonylamino)-3-(4-oxidanylidene-5~{H}-pyrimidin-2-yl)propanoic acid


Mass: 405.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19N3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.2 M sodium phosphate monobasic, 0.8 M potassium phosphate dibasic, 0.1 M CAPS/sodium hydroxide (pH 10.5), 0.2 M lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→47.09 Å / Num. obs: 28703 / % possible obs: 99.81 % / Redundancy: 14.6 % / Biso Wilson estimate: 20.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Net I/σ(I): 34.2
Reflection shellResolution: 1.6→1.657 Å / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 4.93 / Num. unique obs: 1867 / CC1/2: 0.9943

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PHENIX1.14_3260model building
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G1E

5g1e


Resolution: 1.6→47.09 Å / SU ML: 0.1816 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 21.3885 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2336 2018 7.03 %
Rwork0.2002 26685 -
obs0.2025 28703 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 30 178 1431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00521271
X-RAY DIFFRACTIONf_angle_d0.77231713
X-RAY DIFFRACTIONf_chiral_restr0.0588200
X-RAY DIFFRACTIONf_plane_restr0.0044218
X-RAY DIFFRACTIONf_dihedral_angle_d7.6036755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.30291410.2911854X-RAY DIFFRACTION98.96
1.64-1.680.27081440.26811891X-RAY DIFFRACTION99.95
1.68-1.730.26511430.22981889X-RAY DIFFRACTION99.9
1.73-1.790.22531390.21211898X-RAY DIFFRACTION99.9
1.79-1.850.24781420.20551881X-RAY DIFFRACTION99.95
1.85-1.930.22991410.19561901X-RAY DIFFRACTION99.9
1.93-2.010.22731420.18521857X-RAY DIFFRACTION100
2.01-2.120.2291440.17891899X-RAY DIFFRACTION99.8
2.12-2.250.2271450.19081892X-RAY DIFFRACTION99.76
2.25-2.430.2361470.19841932X-RAY DIFFRACTION100
2.43-2.670.21761430.19991902X-RAY DIFFRACTION99.95
2.67-3.060.24381490.20631925X-RAY DIFFRACTION99.95
3.06-3.850.22131430.18811941X-RAY DIFFRACTION99.86
3.85-47.090.23381550.19872023X-RAY DIFFRACTION99.27

+
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