PDBsum entry: 2j0q

Hydrolase

PDB-id

2j0q


	Asymmetric unit

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Description

Header details

Protein chains

DNA/RNA

Ligands

ANP ×2

Metal ions

_MG ×2

Waters ×1

* Residue conservation analysis

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		Biological unit, pentamer - as defined in PDB file (see also PQS)

PDB id:

2j0q

Name:

Hydrolase

Title:

The crystal structure of the exon junction complex at 3.2 a resolution

Structure:

Atp-dependent RNA helicase ddx48. Chain: a, b. Synonym: eif4aiii RNA-helicase, dead box protein 48, eukaryotic initiation factor 4a-like nuk-34, hnmp 265, nuclear matrix protein 265, eukaryotic translation initiation factor 4a isoform 3. Engineered: yes. Protein mago nashi homolog. Chain: c, f.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes

Biological unit:

Pentamer (from PDB file)

UniProt:

Chains A, B: P38919 (IF4A3_HUMAN)

Seq:

Struc:


Seq:				411 a.a.

Struc:				390 a.a.

Chains C, F: P61326 (MGN_HUMAN)

Seq:				146 a.a.

Struc:				143 a.a.

Chains D, G: Q9Y5S9 (RBM8A_HUMAN)

Seq:				174 a.a.

Struc:				89 a.a.

Chain I: O15234 (CASC3_HUMAN)

Seq:

Struc:


Seq:

Struc:


Seq:				703 a.a.

Struc:				63 a.a.

Chain T: O15234 (CASC3_HUMAN)

Seq:

Struc:

Seq:

Struc:

Seq:

703 a.a.

Struc:

65 a.a.

Key:		PfamA domain			PfamB domain
		Secondary structure			CATH domain

Resolution:

3.20Å

R-factor:

0.235

R-free:

0.277

Authors:

F.Bono,J.Ebert,E.Lorentzen,E.Conti

Key ref:

F.Bono et al. (2006). The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA.. Cell, 126, 713-725. [PubMed id: 16923391] [DOI: 10.1016/j.cell.2006.08.006]

Date:

04-Aug-06

Release date:

30-Aug-06

Related entries:

1p27 crystal structure of the human y14/magoh complex
2j0s the crystal structure of the exon junction complex at 2.2 a resolution.
2j0u the crystal structure of eif4aiii-barentsz complex at 3.0 a resolution

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Key reference

DOI no: 10.1016/j.cell.2006.08.006 Cell 126:713-725 (2006)

PubMed id: 16923391

The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA.

F.Bono, J.Ebert, E.Lorentzen, E.Conti.

ABSTRACT

The exon junction complex (EJC) plays a major role in posttranscriptional regulation of mRNA in metazoa. The EJC is deposited onto mRNA during splicing and is transported to the cytoplasm where it influences translation, surveillance, and localization of the spliced mRNA. The complex is formed by the association of four proteins (eIF4AIII, Barentsz [Btz], Mago, and Y14), mRNA, and ATP. The 2.2 A resolution structure of the EJC reveals how it stably locks onto mRNA. The DEAD-box protein eIF4AIII encloses an ATP molecule and provides the binding sites for six ribonucleotides. Btz wraps around eIF4AIII and stacks against the 5' nucleotide. An intertwined network of interactions anchors Mago-Y14 and Btz at the interface between the two domains of eIF4AIII, effectively stabilizing the ATP bound state. Comparison with the structure of the eIF4AIII-Btz subcomplex that we have also determined reveals that large conformational changes are required upon EJC assembly and disassembly.

