6YW5

The structure of the small subunit of the mitoribosome from Neurospora crassa


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
L [auth LL]SCOP2 FamilyCold shock DNA-binding domain-like8101686 4001909 SCOP2 (2022-06-29)
L [auth LL]SCOP2 SuperfamilyNucleic acid-binding proteins8101687 3000135 SCOP2 (2022-06-29)
P [auth PP]SCOP2B SuperfamilyRibosomal protein S168101499 3000680 SCOP2B (2022-06-29)
S [auth SS]SCOP2 FamilyRibosomal protein S198101606 4001081 SCOP2 (2022-06-29)
S [auth SS]SCOP2 SuperfamilyRibosomal protein S198101607 3000686 SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
DA [auth 44]F_UNCLASSIFIEDe6yw5442 A: alpha bundlesX: Long alpha-hairpinH: Fe,Mn superoxide dismutase (SOD), N-terminal domain (From Topology)T: Fe,Mn superoxide dismutase (SOD), N-terminal domainF: F_UNCLASSIFIEDECOD (1.6)
DA [auth 44]PF02777e6yw5441 A: a+b three layersX: Fe,Mn superoxide dismutase (SOD)-C (From Topology)H: Fe,Mn superoxide dismutase (SOD)-C (From Topology)T: Fe,Mn superoxide dismutase (SOD)-CF: PF02777ECOD (1.6)
EA [auth 55]F_UNCLASSIFIEDe6yw5551 A: alpha bundlesX: Long alpha-hairpinH: Fe,Mn superoxide dismutase (SOD), N-terminal domain (From Topology)T: Fe,Mn superoxide dismutase (SOD), N-terminal domainF: F_UNCLASSIFIEDECOD (1.6)
EA [auth 55]PF02777e6yw5552 A: a+b three layersX: Fe,Mn superoxide dismutase (SOD)-C (From Topology)H: Fe,Mn superoxide dismutase (SOD)-C (From Topology)T: Fe,Mn superoxide dismutase (SOD)-CF: PF02777ECOD (1.6)
J [auth JJ]PF00338e6yw5JJ1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal protein S10 (From Topology)T: Ribosomal protein S10F: PF00338ECOD (1.6)
K [auth KK]PF00411e6yw5KK1 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: PF00411ECOD (1.6)
L [auth LL]PF00164e6yw5LL1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF00164ECOD (1.6)
M [auth MM]PF00416e6yw5MM1 A: alpha arraysX: HhH/H2THH: H2TH (From Topology)T: H2THF: PF00416ECOD (1.6)
N [auth NN]PF00253e6yw5NN1 A: few secondary structure elementsX: Glucocorticoid receptor-likeH: LIM domain-likeT: LIM domain-likeF: PF00253ECOD (1.6)
P [auth PP]PF00886e6yw5PP1 A: a+b two layersX: Ribosomal protein S16 (From Topology)H: Ribosomal protein S16 (From Topology)T: Ribosomal protein S16F: PF00886ECOD (1.6)
S [auth SS]PF00203e6yw5SS1 A: a+b two layersX: Ribosomal protein S19 (From Topology)H: Ribosomal protein S19 (From Topology)T: Ribosomal protein S19F: PF00203ECOD (1.6)
T [auth TT]PF01165e6yw5TT1 A: extended segmentsX: 30S ribosomal protein S21 (From Topology)H: 30S ribosomal protein S21 (From Topology)T: 30S ribosomal protein S21F: PF01165ECOD (1.6)
Y [auth YY]PF08293e6yw5YY1 A: extended segmentsX: Mitoribosomal protein mS33 (From Topology)H: Mitoribosomal protein mS33 (From Topology)T: Mitoribosomal protein mS33F: PF08293ECOD (1.6)
AA [auth 11]F_UNCLASSIFIEDe6yw5111 A: few secondary structure elementsX: p8-MTCP1-related (From Topology)H: p8-MTCP1-related (From Topology)T: p8-MTCP1-relatedF: F_UNCLASSIFIEDECOD (1.6)
HA [auth 88]PF16113e6yw5881 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: PF16113ECOD (1.6)
F [auth FF]PF01250e6yw5FF1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal protein S6 (From Topology)T: Ribosomal protein S6F: PF01250ECOD (1.6)
H [auth HH]F_UNCLASSIFIEDe6yw5HH1 A: a+b two layersX: R3H domain-likeH: Ribosomal protein S8, N-terminal domain (From Topology)T: Ribosomal protein S8, N-terminal domainF: F_UNCLASSIFIEDECOD (1.6)
H [auth HH]PF00410e6yw5HH2 A: a+b two layersX: Ribosomal protein S8, C-terminal domain (From Topology)H: Ribosomal protein S8, C-terminal domain (From Topology)T: Ribosomal protein S8, C-terminal domainF: PF00410ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
DA [auth 44],
EA [auth 55]
PF02777Iron/manganese superoxide dismutases, C-terminal domain (Sod_Fe_C)Iron/manganese superoxide dismutases, C-terminal domainsuperoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplas ...superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. C-terminal domain is a mixed alpha/beta fold.
