Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2XB2

Crystal structure of the core Mago-Y14-eIF4AIII-Barentsz-UPF3b assembly shows how the EJC is bridged to the NMD machinery

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000184	biological_process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
A	0000398	biological_process	mRNA splicing, via spliceosome
A	0003676	molecular_function	nucleic acid binding
A	0003723	molecular_function	RNA binding
A	0003724	molecular_function	RNA helicase activity
A	0003729	molecular_function	mRNA binding
A	0004386	molecular_function	helicase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005681	cellular_component	spliceosomal complex
A	0005730	cellular_component	nucleolus
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006364	biological_process	rRNA processing
A	0006397	biological_process	mRNA processing
A	0006406	biological_process	mRNA export from nucleus
A	0006417	biological_process	regulation of translation
A	0008143	molecular_function	poly(A) binding
A	0008306	biological_process	associative learning
A	0008380	biological_process	RNA splicing
A	0010629	biological_process	negative regulation of gene expression
A	0014070	biological_process	response to organic cyclic compound
A	0016020	cellular_component	membrane
A	0016607	cellular_component	nuclear speck
A	0016787	molecular_function	hydrolase activity
A	0016887	molecular_function	ATP hydrolysis activity
A	0017148	biological_process	negative regulation of translation
A	0030425	cellular_component	dendrite
A	0035145	cellular_component	exon-exon junction complex
A	0035368	molecular_function	selenocysteine insertion sequence binding
A	0035613	molecular_function	RNA stem-loop binding
A	0035640	biological_process	exploration behavior
A	0043021	molecular_function	ribonucleoprotein complex binding
A	0043025	cellular_component	neuronal cell body
A	0045727	biological_process	positive regulation of translation
A	0048701	biological_process	embryonic cranial skeleton morphogenesis
A	0051028	biological_process	mRNA transport
A	0071006	cellular_component	U2-type catalytic step 1 spliceosome
A	0071013	cellular_component	catalytic step 2 spliceosome
A	0072715	biological_process	cellular response to selenite ion
A	0090394	biological_process	negative regulation of excitatory postsynaptic potential
A	0098794	cellular_component	postsynapse
A	0098978	cellular_component	glutamatergic synapse
A	0099578	biological_process	regulation of translation at postsynapse, modulating synaptic transmission
A	1904570	biological_process	negative regulation of selenocysteine incorporation
A	1990416	biological_process	cellular response to brain-derived neurotrophic factor stimulus
A	1990904	cellular_component	ribonucleoprotein complex
A	2000622	biological_process	regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
C	0000184	biological_process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
C	0000381	biological_process	regulation of alternative mRNA splicing, via spliceosome
C	0000398	biological_process	mRNA splicing, via spliceosome
C	0003723	molecular_function	RNA binding
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005681	cellular_component	spliceosomal complex
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006397	biological_process	mRNA processing
C	0006406	biological_process	mRNA export from nucleus
C	0006417	biological_process	regulation of translation
C	0008380	biological_process	RNA splicing
C	0016607	cellular_component	nuclear speck
C	0035145	cellular_component	exon-exon junction complex
C	0050684	biological_process	regulation of mRNA processing
C	0051028	biological_process	mRNA transport
C	0071013	cellular_component	catalytic step 2 spliceosome
C	1990501	cellular_component	exon-exon junction subcomplex mago-y14
C	2000622	biological_process	regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
D	0003676	molecular_function	nucleic acid binding
D	0003723	molecular_function	RNA binding
D	0003729	molecular_function	mRNA binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0006396	biological_process	RNA processing
S	0003729	molecular_function	mRNA binding
S	0006397	biological_process	mRNA processing
S	0035145	cellular_component	exon-exon junction complex
T	0003729	molecular_function	mRNA binding
T	0006397	biological_process	mRNA processing
T	0035145	cellular_component	exon-exon junction complex
X	0000184	biological_process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
X	0000398	biological_process	mRNA splicing, via spliceosome
X	0003676	molecular_function	nucleic acid binding
X	0003723	molecular_function	RNA binding
X	0003724	molecular_function	RNA helicase activity
X	0003729	molecular_function	mRNA binding
X	0004386	molecular_function	helicase activity
X	0005515	molecular_function	protein binding
X	0005524	molecular_function	ATP binding
X	0005634	cellular_component	nucleus
X	0005654	cellular_component	nucleoplasm
X	0005681	cellular_component	spliceosomal complex
X	0005730	cellular_component	nucleolus
X	0005737	cellular_component	cytoplasm
X	0005829	cellular_component	cytosol
X	0006364	biological_process	rRNA processing
X	0006397	biological_process	mRNA processing
X	0006406	biological_process	mRNA export from nucleus
X	0006417	biological_process	regulation of translation
X	0008143	molecular_function	poly(A) binding
X	0008306	biological_process	associative learning
X	0008380	biological_process	RNA splicing
X	0010629	biological_process	negative regulation of gene expression
X	0014070	biological_process	response to organic cyclic compound
X	0016020	cellular_component	membrane
X	0016607	cellular_component	nuclear speck
X	0016787	molecular_function	hydrolase activity
X	0016887	molecular_function	ATP hydrolysis activity
X	0017148	biological_process	negative regulation of translation
X	0030425	cellular_component	dendrite
X	0035145	cellular_component	exon-exon junction complex
X	0035368	molecular_function	selenocysteine insertion sequence binding
X	0035613	molecular_function	RNA stem-loop binding
X	0035640	biological_process	exploration behavior
X	0043021	molecular_function	ribonucleoprotein complex binding
X	0043025	cellular_component	neuronal cell body
X	0045727	biological_process	positive regulation of translation
X	0048701	biological_process	embryonic cranial skeleton morphogenesis
X	0051028	biological_process	mRNA transport
X	0071006	cellular_component	U2-type catalytic step 1 spliceosome
X	0071013	cellular_component	catalytic step 2 spliceosome
X	0072715	biological_process	cellular response to selenite ion
X	0090394	biological_process	negative regulation of excitatory postsynaptic potential
X	0098794	cellular_component	postsynapse
X	0098978	cellular_component	glutamatergic synapse
X	0099578	biological_process	regulation of translation at postsynapse, modulating synaptic transmission
X	1904570	biological_process	negative regulation of selenocysteine incorporation
X	1990416	biological_process	cellular response to brain-derived neurotrophic factor stimulus
X	1990904	cellular_component	ribonucleoprotein complex
X	2000622	biological_process	regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
Y	0000184	biological_process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
Y	0000381	biological_process	regulation of alternative mRNA splicing, via spliceosome
Y	0000398	biological_process	mRNA splicing, via spliceosome
Y	0003723	molecular_function	RNA binding
Y	0005515	molecular_function	protein binding
Y	0005634	cellular_component	nucleus
Y	0005654	cellular_component	nucleoplasm
Y	0005681	cellular_component	spliceosomal complex
Y	0005737	cellular_component	cytoplasm
Y	0005829	cellular_component	cytosol
Y	0006397	biological_process	mRNA processing
Y	0006406	biological_process	mRNA export from nucleus
Y	0006417	biological_process	regulation of translation
Y	0008380	biological_process	RNA splicing
Y	0016607	cellular_component	nuclear speck
Y	0035145	cellular_component	exon-exon junction complex
Y	0050684	biological_process	regulation of mRNA processing
Y	0051028	biological_process	mRNA transport
Y	0071013	cellular_component	catalytic step 2 spliceosome
Y	1990501	cellular_component	exon-exon junction subcomplex mago-y14
Y	2000622	biological_process	regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
Z	0003676	molecular_function	nucleic acid binding
Z	0003723	molecular_function	RNA binding
Z	0003729	molecular_function	mRNA binding
Z	0005634	cellular_component	nucleus
Z	0005737	cellular_component	cytoplasm
Z	0006396	biological_process	RNA processing

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG A 1412

Chain	Residue
A	THR89
A	ASP187
A	GLU188
A	ANP1413

site_id	AC2
Number of Residues	19
Details	BINDING SITE FOR RESIDUE ANP A 1413

Chain	Residue
A	SER84
A	GLY85
A	THR86
A	GLY87
A	LYS88
A	THR89
A	ALA90
A	GLU188
A	GLY340
A	ASP342
A	ARG367
A	ARG370
A	TYR371
A	MG1412
A	PHE40
A	PHE58
A	LYS60
A	PRO61
A	GLN65

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG X 1412

Chain	Residue
X	THR89
X	ASP187
X	GLU188
X	ANP1413

site_id	AC4
Number of Residues	19
Details	BINDING SITE FOR RESIDUE ANP X 1413

Chain	Residue
X	PHE40
X	PHE58
X	LYS60
X	PRO61
X	GLN65
X	SER84
X	GLY85
X	THR86
X	GLY87
X	LYS88
X	THR89
X	ALA90
X	GLU188
X	GLY340
X	ASP342
X	ARG367
X	ARG370
X	TYR371
X	MG1412

Functional Information from PROSITE/UniProt

site_id	PS00039
Number of Residues	9
Details	DEAD_ATP_HELICASE DEAD-box subfamily ATP-dependent helicases signature. VLDEADEmL

Chain	Residue	Details
A	VAL185-LEU193

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	MOD_RES: Omega-N-methylarginine => ECO:0007744\|PubMed:24129315

Chain	Residue	Details
G	LYS447
U	LYS447
A	ARG367
X	LYS60
X	GLN65
X	GLY85
X	ASP342
X	ARG367
A	GLY85
A	ASP342

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:21406692, ECO:0007744\|PubMed:23186163

Chain	Residue	Details
S	SER265
T	SER265

site_id	SWS_FT_FI3
Number of Residues	2
Details	MOD_RES: N-acetylalanine; in Eukaryotic initiation factor 4A-III, N-terminally processed => ECO:0000269\|Ref.8, ECO:0007744\|PubMed:19369195, ECO:0007744\|PubMed:19413330, ECO:0007744\|PubMed:20068231, ECO:0007744\|PubMed:21406692, ECO:0007744\|PubMed:22223895, ECO:0007744\|PubMed:22814378

Chain	Residue	Details
A	ALA2
X	ALA2

site_id	SWS_FT_FI4
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:P60842

Chain	Residue	Details
A	SER10
X	SER10

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:20068231, ECO:0007744\|PubMed:21406692, ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	SER12
X	SER12

site_id	SWS_FT_FI6
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:P60842

Chain	Residue	Details
A	LYS124
X	LYS124

site_id	SWS_FT_FI7
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:18669648, ECO:0007744\|PubMed:20068231, ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	THR163
X	THR163

site_id	SWS_FT_FI8
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:P60843

Chain	Residue	Details
A	LYS198
X	LYS198

site_id	SWS_FT_FI9
Number of Residues	4
Details	MOD_RES: N6-acetyllysine => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
X	LYS296
X	LYS321
A	LYS296
A	LYS321

site_id	SWS_FT_FI10
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744\|PubMed:25218447, ECO:0007744\|PubMed:25755297, ECO:0007744\|PubMed:25772364, ECO:0007744\|PubMed:28112733

Chain	Residue	Details
A	LYS19
X	LYS19

site_id	SWS_FT_FI11
Number of Residues	6
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744\|PubMed:28112733

Chain	Residue	Details
X	LYS314
X	LYS382
A	LYS314
A	LYS382

site_id	SWS_FT_FI12
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0000250\|UniProtKB:P60842

Chain	Residue	Details
X	LYS152
X	LYS374
A	LYS152
A	LYS374

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)