3J16

Models of ribosome-bound Dom34p and Rli1p and their ribosomal binding partners

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004521	molecular_function	RNA endonuclease activity
A	0005515	molecular_function	protein binding
A	0005737	cellular_component	cytoplasm
A	0006412	biological_process	translation
A	0006417	biological_process	regulation of translation
A	0016070	biological_process	RNA metabolic process
A	0032790	biological_process	ribosome disassembly
A	0043022	molecular_function	ribosome binding
A	0045727	biological_process	positive regulation of translation
A	0045948	biological_process	positive regulation of translational initiation
A	0046872	molecular_function	metal ion binding
A	0051301	biological_process	cell division
A	0051321	biological_process	meiotic cell cycle
A	0070481	biological_process	nuclear-transcribed mRNA catabolic process, non-stop decay
A	0070651	biological_process	nonfunctional rRNA decay
A	0070966	biological_process	nuclear-transcribed mRNA catabolic process, no-go decay
A	0071025	biological_process	RNA surveillance
A	0072344	biological_process	rescue of stalled ribosome
A	1990533	cellular_component	Dom34-Hbs1 complex
B	0000054	biological_process	ribosomal subunit export from nucleus
B	0000166	molecular_function	nucleotide binding
B	0003743	molecular_function	translation initiation factor activity
B	0005506	molecular_function	iron ion binding
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0005852	cellular_component	eukaryotic translation initiation factor 3 complex
B	0006364	biological_process	rRNA processing
B	0006412	biological_process	translation
B	0006413	biological_process	translational initiation
B	0006415	biological_process	translational termination
B	0016887	molecular_function	ATP hydrolysis activity
B	0032790	biological_process	ribosome disassembly
B	0042254	biological_process	ribosome biogenesis
B	0042273	biological_process	ribosomal large subunit biogenesis
B	0043024	molecular_function	ribosomal small subunit binding
B	0045727	biological_process	positive regulation of translation
B	0060255	biological_process	regulation of macromolecule metabolic process
C	0000462	biological_process	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
C	0003735	molecular_function	structural constituent of ribosome
C	0005654	cellular_component	nucleoplasm
C	0005730	cellular_component	nucleolus
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0005840	cellular_component	ribosome
C	0006364	biological_process	rRNA processing
C	0006412	biological_process	translation
C	0022627	cellular_component	cytosolic small ribosomal subunit
C	0030686	cellular_component	90S preribosome
C	0032040	cellular_component	small-subunit processome
C	0042254	biological_process	ribosome biogenesis
C	1990904	cellular_component	ribonucleoprotein complex
D	0000462	biological_process	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
D	0002181	biological_process	cytoplasmic translation
D	0003735	molecular_function	structural constituent of ribosome
D	0005737	cellular_component	cytoplasm
D	0005739	cellular_component	mitochondrion
D	0005829	cellular_component	cytosol
D	0005840	cellular_component	ribosome
D	0006412	biological_process	translation
D	0022627	cellular_component	cytosolic small ribosomal subunit
D	1990904	cellular_component	ribonucleoprotein complex
E	0002181	biological_process	cytoplasmic translation
E	0003735	molecular_function	structural constituent of ribosome
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0005840	cellular_component	ribosome
E	0006412	biological_process	translation
E	0006451	biological_process	translational readthrough
E	0010494	cellular_component	cytoplasmic stress granule
E	0022627	cellular_component	cytosolic small ribosomal subunit
E	1990904	cellular_component	ribonucleoprotein complex
F	0002181	biological_process	cytoplasmic translation
F	0003735	molecular_function	structural constituent of ribosome
F	0005515	molecular_function	protein binding
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0005840	cellular_component	ribosome
F	0006412	biological_process	translation
F	0019843	molecular_function	rRNA binding
F	0022625	cellular_component	cytosolic large ribosomal subunit
F	1990904	cellular_component	ribonucleoprotein complex
G	0000027	biological_process	ribosomal large subunit assembly
G	0002181	biological_process	cytoplasmic translation
G	0003735	molecular_function	structural constituent of ribosome
G	0005515	molecular_function	protein binding
G	0005737	cellular_component	cytoplasm
G	0005840	cellular_component	ribosome
G	0022625	cellular_component	cytosolic large ribosomal subunit
G	0030686	cellular_component	90S preribosome
G	0042254	biological_process	ribosome biogenesis
G	0070180	molecular_function	large ribosomal subunit rRNA binding
G	1990904	cellular_component	ribonucleoprotein complex
H	0000027	biological_process	ribosomal large subunit assembly
H	0002181	biological_process	cytoplasmic translation
H	0003723	molecular_function	RNA binding
H	0003735	molecular_function	structural constituent of ribosome
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0005840	cellular_component	ribosome
H	0006412	biological_process	translation
H	0022625	cellular_component	cytosolic large ribosomal subunit
H	0022626	cellular_component	cytosolic ribosome
H	0034517	biological_process	ribophagy
H	0070180	molecular_function	large ribosomal subunit rRNA binding
H	1990904	cellular_component	ribonucleoprotein complex
I	0002181	biological_process	cytoplasmic translation
I	0003735	molecular_function	structural constituent of ribosome
I	0005737	cellular_component	cytoplasm
I	0005829	cellular_component	cytosol
I	0005840	cellular_component	ribosome
I	0006412	biological_process	translation
I	0022625	cellular_component	cytosolic large ribosomal subunit
I	0070180	molecular_function	large ribosomal subunit rRNA binding
I	1990904	cellular_component	ribonucleoprotein complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 701