Selected figure(s)

Figure 2.
Figure 2. Structure of EJC
View of the human EJC in two orientations related by a 180° rotation about a vertical axis. In the complex, Btz (shown in red) stretches around the DEAD-box helicase eIF4AIII (in yellow). Both proteins interact with RNA (in black), which is bound at a cleft formed between the two RecA-like domains of eIF4AIII. ATP (in gray) binds at an interface between the two domains of eIF4AIII, distinct from the RNA binding cleft. The other two protein components of the EJC, Mago (blue), and Y14 (magenta), bind mainly to domain 2 of eIF4AIII, but the interaction surface also extends over to the interface with domain 1. The dotted line in red shows the approximate path of a portion of Btz not present in the electron density (residues 198–213; Figure 1). The helix at the C-terminal stretch of Btz is present in the 3.2 Å resolution structure (shown), while it is partially disordered in the 2.2 Å structure. The two EJC structures are otherwise virtually identical. All ribbon drawings were rendered using PyMOL (DeLano, W.L., 2002, http://www.pymol.org).
Figure 4.
Figure 4. Interaction Networks between the Protein Components of the EJC
(A) The C-terminal stretch of Btz (red) is anchored to domain 1 of eIF4AIII (yellow). The close up is in a similar orientation as Figure 2A. It shows a subset of Btz residues contacting a region of the DEAD-box protein that is conserved in eIF4AIII orthologs but not in paralogs such as eIF4AI.
(B) Group of interactions between Mago (blue), Btz, and eIF4AIII. Mago and Btz protrude into the cleft that is formed between the two domains of eIF4AIII.
(C) The C-terminal helix of eIF4AIII engages in a cluster of interactions between Y14 (magenta) and Mago.
(D) Interactions of Mago-Y14 with the eIF4AIII linker (residues 241–250, in yellow) connecting the two RecA-like domains (in gray). The linker is wedged into Mago-Y14. It interacts on one side with the loops of Mago shown in panel (B) and on the other side with Y14 and with the C-terminal region of Mago (see Ile146 in Figure 3E).

The above figures are reprinted by permission from Cell Press: Cell (2006, 126, 713-725) copyright 2006.

Figures were selected by the author.

Literature references that cite this PDB file's key reference

PubMed id Reference

19859661 P.Nicholson, H.Yepiskoposyan, S.Metze, R.Zamudio Orozco, N.Kleinschmidt, and O.Mühlemann (2010).
Nonsense-mediated mRNA decay in human cells: mechanistic insights, functions beyond quality control and the double-life of NMD factors.

Cell Mol Life Sci, 67, 677-700.

19474341 A.R.Karow, and D.Klostermeier (2009).
A conformational change in the helicase core is necessary but not sufficient for RNA unwinding by the DEAD box helicase YxiN.

Nucleic Acids Res, 37, 4464-4471.

19050012 D.Klostermeier, and M.G.Rudolph (2009).
A novel dimerization motif in the C-terminal domain of the Thermus thermophilus DEAD box helicase Hera confers substantial flexibility.

Nucleic Acids Res, 37, 421-430.

PDB codes: 3eaq 3ear 3eas

19219046 H.von Moeller, C.Basquin, and E.Conti (2009).
The mRNA export protein DBP5 binds RNA and the cytoplasmic nucleoporin NUP214 in a mutually exclusive manner.

Nat Struct Mol Biol, 16, 247-254.

PDB codes: 3fhc 3fht

19033377 K.H.Nielsen, H.Chamieh, C.B.Andersen, F.Fredslund, K.Hamborg, H.Le Hir, and G.R.Andersen (2009).
Mechanism of ATP turnover inhibition in the EJC.

RNA, 15, 67-75.

PDB code: 3ex7

19700770 M.N.Murphy, P.Gong, K.Ralto, L.Manelyte, N.J.Savery, and K.Theis (2009).
An N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor Mfd.

Nucleic Acids Res, 37, 6042-6053.

PDB code: 3hjh

19478851 N.H.Gehring, S.Lamprinaki, M.W.Hentze, and A.E.Kulozik (2009).
The hierarchy of exon-junction complex assembly by the spliceosome explains key features of mammalian nonsense-mediated mRNA decay.

PLoS Biol, 7, e1000120.

