5JB3

Cryo-EM structure of a full archaeal ribosomal translation initiation complex in the P-REMOTE conformation

Functional Information from GO Data

Chain	GOid	namespace	contents
1	0001731	biological_process	formation of translation preinitiation complex
1	0002188	biological_process	translation reinitiation
1	0003743	molecular_function	translation initiation factor activity
1	0006412	biological_process	translation
1	0006413	biological_process	translational initiation
1	0006417	biological_process	regulation of translation
3	0001682	biological_process	tRNA 5'-leader removal
3	0003723	molecular_function	RNA binding
3	0003735	molecular_function	structural constituent of ribosome
3	0004526	molecular_function	ribonuclease P activity
3	0005737	cellular_component	cytoplasm
3	0005840	cellular_component	ribosome
3	0006364	biological_process	rRNA processing
3	0006412	biological_process	translation
3	0008033	biological_process	tRNA processing
3	0019843	molecular_function	rRNA binding
3	0042254	biological_process	ribosome biogenesis
3	1990904	cellular_component	ribonucleoprotein complex
6	0003723	molecular_function	RNA binding
6	0003743	molecular_function	translation initiation factor activity
6	0006412	biological_process	translation
6	0006413	biological_process	translational initiation
7	0000049	molecular_function	tRNA binding
7	0000166	molecular_function	nucleotide binding
7	0001731	biological_process	formation of translation preinitiation complex
7	0003743	molecular_function	translation initiation factor activity
7	0003746	molecular_function	translation elongation factor activity
7	0003924	molecular_function	GTPase activity
7	0005515	molecular_function	protein binding
7	0005525	molecular_function	GTP binding
7	0006412	biological_process	translation
7	0006413	biological_process	translational initiation
7	0006414	biological_process	translational elongation
7	0016787	molecular_function	hydrolase activity
7	0046872	molecular_function	metal ion binding
8	0003743	molecular_function	translation initiation factor activity
8	0006412	biological_process	translation
8	0006413	biological_process	translational initiation
9	0003676	molecular_function	nucleic acid binding
9	0003723	molecular_function	RNA binding
9	0003743	molecular_function	translation initiation factor activity
9	0005515	molecular_function	protein binding
9	0006412	biological_process	translation
9	0006413	biological_process	translational initiation
9	0043022	molecular_function	ribosome binding
A	0003735	molecular_function	structural constituent of ribosome
A	0005840	cellular_component	ribosome
A	0006412	biological_process	translation
A	1990904	cellular_component	ribonucleoprotein complex
B	0003735	molecular_function	structural constituent of ribosome
B	0005840	cellular_component	ribosome
B	0006412	biological_process	translation
B	0015935	cellular_component	small ribosomal subunit
B	1990904	cellular_component	ribonucleoprotein complex
D	0003723	molecular_function	RNA binding
D	0003735	molecular_function	structural constituent of ribosome
D	0005840	cellular_component	ribosome
D	0006412	biological_process	translation
D	0015935	cellular_component	small ribosomal subunit
D	0019843	molecular_function	rRNA binding
D	0042274	biological_process	ribosomal small subunit biogenesis
D	0043226	cellular_component	organelle
D	1990904	cellular_component	ribonucleoprotein complex
E	0003723	molecular_function	RNA binding
E	0003735	molecular_function	structural constituent of ribosome
E	0005840	cellular_component	ribosome
E	0006412	biological_process	translation
E	0019843	molecular_function	rRNA binding
E	0022627	cellular_component	cytosolic small ribosomal subunit