Chain	Residue
B	LYS116
B	SER117
B	GLN171
B	GLU247
B	ATP702

---

site_id	AC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE ATP B 702

Chain	Residue
B	ILE114
B	GLY115
B	LYS116
B	SER117
B	THR118
B	SER299
B	MG701
B	HOH801
B	TYR87
B	PHE92
B	ASN112
B	GLY113

---

site_id	AC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE SF4 B 703

Chain	Residue
B	CYS29
B	PRO30
B	CYS38
B	ILE39
B	ILE50
B	CYS55
B	ILE56
B	CYS58
B	GLY59
B	ILE60
B	CYS61

---

site_id	AC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF4 B 704

Chain	Residue
B	CYS16
B	LYS17
B	PRO18
B	CYS21
B	ARG22
B	CYS25
B	CYS65
B	PRO66
B	PHE67
B	ALA69

---

Functional Information from PROSITE/UniProt

site_id	PS00049
Number of Residues	27
Details	RIBOSOMAL_L14 Ribosomal protein L14 signature. AIVVrqakswrrr.DGvflyFedNagVI

Chain	Residue	Details
I	ALA76-ILE102

---

site_id	PS00198
Number of Residues	12
Details	4FE4S_FER_1 4Fe-4S ferredoxin-type iron-sulfur binding region signature. CiGCGiCVkKCP

Chain	Residue	Details
B	CYS55-PRO66

---

site_id	PS00211
Number of Residues	15
Details	ABC_TRANSPORTER_1 ABC transporters family signature. LSGGELQRVAIVLAL

Chain	Residue	Details
B	LEU468-LEU482

---

site_id	PS00359
Number of Residues	15
Details	RIBOSOMAL_L11 Ribosomal protein L11 signature. KeIlGTaqSVGcRV.D

Chain	Residue	Details
H	LYS130-ASP144

---

site_id	PS00529
Number of Residues	23
Details	RIBOSOMAL_S24E Ribosomal protein S24e signature. FGggKSvGFGlVYNSvaeakkfE

Chain	Residue	Details
D	PHE64-GLU86

---

site_id	PS00578
Number of Residues	12
Details	RIBOSOMAL_S6E Ribosomal protein S6e signature. ISGGnDkqGfPM

Chain	Residue	Details
C	ILE52-MET63

---

site_id	PS00700
Number of Residues	22
Details	RIBOSOMAL_L6_2 Ribosomal protein L6 signature 2. QicrVrnKdiRkFlDGIYVshK

Chain	Residue	Details
F	GLN163-LYS184

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	32
Details	Domain: {"description":"4Fe-4S ferredoxin-type 1","evidences":[{"source":"PROSITE-ProRule","id":"PRU00711","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	29
Details	Domain: {"description":"4Fe-4S ferredoxin-type 2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00711","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	250
Details	Domain: {"description":"ABC transporter 1","evidences":[{"source":"PROSITE-ProRule","id":"PRU00434","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	223
Details	Domain: {"description":"ABC transporter 2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00434","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	14
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00434","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17287358","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"17287358","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	13
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22106047","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	1
Details	Modified residue: {"description":"N6,N6,N6-trimethyllysine; by RKM2","evidences":[{"source":"PubMed","id":"17005568","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	1
Details	Modified residue: {"description":"N5-methylarginine; by RMT2","evidences":[{"source":"PubMed","id":"11856739","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18957409","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	1
Details	Modified residue: {"description":"N-acetylserine","evidences":[{"source":"PubMed","id":"16096273","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22814378","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	2
Details	Modified residue: {"description":"N6,N6-dimethyllysine; by RKM1","evidences":[{"source":"PubMed","id":"17327221","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	33
Details	Region: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	21
Details	Compositional bias: {"description":"Basic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI17
Number of Residues	1
Details	Modified residue: {"description":"N-acetylserine","evidences":[{"source":"PubMed","id":"10601260","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"1544921","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22814378","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI18
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---