6ES4 | pdb_00006es4

A cryptic RNA-binding domain mediates Syncrip recognition and exosomal partitioning of miRNA targets

• PDB DOI: https://doi.org/10.2210/pdb6ES4/pdb

• Classification: RNA
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-19 Released: 2018-03-07 
• Deposition Author(s): 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 Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.205 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

A cryptic RNA-binding domain mediates Syncrip recognition and exosomal partitioning of miRNA targets.

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.

(2018) Nat Commun 9: 831-831

• PubMed: 29483512 
• DOI: https://doi.org/10.1038/s41467-018-03182-3
• Primary Citation Related Structures: 
  6ES4


• PubMed Abstract: 
  

  Exosomal miRNA transfer is a mechanism for cell-cell communication that is important in the immune response, in the functioning of the nervous system and in cancer. Syncrip/hnRNPQ is a highly conserved RNA-binding protein that mediates the exosomal partition of a set of miRNAs. Here, we report that Syncrip's amino-terminal domain, which was previously thought to mediate protein-protein interactions, is a cryptic, conserved and sequence-specific RNA-binding domain, designated NURR (N-terminal unit for RNA recognition). The NURR domain mediates the specific recognition of a short hEXO sequence defining Syncrip exosomal miRNA targets, and is coupled by a non-canonical structural element to Syncrip's RRM domains to achieve high-affinity miRNA binding. As a consequence, Syncrip-mediated selection of the target miRNAs implies both recognition of the hEXO sequence by the NURR domain and binding of the RRM domains 5' to this sequence. This structural arrangement enables Syncrip-mediated selection of miRNAs with different seed sequences.

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Organizational Affiliation: 
• Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6XA, UK.
School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
Department of Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Street 2, 12489, Berlin, Germany.
Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy.
Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK. [e-mail].
Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6XA, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 50.68 kDa 
• Atom Count: 3,279 
• Modeled Residue Count: 412 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Syncrip, isoform K	A, B	222	Drosophila melanogaster	Mutation(s): 0  Gene Names: Syp, AI945337, anon-WO0118547.613, Dmel\CG17838, l(3)03806, syp, CG17838, Dmel_CG17838
UniProt
Find proteins for A0A0B4KHI4 (Drosophila melanogaster) Explore A0A0B4KHI4  Go to UniProtKB:  A0A0B4KHI4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], L [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, B	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.205 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.783	α = 90
b = 128.528	β = 101.12
c = 79.585	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
SOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-03-07 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MC_PC_13051

Revision History  

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Structure summary