E	1990904	cellular_component	ribonucleoprotein complex
F	0003723	molecular_function	RNA binding
F	0003735	molecular_function	structural constituent of ribosome
F	0005840	cellular_component	ribosome
F	0006412	biological_process	translation
F	0015935	cellular_component	small ribosomal subunit
F	0019843	molecular_function	rRNA binding
F	0022627	cellular_component	cytosolic small ribosomal subunit
F	1990904	cellular_component	ribonucleoprotein complex
G	0003735	molecular_function	structural constituent of ribosome
G	0005840	cellular_component	ribosome
G	0006412	biological_process	translation
G	1990904	cellular_component	ribonucleoprotein complex
H	0003723	molecular_function	RNA binding
H	0003735	molecular_function	structural constituent of ribosome
H	0005840	cellular_component	ribosome
H	0006412	biological_process	translation
H	0015935	cellular_component	small ribosomal subunit
H	0019843	molecular_function	rRNA binding
H	1990904	cellular_component	ribonucleoprotein complex
I	0003723	molecular_function	RNA binding
I	0003735	molecular_function	structural constituent of ribosome
I	0005840	cellular_component	ribosome
I	0006412	biological_process	translation
I	0019843	molecular_function	rRNA binding
I	1990904	cellular_component	ribonucleoprotein complex
J	0003735	molecular_function	structural constituent of ribosome
J	0005840	cellular_component	ribosome
J	0006412	biological_process	translation
J	1990904	cellular_component	ribonucleoprotein complex
K	0000462	biological_process	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
K	0003723	molecular_function	RNA binding
K	0003735	molecular_function	structural constituent of ribosome
K	0005840	cellular_component	ribosome
K	0006412	biological_process	translation
K	0015935	cellular_component	small ribosomal subunit
K	0022627	cellular_component	cytosolic small ribosomal subunit
K	1990904	cellular_component	ribonucleoprotein complex
L	0000049	molecular_function	tRNA binding
L	0003723	molecular_function	RNA binding
L	0003735	molecular_function	structural constituent of ribosome
L	0005840	cellular_component	ribosome
L	0006412	biological_process	translation
L	0015935	cellular_component	small ribosomal subunit
L	1990904	cellular_component	ribonucleoprotein complex
M	0003723	molecular_function	RNA binding
M	0003735	molecular_function	structural constituent of ribosome
M	0005840	cellular_component	ribosome
M	0006412	biological_process	translation
M	0019843	molecular_function	rRNA binding
M	1990904	cellular_component	ribonucleoprotein complex
N	0003723	molecular_function	RNA binding
N	0003735	molecular_function	structural constituent of ribosome
N	0005840	cellular_component	ribosome
N	0006412	biological_process	translation
N	0015935	cellular_component	small ribosomal subunit
N	0019843	molecular_function	rRNA binding
N	1990904	cellular_component	ribonucleoprotein complex
O	0003676	molecular_function	nucleic acid binding
O	0003723	molecular_function	RNA binding
O	0003735	molecular_function	structural constituent of ribosome
O	0005829	cellular_component	cytosol
O	0005840	cellular_component	ribosome
O	0006412	biological_process	translation
O	0015935	cellular_component	small ribosomal subunit
O	0019843	molecular_function	rRNA binding
O	1990904	cellular_component	ribonucleoprotein complex
P	0002181	biological_process	cytoplasmic translation
P	0003723	molecular_function	RNA binding
P	0003735	molecular_function	structural constituent of ribosome
P	0005840	cellular_component	ribosome
P	0006412	biological_process	translation
P	0008270	molecular_function	zinc ion binding
P	0015935	cellular_component	small ribosomal subunit
P	0019843	molecular_function	rRNA binding