Domain
A [auth AA]PF11709Mitochondrial ribosomal protein subunit (Mit_ribos_Mrp51)Mitochondrial ribosomal protein subunit- Family
J [auth JJ]PF00338Ribosomal protein S10p/S20e (Ribosomal_S10)Ribosomal protein S10p/S20eThis family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes.Domain
K [auth KK]PF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
L [auth LL]PF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
M [auth MM]PF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
N [auth NN]PF00253Ribosomal protein S14p/S29e (Ribosomal_S14)Ribosomal protein S14p/S29e- Family
O [auth OO]PF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15- Domain
P [auth PP]PF00886Ribosomal protein S16 (Ribosomal_S16)Ribosomal protein S16- Family
Q [auth QQ]PF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17- Domain
R [auth RR]PF01084Ribosomal protein S18 (Ribosomal_S18)Ribosomal protein S18- Family
S [auth SS]PF00203Ribosomal protein S19 (Ribosomal_S19)Ribosomal protein S19- Domain
B [auth BB]PF00318Ribosomal protein S2 (Ribosomal_S2)Ribosomal protein S2- Family
T [auth TT]PF01165Ribosomal protein S21 (Ribosomal_S21)Ribosomal protein S21- Family
U [auth UU]PF13741Mitochondrial ribosomal protein S25 (MRP-S25)Mitochondrial ribosomal protein S25- Family
X [auth XX]PF10236Mitochondrial ribosomal death-associated protein 3 (DAP3)Mitochondrial ribosomal death-associated protein 3- Family
Y [auth YY]PF08293Mitochondrial ribosomal subunit S27 (MRP-S33)Mitochondrial ribosomal subunit S27- Family
Z [auth ZZ]PF10213Mitochondrial ribosomal subunit protein (MRP-S28)Mitochondrial ribosomal subunit protein- Family
BA [auth 22]PF08213Mitochondrial mRNA-processing protein COX24, C-terminal (COX24_C)Mitochondrial mRNA-processing protein COX24, C-terminalThis domain of unknown function is found at the C terminal end of Mitochondrial small ribosomal subunit protein mS38, also known as Mitochondrial mRNA-processing protein COX24 in yeast which is involved in the splicing of the COX1 mRNA [1]. COX24 is ...This domain of unknown function is found at the C terminal end of Mitochondrial small ribosomal subunit protein mS38, also known as Mitochondrial mRNA-processing protein COX24 in yeast which is involved in the splicing of the COX1 mRNA [1]. COX24 is a component of the mitochondrial ribosome (mitoribosome), responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. The mitoribosomes are attached to the mitochondrial inner membrane and translation products are cotranslationally integrated into the membrane [2,3]. This domain is also found in COX24 mammalian homologue Aurora kinase A-interacting protein [4]. This entry also includes uncharacterised proteins from bacteria.
Domain
CA [auth 33]PF09597IGR protein motif (IGR)IGR protein motifThis domain is found in fungal proteins and contains a conserved IGR motif. Its function is unknown.Domain
FA [auth 66]PF12298Eukaryotic mitochondrial regulator protein (Bot1p)Eukaryotic mitochondrial regulator protein- Family
HA [auth 88]PF16113Enoyl-CoA hydratase/isomerase (ECH_2)Enoyl-CoA hydratase/isomeraseThis family contains a diverse set of enzymes including: enoyl-CoA hydratase, napthoate synthase, carnitate racemase, 3-hydroxybutyryl-CoA dehydratase and dodecanoyl-CoA delta-isomerase. This family differs from Pfam:PF00378 in the structure of it's ...This family contains a diverse set of enzymes including: enoyl-CoA hydratase, napthoate synthase, carnitate racemase, 3-hydroxybutyryl-CoA dehydratase and dodecanoyl-CoA delta-isomerase. This family differs from Pfam:PF00378 in the structure of it's C-terminus.
