[English] 日本語
Yorodumi
- PDB-6es4: A cryptic RNA-binding domain mediates Syncrip recognition and exo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6es4
TitleA cryptic RNA-binding domain mediates Syncrip recognition and exosomal partitioning of miRNA targets
ComponentsSyncrip, isoform K
KeywordsRNA / miRNA / exosome / Syncrip / RNA-binding
Function / homology
Function and homology information


regulation of neuromuscular synaptic transmission / Processing of Capped Intron-Containing Pre-mRNA / postsynapse of neuromuscular junction / regulation of oskar mRNA translation / mRNA Splicing - Major Pathway / negative regulation of synaptic assembly at neuromuscular junction / oocyte dorsal/ventral axis specification / dorsal appendage formation / ribonucleoprotein granule / basal cortex ...regulation of neuromuscular synaptic transmission / Processing of Capped Intron-Containing Pre-mRNA / postsynapse of neuromuscular junction / regulation of oskar mRNA translation / mRNA Splicing - Major Pathway / negative regulation of synaptic assembly at neuromuscular junction / oocyte dorsal/ventral axis specification / dorsal appendage formation / ribonucleoprotein granule / basal cortex / mRNA stabilization / lncRNA binding / precatalytic spliceosome / mRNA 3'-UTR binding / mRNA splicing, via spliceosome / mRNA 5'-UTR binding / ribonucleoprotein complex / mRNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Heterogeneous nuclear ribonucleoprotein Q acidic domain / Heterogeneous nuclear ribonucleoprotein Q acidic domain / HnRNP R/Q splicing factor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Syncrip, isoform K / Syncrip, isoform Q
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.2 Å
AuthorsHobor, F. / Dallmann, A. / Ball, N.J. / Cicchini, C. / Battistelli, C. / Ogrodowicz, R.W. / Christodoulou, E. / Martin, S.R. / Castello, A. / Tripodi, M. ...Hobor, F. / Dallmann, A. / Ball, N.J. / Cicchini, C. / Battistelli, C. / Ogrodowicz, R.W. / Christodoulou, E. / Martin, S.R. / Castello, A. / Tripodi, M. / Taylor, I.A. / Ramos, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_PC_13051 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: A cryptic RNA-binding domain mediates Syncrip recognition and exosomal partitioning of miRNA targets.
Authors: Hobor, F. / Dallmann, A. / Ball, N.J. / Cicchini, C. / Battistelli, C. / Ogrodowicz, R.W. / Christodoulou, E. / Martin, S.R. / Castello, A. / Tripodi, M. / Taylor, I.A. / Ramos, A.
History
DepositionOct 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Syncrip, isoform K
B: Syncrip, isoform K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,67615
Polymers49,6312
Non-polymers1,04513
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-56 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.783, 128.528, 79.585
Angle α, β, γ (deg.)90.000, 101.120, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Syncrip, isoform K


Mass: 24815.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Syp, AI945337, anon-WO0118547.613, Dmel\CG17838, l(3)03806, syp, CG17838, Dmel_CG17838
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4KHH8, UniProt: A0A0B4KHI4*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.2 M ammonium sulphate, 0.1 M sodium citrate pH 6, Seeding

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 33579 / % possible obs: 99 % / Redundancy: 3.36 % / Biso Wilson estimate: 44.1 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.045 / Net I/σ(I): 19.15
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.31 / Num. unique obs: 5270 / CC1/2: 0.868 / Rrim(I) all: 0.421 / % possible all: 96.8

-
Phasing

Phasing
Method
SAD
molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.43 Å39.05 Å
Translation6.43 Å39.05 Å

-
Processing

Software
NameVersionClassification
SCALAdata scaling
PHASER2.5.6phasing
SOLVEphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.2→37.561 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.24
RfactorNum. reflection% reflection
Rfree0.2055 1650 4.92 %
Rwork0.1737 --
obs0.1752 33546 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.1 Å2 / Biso mean: 61.0577 Å2 / Biso min: 25.9 Å2
Refinement stepCycle: final / Resolution: 2.2→37.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3125 0 59 76 3260
Biso mean--92.36 52.36 -
Num. residues----412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033259
X-RAY DIFFRACTIONf_angle_d0.7534407
X-RAY DIFFRACTIONf_chiral_restr0.027480
X-RAY DIFFRACTIONf_plane_restr0.003565
X-RAY DIFFRACTIONf_dihedral_angle_d13.2451191
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.26480.29251530.24042587274097
2.2648-2.33790.25571370.217326312768100
2.3379-2.42140.27341240.206827422866100
2.4214-2.51840.27741430.204225962739100
2.5184-2.6330.24391290.201326812810100
2.633-2.77170.26411320.201526872819100
2.7717-2.94530.2161470.202326262773100
2.9453-3.17260.221330.194526902823100
3.1726-3.49170.20761510.17932639279099
3.4917-3.99650.18921510.16272648279999
3.9965-5.03320.16351240.13742674279899
5.0332-37.56670.18441260.1612695282198
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)
11.06981.03380.98664.12753.81143.846-0.10510.0554-0.0758-0.1639-0.04420.1668-0.03450.01060.14170.7055-0.08460.0080.5619-0.15030.548327.9347120.0156113.3148
22.40940.4232-0.15342.94-0.30733.1671-0.03550.00290.21140.1494-0.04420.21430.04590.04390.08060.1903-0.00550.01320.2968-0.00780.329722.757997.254493.2616
31.924-2.5977-1.08944.45482.6563.0586-0.2389-0.1851-0.07330.84230.28770.3908-0.8017-0.2001-0.06020.75970.15360.07790.4924-0.07480.55438.60349.819781.9799
43.17860.0958-0.52134.4766-2.04353.20530.0717-0.0607-0.384-0.5069-0.1780.07540.65660.17630.07870.46320.1199-0.03140.3370.02320.33923.90172.284799.1353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 22:121)A22 - 121
2X-RAY DIFFRACTION2(chain A and resid 122:243)A122 - 243
3X-RAY DIFFRACTION3(chain B and resid 22:104)B22 - 104
4X-RAY DIFFRACTION4(chain B and resid 122:243)B122 - 243

+
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