19244245 R.Collins, T.Karlberg, L.Lehtiö, P.Schütz, S.van den Berg, L.G.Dahlgren, M.Hammarström, J.Weigelt, and H.Schüler (2009).
The DEXD/H-box RNA Helicase DDX19 Is Regulated by an {alpha}-Helical Switch.

J Biol Chem, 284, 10296-10300.

PDB codes: 3ews 3g0h

19322199 S.Chimnaronk, T.Suzuki, T.Manita, Y.Ikeuchi, M.Yao, T.Suzuki, and I.Tanaka (2009).
RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon.

EMBO J, 28, 1362-1373.

PDB code: 2zpa

19589129 S.H.Ling, Z.Cheng, and H.Song (2009).
Structural aspects of RNA helicases in eukaryotic mRNA decay.

Biosci Rep, 29, 339-349.

19324961 U.Schmidt, K.B.Im, C.Benzing, S.Janjetovic, K.Rippe, P.Lichter, and M.Wachsmuth (2009).
Assembly and mobility of exon-exon junction complexes in living cells.

RNA, 15, 862-876.

18573084 A.M.Pyle (2008).
Translocation and unwinding mechanisms of RNA and DNA helicases.

Annu Rev Biophys, 37, 317-336.

18184816 B.Theissen, A.R.Karow, J.Köhler, A.Gubaev, and D.Klostermeier (2008).
Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase.

Proc Natl Acad Sci U S A, 105, 548-553.

19008861 D.Luo, T.Xu, R.P.Watson, D.Scherer-Becker, A.Sampath, W.Jahnke, S.S.Yeong, C.H.Wang, S.P.Lim, A.Strongin, S.G.Vasudevan, and J.Lescar (2008).
Insights into RNA unwinding and ATP hydrolysis by the flavivirus NS3 protein.

EMBO J, 27, 3209-3219.

PDB codes: 2jlq 2jlr 2jls 2jlu 2jlv 2jlw 2jlx 2jly 2jlz

18952819 D.M.Mishler, A.B.Christ, and J.A.Steitz (2008).
Flexibility in the site of exon junction complex deposition revealed by functional group and RNA secondary structure alterations in the splicing substrate.

RNA, 14, 2657-2670.

19088201 F.Liu, A.Putnam, and E.Jankowsky (2008).
ATP hydrolysis is required for DEAD-box protein recycling but not for duplex unwinding.

Proc Natl Acad Sci U S A, 105, 20209-20214.

18600222 G.Langer, S.X.Cohen, V.S.Lamzin, and A.Perrakis (2008).
Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7.

Nat Protoc, 3, 1171-1179.

18066079 H.Chamieh, L.Ballut, F.Bonneau, and H.Le Hir (2008).
NMD factors UPF2 and UPF3 bridge UPF1 to the exon junction complex and stimulate its RNA helicase activity.

Nat Struct Mol Biol, 15, 85-93.

18165229 J.A.Worrall, F.S.Howe, A.R.McKay, C.V.Robinson, and B.F.Luisi (2008).
Allosteric activation of the ATPase activity of the Escherichia coli RhlB RNA helicase.

J Biol Chem, 283, 5567-5576.

18332124 J.Banroques, O.Cordin, M.Doère, P.Linder, and N.K.Tanner (2008).
A conserved phenylalanine of motif IV in superfamily 2 helicases is required for cooperative, ATP-dependent binding of RNA substrates in DEAD-box proteins.

Mol Cell Biol, 28, 3359-3371.

18974867 J.R.Boyne, K.J.Colgan, and A.Whitehouse (2008).
Recruitment of the complete hTREX complex is required for Kaposi's sarcoma-associated herpesvirus intronless mRNA nuclear export and virus replication.

PLoS Pathog, 4, e1000194.

18270573 L.Lindqvist, M.Oberer, M.Reibarkh, R.Cencic, M.E.Bordeleau, E.Vogt, A.Marintchev, J.Tanaka, F.Fagotto, M.Altmann, G.Wagner, and J.Pelletier (2008).
Selective pharmacological targeting of a DEAD box RNA helicase.

