1OO0 | pdb_00001oo0

Crystal structure of the Drosophila Mago nashi-Y14 complex

PDB DOI: https://doi.org/10.2210/pdb1OO0/pdb

Classification: SIGNALING PROTEIN
Organism(s): Drosophila melanogaster
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2003-03-02 Released: 2003-05-27
Deposition Author(s): Shi, H., Xu, R.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.262 (Depositor)
R-Value Work:
0.215 (Depositor), 0.228 (DCC)
R-Value Observed:
0.215 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the Drosophila Mago nashi-Y14 complex

Shi, H., Xu, R.M.

(2003) Genes Dev 17: 971-976

PubMed: 12704080 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1101/gad.260403
Primary Citation Related Structures:
1OO0

PubMed Abstract:
Pre-mRNA splicing is essential for generating mature mRNA and is also important for subsequent mRNA export and quality control. The splicing history is imprinted on spliced mRNA through the deposition of a splicing-dependent multiprotein complex, the exon junction complex (EJC), at approximately 20 nucleotides upstream of exon-exon junctions. The EJC is a dynamic structure containing proteins functioning in the nuclear export and nonsense-mediated decay of spliced mRNAs. Mago nashi (Mago) and Y14 are core components of the EJC, and they form a stable heterodimer that strongly associates with spliced mRNA. Here we report a 1.85 A-resolution structure of the Drosophila Mago-Y14 complex. Surprisingly, the structure shows that the canonical RNA-binding surface of the Y14 RNA recognition motif (RRM) is involved in extensive protein-protein interactions with Mago. This unexpected finding provides important insights for understanding the molecular mechanisms of EJC assembly and RRM-mediated protein-protein interactions.

Organizational Affiliation

W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, New York 11724, USA.

Macromolecule Content

Total Structure Weight: 30.7 kDa
Atom Count: 2,111
Modeled Residue Count: 236
Deposited Residue Count: 257
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mago nashi protein	A	147	Drosophila melanogaster	Mutation(s): 0 Gene Names: MAGO
UniProt
Find proteins for P49028 (Drosophila melanogaster) Explore P49028 Go to UniProtKB: P49028
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49028
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CG8781-PA	B	110	Drosophila melanogaster	Mutation(s): 0 Gene Names: TSU
UniProt
Find proteins for Q9V535 (Drosophila melanogaster) Explore Q9V535 Go to UniProtKB: Q9V535
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9V535
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A]	H [auth A], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth B]
SR Query on SR Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.262 (Depositor)
R-Value Work: 0.215 (Depositor), 0.228 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.027	α = 90
b = 52.387	β = 104.9
c = 52.862	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-05-27

Deposition Author(s):

Shi, H.

Xu, R.M.

Revision History (Full details and data files)

Version 1.0: 2003-05-27
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations