[English] 日本語
Yorodumi
- PDB-6rlc: Crystal structure of the PDZ tandem of syntenin in complex with f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rlc
TitleCrystal structure of the PDZ tandem of syntenin in complex with fragment F13
ComponentsSyntenin-1
KeywordsSIGNALING PROTEIN / signaling protein cell adhesion PDZ domain syntenin syndecan drug design
Function / homology
Function and homology information


interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / Neurofascin interactions / presynapse assembly / neurexin family protein binding / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion ...interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / Neurofascin interactions / presynapse assembly / neurexin family protein binding / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / frizzled binding / negative regulation of receptor internalization / protein targeting to membrane / Ephrin signaling / RIPK1-mediated regulated necrosis / positive regulation of transforming growth factor beta receptor signaling pathway / growth factor binding / positive regulation of epithelial to mesenchymal transition / positive regulation of phosphorylation / cell adhesion molecule binding / regulation of mitotic cell cycle / ionotropic glutamate receptor binding / phosphatidylinositol-4,5-bisphosphate binding / protein sequestering activity / ephrin receptor binding / adherens junction / positive regulation of JNK cascade / Regulation of necroptotic cell death / azurophil granule lumen / extracellular vesicle / melanosome / presynapse / actin cytoskeleton organization / positive regulation of cell growth / chemical synaptic transmission / nuclear membrane / Ras protein signal transduction / blood microparticle / cytoskeleton / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein heterodimerization activity / focal adhesion / Neutrophil degranulation / positive regulation of cell population proliferation / protein-containing complex binding / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / 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
ACETATE ION / Chem-K7Z / Syntenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFeracci, M. / Barral, K.
Funding support Belgium, France, 7items
OrganizationGrant numberCountry
KU LeuvenGOA/12/016 Belgium
French National Research AgencyAMIDEX project ANR-11-IDEX-0001-02 France
Other privateSTK-FAF-FA/2016/828 Belgium
Fondation ARCARC PDF20151203700 France
Fondation ARCPJA 2016204584 France
Research Foundation - FlandersFWO, G.0C57.18N Belgium
Other privateNational League Against Cancer France
CitationJournal: J Extracell Vesicles / Year: 2020
Title: Pharmacological inhibition of syntenin PDZ2 domain impairs breast cancer cell activities and exosome loadifing with syndecan and EpCAM cargo.
Authors: Leblanc, R. / Kashyap, R. / Barral, K. / Egea-Jimenez, A.L. / Kovalskyy, D. / Feracci, M. / Garcia, M. / Derviaux, C. / Betzi, S. / Ghossoub, R. / Platonov, M. / Roche, P. / Morelli, X. / ...Authors: Leblanc, R. / Kashyap, R. / Barral, K. / Egea-Jimenez, A.L. / Kovalskyy, D. / Feracci, M. / Garcia, M. / Derviaux, C. / Betzi, S. / Ghossoub, R. / Platonov, M. / Roche, P. / Morelli, X. / Hoffer, L. / Zimmermann, P.
History
DepositionMay 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / struct_ncs_dom_lim
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Syntenin-1
D: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,51511
Polymers72,0754
Non-polymers1,4407
Water2,666148
1
A: Syntenin-1
B: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7876
Polymers36,0372
Non-polymers7504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Syntenin-1
D: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7285
Polymers36,0372
Non-polymers6913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.230, 57.512, 101.094
Angle α, β, γ (deg.)93.99, 96.08, 107.70
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA111 - 2714 - 164
21PROPROBB111 - 2714 - 164
12PHEPHEAA111 - 2734 - 166
22PHEPHECC111 - 2734 - 166
13PROPROAA111 - 2714 - 164
23PROPRODD111 - 2714 - 164
14PROPROBB111 - 2714 - 164
24PROPROCC111 - 2714 - 164
15PROPROBB111 - 2714 - 164
25PROPRODD111 - 2714 - 164
16PROPROCC111 - 2714 - 164
26PROPRODD111 - 2714 - 164

NCS ensembles :
IDDetails
6C,D
1A,B
2A,C
3A,D
4B,C
5B,C

-
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: 18018.688 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 K-12 (bacteria) / References: UniProt: O00560
#2: Chemical
ChemComp-K7Z / (2~{S})-2-[3-(4-chlorophenyl)sulfanylpropanoylamino]-3-methyl-butanoic acid


Mass: 315.816 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H18ClNO3S
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM Sodium Acetate pH 4.6, 200mM Ammonium Acetate, 22% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→50.02 Å / Num. all: 106108 / Num. obs: 30520 / % possible obs: 96.78 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.04369 / Rrim(I) all: 0.08199 / Net I/σ(I): 9.74
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.3676 / Mean I/σ(I) obs: 3.02 / Num. unique all: 10728 / Num. unique obs: 3035 / CC1/2: 0.925 / Rpim(I) all: 0.2293 / Rrim(I) all: 0.4347 / % possible all: 95.92

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50.02 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.916 / SU B: 21.245 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R: 0.466 / ESU R Free: 0.289 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30141 1497 4.9 %RANDOM
Rwork0.25901 ---
obs0.26105 29031 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.873 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20.04 Å20.36 Å2
2--1.05 Å2-1.02 Å2
3----2.01 Å2
Refinement stepCycle: 1 / Resolution: 2.2→50.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4949 0 92 148 5189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135117
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174904
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.656890
X-RAY DIFFRACTIONr_angle_other_deg1.2391.60211394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0525651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18623.361238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65215938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9721528
X-RAY DIFFRACTIONr_chiral_restr0.0630.2712
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025683
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02981
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9432.1782613
X-RAY DIFFRACTIONr_mcbond_other0.9322.1732609
X-RAY DIFFRACTIONr_mcangle_it1.5693.2563263
X-RAY DIFFRACTIONr_mcangle_other1.5643.2553262
X-RAY DIFFRACTIONr_scbond_it1.0872.4142504
X-RAY DIFFRACTIONr_scbond_other1.0872.4162505
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7873.5543628
X-RAY DIFFRACTIONr_long_range_B_refined5.3782.44273377
X-RAY DIFFRACTIONr_long_range_B_other5.3782.44273378
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A46330.11
12B46330.11
21A47440.1
22C47440.1
31A45700.1
32D45700.1
41B46550.09
42C46550.09
51B46810.08
52D46810.08
61C46590.1
62D46590.1
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 110 -
Rwork0.344 2161 -
obs--95.74 %
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)
10.7404-0.3963-0.79446.1482.90011.9222-0.00250.220.2016-0.50120.1286-0.0317-0.2059-0.1288-0.12610.4381-0.1071-0.06340.09410.08310.134613.830816.94279.0831
20.70030.29360.13014.37160.98952.4459-0.003-0.0868-0.13810.07410.0454-0.22770.52030.1678-0.04240.4773-0.0591-0.01340.05170.01970.034915.52425.965332.1475
30.3769-0.7585-0.76055.21332.52161.82140.0180.13720.0528-0.2407-0.04890.2252-0.1172-0.20810.03080.3961-0.0884-0.07520.07950.05470.117727.7752-4.7359-40.8878
40.72520.2877-0.53693.9743.37646.3864-0.2323-0.0336-0.34670.83970.1922-0.14431.56770.33020.040.7129-0.02280.04070.05390.01580.184728.2895-16.3293-18.3197
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A111 - 273
2X-RAY DIFFRACTION2B111 - 272
3X-RAY DIFFRACTION3C111 - 273
4X-RAY DIFFRACTION4D110 - 272

+
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