3EX7

The crystal structure of EJC in its transition state

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000184	biological_process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
A	0000381	biological_process	regulation of alternative mRNA splicing, via spliceosome
A	0000398	biological_process	mRNA splicing, via spliceosome
A	0003723	molecular_function	RNA binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005681	cellular_component	spliceosomal complex
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006397	biological_process	mRNA processing
A	0006406	biological_process	mRNA export from nucleus
A	0006417	biological_process	regulation of translation
A	0008380	biological_process	RNA splicing
A	0016607	cellular_component	nuclear speck
A	0035145	cellular_component	exon-exon junction complex
A	0050684	biological_process	regulation of mRNA processing
A	0051028	biological_process	mRNA transport
A	0071013	cellular_component	catalytic step 2 spliceosome
A	1990501	cellular_component	exon-exon junction subcomplex mago-y14
A	2000622	biological_process	regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
B	0003676	molecular_function	nucleic acid binding
B	0003723	molecular_function	RNA binding
B	0003729	molecular_function	mRNA binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0006396	biological_process	RNA processing
C	0000166	molecular_function	nucleotide binding
C	0000184	biological_process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
C	0000398	biological_process	mRNA splicing, via spliceosome
C	0003676	molecular_function	nucleic acid binding
C	0003723	molecular_function	RNA binding
C	0003724	molecular_function	RNA helicase activity
C	0003729	molecular_function	mRNA binding
C	0004386	molecular_function	helicase activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005681	cellular_component	spliceosomal complex
C	0005730	cellular_component	nucleolus
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006364	biological_process	rRNA processing
C	0006397	biological_process	mRNA processing
C	0006406	biological_process	mRNA export from nucleus
C	0006417	biological_process	regulation of translation
C	0008143	molecular_function	poly(A) binding
C	0008306	biological_process	associative learning
C	0008380	biological_process	RNA splicing
C	0010629	biological_process	negative regulation of gene expression
C	0016020	cellular_component	membrane
C	0016607	cellular_component	nuclear speck
C	0016787	molecular_function	hydrolase activity
C	0016887	molecular_function	ATP hydrolysis activity
C	0017148	biological_process	negative regulation of translation
C	0030425	cellular_component	dendrite
C	0035145	cellular_component	exon-exon junction complex
C	0035368	molecular_function	selenocysteine insertion sequence binding
C	0035613	molecular_function	RNA stem-loop binding
C	0035640	biological_process	exploration behavior
C	0043021	molecular_function	ribonucleoprotein complex binding
C	0043025	cellular_component	neuronal cell body
C	0045727	biological_process	positive regulation of translation
C	0048701	biological_process	embryonic cranial skeleton morphogenesis
C	0051028	biological_process	mRNA transport
C	0071006	cellular_component	U2-type catalytic step 1 spliceosome
C	0071013	cellular_component	catalytic step 2 spliceosome
C	0072715	biological_process	cellular response to selenite ion
C	0090394	biological_process	negative regulation of excitatory postsynaptic potential
C	0098794	cellular_component	postsynapse
C	0098978	cellular_component	glutamatergic synapse
C	0099578	biological_process	regulation of translation at postsynapse, modulating synaptic transmission
C	1904570	biological_process	negative regulation of selenocysteine incorporation
C	1990416	biological_process	cellular response to brain-derived neurotrophic factor stimulus
C	1990904	cellular_component	ribonucleoprotein complex
C	2000622	biological_process	regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
D	0003723	molecular_function	RNA binding
D	0003729	molecular_function	mRNA binding
D	0006397	biological_process	mRNA processing
D	0035145	cellular_component	exon-exon junction complex
E	0000184	biological_process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
E	0000381	biological_process	regulation of alternative mRNA splicing, via spliceosome
E	0000398	biological_process	mRNA splicing, via spliceosome
E	0003723	molecular_function	RNA binding
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005681	cellular_component	spliceosomal complex
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006397	biological_process	mRNA processing
E	0006406	biological_process	mRNA export from nucleus
E	0006417	biological_process	regulation of translation
E	0008380	biological_process	RNA splicing
E	0016607	cellular_component	nuclear speck
E	0035145	cellular_component	exon-exon junction complex
E	0050684	biological_process	regulation of mRNA processing
E	0051028	biological_process	mRNA transport
E	0071013	cellular_component	catalytic step 2 spliceosome
E	1990501	cellular_component	exon-exon junction subcomplex mago-y14
E	2000622	biological_process	regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
G	0003676	molecular_function	nucleic acid binding
G	0003723	molecular_function	RNA binding
G	0003729	molecular_function	mRNA binding
G	0005634	cellular_component	nucleus
G	0005737	cellular_component	cytoplasm
G	0006396	biological_process	RNA processing
H	0000166	molecular_function	nucleotide binding
H	0000184	biological_process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
H	0000398	biological_process	mRNA splicing, via spliceosome
H	0003676	molecular_function	nucleic acid binding
H	0003723	molecular_function	RNA binding
H	0003724	molecular_function	RNA helicase activity
H	0003729	molecular_function	mRNA binding
H	0004386	molecular_function	helicase activity
H	0005515	molecular_function	protein binding
H	0005524	molecular_function	ATP binding
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005681	cellular_component	spliceosomal complex
H	0005730	cellular_component	nucleolus
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0006364	biological_process	rRNA processing
H	0006397	biological_process	mRNA processing
H	0006406	biological_process	mRNA export from nucleus
H	0006417	biological_process	regulation of translation
H	0008143	molecular_function	poly(A) binding
H	0008306	biological_process	associative learning
H	0008380	biological_process	RNA splicing
H	0010629	biological_process	negative regulation of gene expression
H	0016020	cellular_component	membrane
H	0016607	cellular_component	nuclear speck
H	0016787	molecular_function	hydrolase activity
H	0016887	molecular_function	ATP hydrolysis activity
H	0017148	biological_process	negative regulation of translation
H	0030425	cellular_component	dendrite
H	0035145	cellular_component	exon-exon junction complex
H	0035368	molecular_function	selenocysteine insertion sequence binding
H	0035613	molecular_function	RNA stem-loop binding
H	0035640	biological_process	exploration behavior
H	0043021	molecular_function	ribonucleoprotein complex binding
H	0043025	cellular_component	neuronal cell body
H	0045727	biological_process	positive regulation of translation
H	0048701	biological_process	embryonic cranial skeleton morphogenesis
H	0051028	biological_process	mRNA transport
H	0071006	cellular_component	U2-type catalytic step 1 spliceosome
H	0071013	cellular_component	catalytic step 2 spliceosome
H	0072715	biological_process	cellular response to selenite ion
H	0090394	biological_process	negative regulation of excitatory postsynaptic potential
H	0098794	cellular_component	postsynapse
H	0098978	cellular_component	glutamatergic synapse
H	0099578	biological_process	regulation of translation at postsynapse, modulating synaptic transmission
H	1904570	biological_process	negative regulation of selenocysteine incorporation
H	1990416	biological_process	cellular response to brain-derived neurotrophic factor stimulus
H	1990904	cellular_component	ribonucleoprotein complex
H	2000622	biological_process	regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
I	0003723	molecular_function	RNA binding
I	0003729	molecular_function	mRNA binding
I	0006397	biological_process	mRNA processing
I	0035145	cellular_component	exon-exon junction complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	21
Details	BINDING SITE FOR RESIDUE ADP C 414