P	0022627	cellular_component	cytosolic small ribosomal subunit
P	0046872	molecular_function	metal ion binding
P	1990904	cellular_component	ribonucleoprotein complex
Q	0003735	molecular_function	structural constituent of ribosome
Q	0005840	cellular_component	ribosome
Q	0006412	biological_process	translation
Q	0022627	cellular_component	cytosolic small ribosomal subunit
Q	0070181	molecular_function	small ribosomal subunit rRNA binding
Q	1990904	cellular_component	ribonucleoprotein complex
R	0003723	molecular_function	RNA binding
R	0003735	molecular_function	structural constituent of ribosome
R	0005840	cellular_component	ribosome
R	0006412	biological_process	translation
R	0019843	molecular_function	rRNA binding
R	0022627	cellular_component	cytosolic small ribosomal subunit
R	1990904	cellular_component	ribonucleoprotein complex
S	0003735	molecular_function	structural constituent of ribosome
S	0005829	cellular_component	cytosol
S	0005840	cellular_component	ribosome
S	0006412	biological_process	translation
S	1990904	cellular_component	ribonucleoprotein complex
T	0000028	biological_process	ribosomal small subunit assembly
T	0003723	molecular_function	RNA binding
T	0003735	molecular_function	structural constituent of ribosome
T	0005840	cellular_component	ribosome
T	0006412	biological_process	translation
T	0015935	cellular_component	small ribosomal subunit
T	0019843	molecular_function	rRNA binding
T	0022627	cellular_component	cytosolic small ribosomal subunit
T	1990904	cellular_component	ribonucleoprotein complex
U	0000028	biological_process	ribosomal small subunit assembly
U	0003723	molecular_function	RNA binding
U	0003735	molecular_function	structural constituent of ribosome
U	0005840	cellular_component	ribosome
U	0006412	biological_process	translation
U	0022627	cellular_component	cytosolic small ribosomal subunit
U	1990904	cellular_component	ribonucleoprotein complex
V	0003723	molecular_function	RNA binding
V	0003735	molecular_function	structural constituent of ribosome
V	0005840	cellular_component	ribosome
V	0006412	biological_process	translation
V	0019843	molecular_function	rRNA binding
V	1990904	cellular_component	ribonucleoprotein complex
W	0003735	molecular_function	structural constituent of ribosome
W	0005840	cellular_component	ribosome
W	0006412	biological_process	translation
W	0008270	molecular_function	zinc ion binding
W	0046872	molecular_function	metal ion binding
W	1990904	cellular_component	ribonucleoprotein complex
X	0000028	biological_process	ribosomal small subunit assembly
X	0003735	molecular_function	structural constituent of ribosome
X	0005840	cellular_component	ribosome
X	0006412	biological_process	translation
X	0022627	cellular_component	cytosolic small ribosomal subunit
X	0030490	biological_process	maturation of SSU-rRNA
X	1990904	cellular_component	ribonucleoprotein complex
Y	0003735	molecular_function	structural constituent of ribosome
Y	0005840	cellular_component	ribosome
Y	0006412	biological_process	translation
Y	0008270	molecular_function	zinc ion binding
Y	0046872	molecular_function	metal ion binding
Y	1990904	cellular_component	ribonucleoprotein complex
Z	0003676	molecular_function	nucleic acid binding
Z	0003723	molecular_function	RNA binding
Z	0003735	molecular_function	structural constituent of ribosome
Z	0005840	cellular_component	ribosome
Z	0006412	biological_process	translation
Z	0015935	cellular_component	small ribosomal subunit
Z	0019843	molecular_function	rRNA binding
Z	0022627	cellular_component	cytosolic small ribosomal subunit
Z	1990904	cellular_component	ribonucleoprotein complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	9
Details	binding site for residue MET 7 501

