6AZ1

Cryo-EM structure of the small subunit of Leishmania ribosome bound to paromomycin


ChainDomainClassArchitectureTopologyHomology
3.40.50.10490 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Glucose-6-phosphate isomerase like protein
1.10.455.10 Mainly Alpha Orthogonal Bundle Ribosomal Protein S7 Ribosomal protein S7/S5
3.30.1370.30 Alpha Beta 2-Layer Sandwich Ribosomal Protein S8 Chain: A, domain 1
3.30.1490.10 Alpha Beta 2-Layer Sandwich Dna Ligase domain 1
3.30.70.600 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Ribosomal protein S10
1.10.10.10 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
3.30.420.80 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase domain 5
3.30.1330.30 Alpha Beta 2-Layer Sandwich 60s Ribosomal Protein L30 Chain: A
4.10.830.10 Few Secondary Structures Irregular 30s Ribosomal Protein S14 Chain N
1.10.287.10 Mainly Alpha Orthogonal Bundle Helix Hairpins S15/NS1, RNA-binding
1.10.60.20 Mainly Alpha Orthogonal Bundle Diphtheria Toxin Repressor domain 2
3.30.1230.20 Alpha Beta 2-Layer Sandwich Hypothetical Cytosolic Protein Chain: A
3.30.70.3370 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits
3.30.1740.20 Alpha Beta 2-Layer Sandwich first zn-finger domain of poly(adp-ribose) polymerase-1 Ribosomal protein S26
2.40.50.140 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
2.130.10.10 Mainly Beta 7 Propeller Methylamine Dehydrogenase Chain H
3.30.230.10 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5 domain 2
2.40.50.1000 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P)
1.10.10.10 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
2.20.25.100 Mainly Beta Single Sheet N-terminal domain of TfIIb Ribosomal protein S27
3.30.300.20 Alpha Beta 2-Layer Sandwich GMP Synthetase Chain A, domain 3
3.30.1140.32 Alpha Beta 2-Layer Sandwich Ribosomal protein S3 C-terminal domain Ribosomal protein S3, C-terminal domain
3.10.290.10 Alpha Beta Roll Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region Chain A
2.40.50.740 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Ribosomal protein S4, central domain
2.30.30.30 Mainly Beta Roll SH3 type barrels.
3.30.160.20 Alpha Beta 2-Layer Sandwich Double Stranded RNA Binding Domain
3.30.230.10 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5 domain 2

Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
PF01015Ribosomal S3Ae family (Ribosomal_S3Ae)Ribosomal S3Ae family- Family
PF00318Ribosomal protein S2 (Ribosomal_S2)Ribosomal protein S2- Family
PF00163Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4)Ribosomal protein S4/S9 N-terminal domain- Family
PF01479S4 domain (S4)S4 domainThe S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.
Domain
PF01092Ribosomal protein S6e (Ribosomal_S6e)Ribosomal protein S6e- Family
PF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.Domain
PF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8- Domain
PF01201Ribosomal protein S8e (Ribosomal_S8e)Ribosomal protein S8e- Family
PF00338Ribosomal protein S10p/S20e (Ribosomal_S10)Ribosomal protein S10p/S20eThis family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes.Domain
PF03501Plectin/S10 domain (S10_plectin)Plectin/S10 domainThis presumed domain is found at the N-terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding.Domain
PF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
PF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
PF01248Ribosomal protein L7Ae/L30e/S12e/Gadd45 family (Ribosomal_L7Ae)Ribosomal protein L7Ae/L30e/S12e/Gadd45 familyThis family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD11 ...This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118 [1].
Domain
PF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
PF00253Ribosomal protein S14p/S29e (Ribosomal_S14)Ribosomal protein S14p/S29e- Family
PF08069Ribosomal S13/S15 N-terminal domain (Ribosomal_S13_N)Ribosomal S13/S15 N-terminal domainThis domain is found at the N-terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [1].Domain
PF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15- Domain
PF00833Ribosomal S17 (Ribosomal_S17e)Ribosomal S17- Family
PF00203Ribosomal protein S19 (Ribosomal_S19)Ribosomal protein S19- Domain
PF01090Ribosomal protein S19e (Ribosomal_S19e)Ribosomal protein S19e- Family
PF01249Ribosomal protein S21e (Ribosomal_S21e)Ribosomal protein S21e- Family
PF01282Ribosomal protein S24e (Ribosomal_S24e)Ribosomal protein S24e- Family
PF01283Ribosomal protein S26e (Ribosomal_S26e)Ribosomal protein S26e- Family
PF01200Ribosomal protein S28e (Ribosomal_S28e)Ribosomal protein S28e- Family
PF04758Ribosomal protein S30 (Ribosomal_S30)Ribosomal protein S30- Family
PF01599Ribosomal protein S27a (Ribosomal_S27)Ribosomal protein S27aThis family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesised as a C-terminal extension of ubiquitin (CEP). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins ...This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesised as a C-terminal extension of ubiquitin (CEP). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis [3]. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [2].
Domain
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
PF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17- Domain
PF16205Ribosomal_S17 N-terminal (Ribosomal_S17_N)Ribosomal_S17 N-terminal- Family
PF03297S25 ribosomal protein (Ribosomal_S25)S25 ribosomal protein- Family
PF01667Ribosomal protein S27 (Ribosomal_S27e)Ribosomal protein S27- Family
PF07650KH domain (KH_2)KH domain- Domain
PF00189Ribosomal protein S3, C-terminal domain (Ribosomal_S3_C)Ribosomal protein S3, C-terminal domainThis family contains a central domain Pfam:PF00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer.Domain
PF00900Ribosomal family S4e (Ribosomal_S4e)Ribosomal family S4e- Family
PF1612140S ribosomal protein S4 C-terminus (40S_S4_C)40S ribosomal protein S4 C-terminus- Family
PF08071RS4NT (NUC023) domain (RS4NT)RS4NT (NUC023) domainThis is the N-terminal domain of Ribosomal S4 / S4e proteins. This domain is associated with S4 and KOW domains [1].Domain
PF01479S4 domain (S4)S4 domainThe S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.
Domain
PF03719Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)Ribosomal protein S5, C-terminal domain- Domain
PF00333Ribosomal protein S5, N-terminal domain (Ribosomal_S5)Ribosomal protein S5, N-terminal domain- Domain
PF01251Ribosomal protein S7e (Ribosomal_S7e)Ribosomal protein S7e- Family

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Ribosomal protein s1e
    ribosomal protein S2
      ribosomal protein S4
        ribosomal protein S6e
          ribosomal protein S7
            ribosomal protein S8
              ribosomal protein S8e
                ribosomal protein S10
                  ribosomal protein S10e
                      ribosomal protein S11
                        ribosomal protein S12
                          ribosomal protein S12e
                            ribosomal protein S13
                              ribosomal protein S14
                                ribosomal protein S15
                                  ribosomal protein S17e
                                    ribosomal protein S19
                                      ribosomal protein S19e
                                        ribosomal protein S21e
                                          ribosomal protein S24e
                                            ribosomal protein S26e
                                              ribosomal protein S28e
                                                ribosomal protein S30e
                                                  ribosomal protein S31e
                                                    LACK1
                                                        ribosomal RNA 18Snonenonenone
                                                        tRNA-Phenonenonenone
                                                        P-site tRNAnonenonenone
                                                        E-site tRNAnonenonenone
                                                        mRNAnonenonenone
                                                        ribosomal protein S9
                                                          ribosomal protein S17
                                                            ribosomal protein S25e
                                                                ribosomal protein S27e
                                                                  ribosomal protein S3
                                                                    ribosomal protein S4e
                                                                      ribosomal protein S5
                                                                        ribosomal protein S7e