Domain
IA [auth 00],
JA [auth 99]
PF04568Mitochondrial ATPase inhibitor, IATP (IATP)Mitochondrial ATPase inhibitor, IATP- Family
D [auth DD]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
E [auth EE]PF03719Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)Ribosomal protein S5, C-terminal domain- Domain
E [auth EE]PF00333Ribosomal protein S5, N-terminal domain (Ribosomal_S5)Ribosomal protein S5, N-terminal domain- Domain
F [auth FF]PF01250Ribosomal protein S6 (Ribosomal_S6)Ribosomal protein S6- Domain
G [auth GG]PF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.Domain
H [auth HH]PF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8- Domain
I [auth II]PF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
DA [auth 44],
EA [auth 55]
Fe superoxide dismutase -
A [auth AA]uS2m
J [auth JJ]37S ribosomal protein S10, mitochondrial
K [auth KK]Mitochondrial ribosomal protein subunit S18
L [auth LL]Mitochondrial 30S ribosomal protein S12
M [auth MM]40S ribosomal protein S13
N [auth NN]Mitochondrial 40S ribosomal protein MRP2
O [auth OO]Ribosomal protein S15
P [auth PP]Ribosomal protein S16, mitochondrial
Q [auth QQ]Mitochondrial 37S ribosomal protein S17
R [auth RR]Mito ribosomal protein S18
S [auth SS]Mitochondrial ribosomal protein S19
B [auth BB]Mito ribosomal protein S2
T [auth TT]Mito ribosomal protein S21
U [auth UU]37S ribosomal protein S25, mitochondrial -
V [auth VV]mS26- -
W [auth WW]mS27- -
X [auth XX]Mitochondrial ribosomal protein DAP3
Y [auth YY]mS33- -
Z [auth ZZ]37S ribosomal protein S24, mitochondrial
AA [auth 11]37S ribosomal protein mrp10, mitochondrial
BA [auth 22]DUF1713 domain-containing protein- -
CA [auth 33]IGR domain-containing protein- -
C [auth CC]Ribosomal protein S5, mitochondrial- -
FA [auth 66]mS42
GA [auth 77]mS46- -
HA [auth 88]3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
IA [auth 00],
JA [auth 99]
mS47 -
KA [auth aa]16S rRNA---
LA [auth V]IF1
D [auth DD]Mito ribosomal protein S4
E [auth EE]37S ribosomal protein S5
F [auth FF]Mito ribosomal protein S6
G [auth GG]Ribosomal_S7 domain-containing protein
H [auth HH]40S ribosomal protein S8
I [auth II]uS9m

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
DA [auth 44],
EA [auth 55]
IPR036324Manganese/iron superoxide dismutase, N-terminal domain superfamilyHomologous Superfamily
DA [auth 44],
EA [auth 55]
IPR019832Manganese/iron superoxide dismutase, C-terminalDomain
DA [auth 44],
EA [auth 55]
IPR036314Manganese/iron superoxide dismutase, C-terminal domain superfamilyHomologous Superfamily
A [auth AA]IPR016712Small ribosomal subunit protein bS1m-likeFamily
J [auth JJ]IPR001848Small ribosomal subunit protein uS10Family
J [auth JJ]IPR027486Small ribosomal subunit protein uS10 domainDomain
J [auth JJ]IPR036838Small ribosomal subunit protein uS10 domain superfamilyHomologous Superfamily
K [auth KK]IPR001971Small ribosomal subunit protein uS11Family
K [auth KK]IPR036967Small ribosomal subunit protein uS11 superfamilyHomologous Superfamily
L [auth LL]IPR006032Small ribosomal subunit protein uS12Family
L [auth LL]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
L [auth LL]IPR005679Ribosomal protein uS12, bacterial-typeFamily
M [auth MM]IPR027437Small ribosomal subunit protein uS13, C-terminalHomologous Superfamily
M [auth MM]IPR001892Small ribosomal subunit protein uS13Family