PLoS ONE, 3, e1583.

18782831 M.H.Linden, R.K.Hartmann, and D.Klostermeier (2008).
The putative RNase P motif in the DEAD box helicase Hera is dispensable for efficient interaction with RNA and helicase activity.

Nucleic Acids Res, 36, 5800-5811.

18719248 N.Rozovsky, A.C.Butterworth, and M.J.Moore (2008).
Interactions between eIF4AI and its accessory factors eIF4B and eIF4H.

RNA, 14, 2136-2148.

18606994 P.Schütz, M.Bumann, A.E.Oberholzer, C.Bieniossek, H.Trachsel, M.Altmann, and U.Baumann (2008).
Crystal structure of the yeast eIF4A-eIF4G complex: an RNA-helicase controlled by protein-protein interactions.

Proc Natl Acad Sci U S A, 105, 9564-9569.

PDB codes: 2vso 2vsx

18256688 P.V.Ivanov, N.H.Gehring, J.B.Kunz, M.W.Hentze, and A.E.Kulozik (2008).
Interactions between UPF1, eRFs, PABP and the exon junction complex suggest an integrated model for mammalian NMD pathways.

EMBO J, 27, 736-747.

18267970 R.Lewis, H.Dürr, K.P.Hopfner, and J.Michaelis (2008).
Conformational changes of a Swi2/Snf2 ATPase during its mechano-chemical cycle.

Nucleic Acids Res, 36, 1881-1890.

19088196 Y.Chen, J.P.Potratz, P.Tijerina, M.Del Campo, A.M.Lambowitz, and R.Russell (2008).
DEAD-box proteins can completely separate an RNA duplex using a single ATP.

Proc Natl Acad Sci U S A, 105, 20203-20208.

18451801 Z.Kerényi, Z.Mérai, L.Hiripi, A.Benkovics, P.Gyula, C.Lacomme, E.Barta, F.Nagy, and D.Silhavy (2008).
Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay.

EMBO J, 27, 1585-1595.

17473849 B.M.Lunde, C.Moore, and G.Varani (2007).
RNA-binding proteins: modular design for efficient function.

Nat Rev Mol Cell Biol, 8, 479-490.

17375189 C.G.Noble, and H.Song (2007).
MLN51 stimulates the RNA-helicase activity of eIF4AIII.

PLoS ONE, 2, e303.

17562711 J.Shen, L.Zhang, and R.Zhao (2007).
Biochemical characterization of the ATPase and helicase activity of UAP56, an essential pre-mRNA splicing and mRNA export factor.

J Biol Chem, 282, 22544-22550.

17558417 K.Büttner, S.Nehring, and K.P.Hopfner (2007).
Structural basis for DNA duplex separation by a superfamily-2 helicase.

Nat Struct Mol Biol, 14, 647-652.

PDB codes: 2p6r 2p6u

17586820 M.H.Viegas, N.H.Gehring, S.Breit, M.W.Hentze, and A.E.Kulozik (2007).
The abundance of RNPS1, a protein component of the exon junction complex, can determine the variability in efficiency of the Nonsense Mediated Decay pathway.

Nucleic Acids Res, 35, 4542-4551.

17846169 S.B.Patel, N.Novikova, and M.Bellini (2007).
Splicing-independent recruitment of spliceosomal small nuclear RNPs to nascent RNA polymerase II transcripts.

J Cell Biol, 178, 937-949.

17606899 Z.Zhang, and A.R.Krainer (2007).
Splicing remodels messenger ribonucleoprotein architecture via eIF4A3-dependent and -independent recruitment of exon junction complex components.

Proc Natl Acad Sci U S A, 104, 11574-11579.

17072313 Q.Yang, and E.Jankowsky (2006).
The DEAD-box protein Ded1 unwinds RNA duplexes by a mode distinct from translocating helicases.

Nat Struct Mol Biol, 13, 981-986.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.