[English] 日本語
Yorodumi
- PDB-5a2p: THE COMPLEX STRUCTURE OF PDZ DOMAINS IN SYNTENIN-1 WITH 4L PEPTIDE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5a2p
TitleTHE COMPLEX STRUCTURE OF PDZ DOMAINS IN SYNTENIN-1 WITH 4L PEPTIDE
Components
  • SYNDECAN-4
  • SYNTENIN-1
KeywordsSIGNALING PROTEIN / CELL ADHESION / PDZ DOMAIN / SYNTENIN-1 / SYNDECAN-4
Function / homology
Function and homology information


A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / Neurofascin interactions / RIPK1-mediated regulated necrosis / Syndecan interactions / Cell surface interactions at the vascular wall / Regulation of necroptotic cell death / Ephrin signaling / Retinoid metabolism and transport ...A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / Neurofascin interactions / RIPK1-mediated regulated necrosis / Syndecan interactions / Cell surface interactions at the vascular wall / Regulation of necroptotic cell death / Ephrin signaling / Retinoid metabolism and transport / regulation of fibroblast migration / interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / inner ear receptor cell stereocilium organization / syndecan binding / presynapse assembly / neurexin family protein binding / positive regulation of exosomal secretion / costamere / frizzled binding / negative regulation of receptor internalization / ureteric bud development / Neutrophil degranulation / positive regulation of transforming growth factor beta receptor signaling pathway / thrombospondin receptor activity / growth factor binding / positive regulation of focal adhesion assembly / fibronectin binding / positive regulation of protein kinase activity / positive regulation of epithelial to mesenchymal transition / negative regulation of T cell proliferation / 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 / neural tube closure / protein kinase C binding / adherens junction / ionotropic glutamate receptor binding / wound healing / melanosome / cell migration / presynapse / cell-cell signaling / positive regulation of cell growth / nuclear membrane / Ras protein signal transduction / cytoskeleton / cell adhesion / positive regulation of cell migration / membrane raft / protein heterodimerization activity / focal adhesion / positive regulation of cell population proliferation / protein-containing complex binding / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / cell surface / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / 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 / PDZ 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
Syndecan-4 / Syntenin-1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.496 Å
AuthorsYoo, J.H. / Yun, J.H. / Cho, H.S. / Lee, W.
CitationJournal: To be Published
Title: Titl the Complex Structure of Pdz Domains in Syntenin-1 with 4L Peptide
Authors: Yun, J.H. / Yoo, J.H. / Cho, H.S. / Lee, W.
History
DepositionMay 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SYNTENIN-1
B: SYNTENIN-1
C: SYNTENIN-1
D: SYNTENIN-1
E: SYNDECAN-4
F: SYNDECAN-4
G: SYNDECAN-4
H: SYNDECAN-4


Theoretical massNumber of molelcules
Total (without water)74,0778
Polymers74,0778
Non-polymers00
Water3,153175
1
C: SYNTENIN-1
D: SYNTENIN-1
G: SYNDECAN-4
H: SYNDECAN-4


Theoretical massNumber of molelcules
Total (without water)37,0384
Polymers37,0384
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-17.4 kcal/mol
Surface area16950 Å2
MethodPISA
2
A: SYNTENIN-1
B: SYNTENIN-1
E: SYNDECAN-4
F: SYNDECAN-4


Theoretical massNumber of molelcules
Total (without water)37,0384
Polymers37,0384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-17.7 kcal/mol
Surface area17020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.200, 64.200, 201.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein
SYNTENIN-1 / SYNDECAN-BINDING PROTEIN 1


Mass: 17607.236 Da / Num. of mol.: 4 / Fragment: PDZ DOMAIN, RESIDUES 112-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9JI92
#2: Protein/peptide
SYNDECAN-4


Mass: 911.954 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) RATTUS NORVEGICUS (Norway rat) / References: UniProt: P34901
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.16 % / Description: NONE

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 0.97955
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97955 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 28305 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.96
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.57 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.496→19.903 Å / SU ML: 0.29 / σ(F): 1.41 / Phase error: 25.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 3966 7.1 %
Rwork0.2192 --
obs0.221 28180 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.496→19.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5148 0 0 175 5323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035216
X-RAY DIFFRACTIONf_angle_d0.8147028
X-RAY DIFFRACTIONf_dihedral_angle_d14.5451912
X-RAY DIFFRACTIONf_chiral_restr0.029828
X-RAY DIFFRACTIONf_plane_restr0.003904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4963-2.52670.3041380.27131837X-RAY DIFFRACTION98
2.5267-2.55860.291480.2821872X-RAY DIFFRACTION100
2.5586-2.59220.3241370.25851808X-RAY DIFFRACTION100
2.5922-2.62770.31051420.26751868X-RAY DIFFRACTION100
2.6277-2.66510.30111420.26921902X-RAY DIFFRACTION100
2.6651-2.70480.31771480.26141804X-RAY DIFFRACTION100
2.7048-2.7470.27841440.27251862X-RAY DIFFRACTION100
2.747-2.79190.27441440.26551873X-RAY DIFFRACTION100
2.7919-2.83990.34211360.26161811X-RAY DIFFRACTION100
2.8399-2.89140.31291420.25851910X-RAY DIFFRACTION100
2.8914-2.94680.32111400.26721821X-RAY DIFFRACTION100
2.9468-3.00680.30651400.25391848X-RAY DIFFRACTION100
3.0068-3.07190.30661440.25871882X-RAY DIFFRACTION100
3.0719-3.14310.26241340.25591838X-RAY DIFFRACTION100
3.1431-3.22140.26791450.23561876X-RAY DIFFRACTION100
3.2214-3.30810.28751420.22751827X-RAY DIFFRACTION100
3.3081-3.4050.25141420.23521877X-RAY DIFFRACTION100
3.405-3.51430.29681340.22051847X-RAY DIFFRACTION100
3.5143-3.63920.26311360.20211843X-RAY DIFFRACTION100
3.6392-3.78390.25981500.23271896X-RAY DIFFRACTION100
3.7839-3.95490.21621440.19841812X-RAY DIFFRACTION100
3.9549-4.16160.17411460.18941838X-RAY DIFFRACTION100
4.1616-4.41970.2131360.16331855X-RAY DIFFRACTION100
4.4197-4.75660.13631500.1561858X-RAY DIFFRACTION100
4.7566-5.22740.19231380.18971840X-RAY DIFFRACTION100
5.2274-5.96590.23581460.21851877X-RAY DIFFRACTION100
5.9659-7.45030.23591350.21421831X-RAY DIFFRACTION99
7.4503-19.90340.16471430.16891810X-RAY DIFFRACTION98

+
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://pdbjlvh1.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