Chain	Residue
4	A76
7	TYR51
7	ARG219
7	ARG280
7	PHE281
7	GLY282
7	LEU294
7	VAL295
7	ALA296

---

site_id	AC2
Number of Residues	2
Details	binding site for residue MG 7 502

Chain	Residue
7	THR23
7	GNP503

---

site_id	AC3
Number of Residues	20
Details	binding site for residue GNP 7 503

Chain	Residue
7	HIS17
7	ASP19
7	HIS20
7	GLY21
7	LYS22
7	THR23
7	THR24
7	MET45
7	THR46
7	ALA94
7	GLY96
7	ASN149
7	ASP152
7	VAL153
7	SER184
7	ALA185
7	LEU186
7	MG502
8	SER122
8	PRO135

---

site_id	AC4
Number of Residues	4
Details	binding site for residue ZN 8 201

Chain	Residue
8	CYS106
8	ASP113
8	THR114
8	CYS127

---

site_id	AC5
Number of Residues	5
Details	binding site for residues 5MU 4 54 and PSU 4 55

Chain	Residue
4	G18
4	G53
4	C56
4	A57
4	A58

---

Functional Information from PROSITE/UniProt

site_id	PS00053
Number of Residues	18
Details	RIBOSOMAL_S8 Ribosomal protein S8 signature. GilIVSTSqGVMshkeAI

Chain	Residue	Details
I	GLY100-ILE117

---

site_id	PS00054
Number of Residues	23
Details	RIBOSOMAL_S11 Ribosomal protein S11 signature. IrALarA.GLkIgrveDvTPiPHD

Chain	Residue	Details
M	ILE102-ASP124

---

site_id	PS00056
Number of Residues	13
Details	RIBOSOMAL_S17 Ribosomal protein S17 signature. GDkVlIaEtRPLS

Chain	Residue	Details
R	GLY83-SER95

---

site_id	PS00323
Number of Residues	25
Details	RIBOSOMAL_S19 Ribosomal protein S19 signature. NGKefvpveIkpemIGhyLGEFapT

Chain	Residue	Details
T	ASN85-THR109

---

site_id	PS00360
Number of Residues	19
Details	RIBOSOMAL_S9 Ribosomal protein S9 signature. GGGfmGQaeAarmAiARAL

Chain	Residue	Details
K	GLY68-LEU86

---

site_id	PS00361
Number of Residues	16
Details	RIBOSOMAL_S10 Ribosomal protein S10 signature. AertGVrmsGPIpLPT

Chain	Residue	Details
L	ALA27-THR42

---

site_id	PS00362
Number of Residues	31
Details	RIBOSOMAL_S15 Ribosomal protein S15 signature. LrkHLeqhPkDlhSmrgLqlIeskirrLvkY

Chain	Residue	Details
Q	LEU105-TYR135

---

site_id	PS00527
Number of Residues	22
Details	RIBOSOMAL_S14 Ribosomal protein S14 signature. R.Cgqygpiiriqg.LMLCRhCFR

Chain	Residue	Details
P	ARG23-ARG44

---

site_id	PS00528
Number of Residues	15
Details	RIBOSOMAL_S4E Ribosomal protein S4e signature. HlKRLAaPtsWyIeR

Chain	Residue	Details
E	HIS9-ARG23

---

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

Chain	Residue	Details
V	PHE60-GLU82

---

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

Chain	Residue	Details
G	ILE63-MET74

---

site_id	PS00585
Number of Residues	33
Details	RIBOSOMAL_S5 Ribosomal protein S5 signature. GRrvrFrVlaAVGNrd.GyVGlGighgk.EVgi.AI

Chain	Residue	Details
F	GLY78-ILE110

---

site_id	PS00628
Number of Residues	20
Details	RIBOSOMAL_S19E Ribosomal protein S19e signature. PekfykaGgsIiRkALQqLE

Chain	Residue	Details
U	PRO87-GLU106

---

site_id	PS00632
Number of Residues	25
Details	RIBOSOMAL_S4 Ribosomal protein S4 signature. LErRLqtiVYKkglArTmrqARqLI

Chain	Residue	Details
D	LEU101-ILE125

---

site_id	PS00646
Number of Residues	14
Details	RIBOSOMAL_S13_1 Ribosomal protein S13 signature. RGiRHelGlpVRGQ

Chain	Residue	Details
O	ARG116-GLN129

---

site_id	PS00712
Number of Residues	16
Details	RIBOSOMAL_S17E Ribosomal protein S17e signature. VtSKkIRNrIAGYvTK

Chain	Residue	Details
S	VAL41-LYS56

---

site_id	PS00961
Number of Residues	9
Details	RIBOSOMAL_S28E Ribosomal protein S28e signature. ETEREAReI

Chain	Residue	Details
X	GLU59-ILE67

---

site_id	PS00962
Number of Residues	12
Details	RIBOSOMAL_S2_1 Ribosomal protein S2 signature 1. LdQYLAAGVHIG

Chain	Residue	Details
B	LEU9-GLY20

---

site_id	PS00963
Number of Residues	25
Details	RIBOSOMAL_S2_2 Ribosomal protein S2 signature 2. PdvLIVtDpraDhqaMrEaveiGIP

Chain	Residue	Details
B	PRO112-PRO136

---

site_id	PS01082
Number of Residues	18
Details	RIBOSOMAL_L7AE Ribosomal protein L7Ae signature. CeekeIPYiyVpSKkeLG

Chain	Residue	Details
3	CYS70-GLY87

---

site_id	PS01168
Number of Residues	33
Details	RIBOSOMAL_S27E Ribosomal protein S27e signature. KCidCgneqivFShPatkvrCliCGatLvePtG

Chain	Residue	Details
W	LYS17-GLY49

---

site_id	PS01191
Number of Residues	13
Details	RIBOSOMAL_S3AE Ribosomal protein S3Ae signature. VlNRVvEvTLkDV

Chain	Residue	Details
A	VAL43-VAL55

---

site_id	PS01193
Number of Residues	20
Details	RIBOSOMAL_S8E Ribosomal protein S8e signature. KkpSGGrivla.RkKrKrELG

Chain	Residue	Details
J	LYS10-GLY29

---

site_id	PS01262
Number of Residues	23
Details	IF1A Eukaryotic initiation factor 1A signature. AlGaGWmdvrCeDGkiRrcRIpG

Chain	Residue	Details
6	ALA31-GLY53

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	141
Details	Region: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	33
Details	Compositional bias: {"description":"Basic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	22
Details	Zinc finger: {"description":"C4-type","evidences":[{"source":"HAMAP-Rule","id":"MF_00371","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00371","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	69
Details	Domain: {"description":"KH type-2","evidences":[{"source":"HAMAP-Rule","id":"MF_01309","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	71
Details	Domain: {"description":"S4 RNA-binding","evidences":[{"source":"HAMAP-Rule","id":"MF_01306","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	62
Details	Domain: {"description":"S4 RNA-binding"}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	63
Details	Domain: {"description":"S5 DRBM","evidences":[{"source":"HAMAP-Rule","id":"MF_01307","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01364","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	21
Details	Zinc finger: {"description":"C4-type","evidences":[{"source":"HAMAP-Rule","id":"MF_00777","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00777","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	21
Details	Compositional bias: {"description":"Basic and acidic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	199
Details	Domain: {"description":"tr-type G","evidences":[{"source":"HAMAP-Rule","id":"MF_00119","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	7
Details	Region: {"description":"G1","evidences":[{"source":"HAMAP-Rule","id":"MF_00119","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	4
Details	Region: {"description":"G2","evidences":[{"source":"HAMAP-Rule","id":"MF_00119","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	3
Details	Region: {"description":"G3","evidences":[{"source":"HAMAP-Rule","id":"MF_00119","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI17
Number of Residues	3
Details	Region: {"description":"G4","evidences":[{"source":"HAMAP-Rule","id":"MF_00119","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI18
Number of Residues	2
Details	Region: {"description":"G5","evidences":[{"source":"HAMAP-Rule","id":"MF_00119","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI19
Number of Residues	10
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00119","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"25690901","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4RCY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4RD1","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI20
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00119","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"25690901","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4RD1","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI21
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00119","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"16407071","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25690901","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2AHO","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI22
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"Q8U082","evidenceCode":"ECO:0000250"},{"source":"HAMAP-Rule","id":"MF_00119","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---