Chain	Residue
C	PHE40
C	THR89
C	ALA90
C	ASP342
C	ARG370
C	TYR371
C	AF3415
C	MG416
C	HOH421
C	HOH497
C	HOH508
C	TYR56
C	HOH569
C	HOH572
C	PHE58
C	LYS60
C	GLN65
C	GLY85
C	THR86
C	GLY87
C	LYS88

---

site_id	AC2
Number of Residues	16
Details	BINDING SITE FOR RESIDUE AF3 C 415

Chain	Residue
C	SER84
C	GLY85
C	LYS88
C	GLU188
C	ALA219
C	GLY340
C	ARG367
C	ARG370
C	ADP414
C	MG416
C	HOH417
C	HOH461
C	HOH569
C	HOH570
C	HOH571
C	HOH572

---

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 416

Chain	Residue
C	THR89
C	ADP414
C	AF3415
C	HOH570
C	HOH571
C	HOH572

---

site_id	AC4
Number of Residues	18
Details	BINDING SITE FOR RESIDUE ADP H 414

Chain	Residue
H	PHE40
H	PHE58
H	LYS60
H	GLN65
H	GLY85
H	THR86
H	GLY87
H	LYS88
H	THR89
H	ALA90
H	ASP342
H	ARG370
H	TYR371
H	AF3415
H	MG416
H	HOH456
H	HOH489
H	HOH492

---

site_id	AC5
Number of Residues	15
Details	BINDING SITE FOR RESIDUE AF3 H 415

Chain	Residue
H	SER84
H	GLY85
H	LYS88
H	GLU188
H	ALA219
H	GLY340
H	ARG367
H	ARG370
H	ADP414
H	MG416
H	HOH419
H	HOH421
H	HOH489
H	HOH490
H	HOH491

---

site_id	AC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG H 416

Chain	Residue
H	THR89
H	ASP187
H	ADP414
H	AF3415
H	HOH490
H	HOH491
H	HOH492

---

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
C	VAL185-LEU193

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	156
Details	Domain: {"description":"RRM","evidences":[{"source":"PROSITE-ProRule","id":"PRU00176","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	340
Details	Domain: {"description":"Helicase ATP-binding","evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	322
Details	Domain: {"description":"Helicase C-terminal","evidences":[{"source":"PROSITE-ProRule","id":"PRU00542","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	56
Details	Motif: {"description":"Q motif"}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	6
Details	Motif: {"description":"DEAD box","evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"PubMed","id":"16923391","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16931718","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19033377","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20479275","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2HYI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2J0Q","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2J0S","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2XB2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EX7","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P60842","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P60843","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"UniProtKB","id":"P60842","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	6
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---