M [auth MM]IPR018269Small ribosomal subunit protein uS13, conserved siteConserved Site
M [auth MM]IPR010979Small ribosomal subunit protein uS13-like, H2THHomologous Superfamily
N [auth NN]IPR001209Small ribosomal subunit protein uS14Family
O [auth OO]IPR005290Small ribosomal subunit protein uS15, bacterial-typeFamily
O [auth OO]IPR009068uS15/NS1, RNA-binding domain superfamilyHomologous Superfamily
O [auth OO]IPR000589Small ribosomal subunit protein uS15Family
P [auth PP]IPR023803Small ribosomal subunit protein bS16 domain superfamilyHomologous Superfamily
P [auth PP]IPR000307Small ribosomal subunit protein bS16Family
P [auth PP]IPR020592Small ribosomal subunit protein bS16, conserved siteConserved Site
Q [auth QQ]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
Q [auth QQ]IPR000266Small ribosomal subunit protein uS17Family
R [auth RR]IPR001648Small ribosomal subunit protein bS18Family
R [auth RR]IPR036870Small ribosomal subunit protein bS18 superfamilyHomologous Superfamily
S [auth SS]IPR002222Small ribosomal subunit protein uS19Family
S [auth SS]IPR023575Small ribosomal subunit protein uS19, superfamilyHomologous Superfamily
S [auth SS]IPR020934Small ribosomal subunit protein uS19, conserved siteConserved Site
B [auth BB]IPR005706Small ribosomal subunit protein uS2, bacteria/mitochondria/plastidFamily
B [auth BB]IPR023591Small ribosomal subunit protein uS2, flavodoxin-like domain superfamilyHomologous Superfamily
B [auth BB]IPR018130Small ribosomal subunit protein uS2, conserved siteConserved Site
B [auth BB]IPR001865Small ribosomal subunit protein uS2Family
T [auth TT]IPR001911Small ribosomal subunit protein bS21Family
U [auth UU]IPR016939Small ribosomal subunit protein mS23, fungiFamily
X [auth XX]IPR017082Small ribosomal subunit protein mS29, fungalFamily
X [auth XX]IPR019368Small ribosomal subunit protein mS29Family
Y [auth YY]IPR013219Small ribosomal subunit protein mS33Family
Z [auth ZZ]IPR017081Small ribosomal subunit protein mS35Family
Z [auth ZZ]IPR039848Small ribosomal subunit protein mS35, mitochondrialFamily
Z [auth ZZ]IPR019349Small ribosomal subunit protein mS35, mitochondrial, conserved domainDomain
AA [auth 11]IPR017264Small ribosomal subunit protein mS37, fungal-typeFamily
BA [auth 22]IPR013177Ribosomal protein mS38, C-terminalDomain
CA [auth 33]IPR013761Sterile alpha motif/pointed domain superfamilyHomologous Superfamily
CA [auth 33]IPR039603Small ribosomal subunit protein mS41Family
CA [auth 33]IPR019083IGR domainDomain
FA [auth 66]IPR021036Small ribosomal subunit protein mS45Family
HA [auth 88]IPR029045ClpP/crotonase-like domain superfamilyHomologous Superfamily
HA [auth 88]IPR032259Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H typeFamily
HA [auth 88]IPR045004Enoyl-CoA hydratase/isomerase domainDomain
HA [auth 88]IPR018376Enoyl-CoA hydratase/isomerase, conserved siteConserved Site
IA [auth 00],
JA [auth 99]
IPR007648Mitochondrial ATPase inhibitorFamily
LA [auth V]IPR034600Large ribosomal subunit protein bL31mFamily
LA [auth V]IPR048874Ribosomal protein bL31m, N-terminal domainDomain
D [auth DD]IPR018079Small ribosomal subunit protein uS4, conserved siteConserved Site
D [auth DD]IPR002942RNA-binding S4 domainDomain
D [auth DD]IPR036986RNA-binding S4 domain superfamilyHomologous Superfamily
D [auth DD]IPR022801Small ribosomal subunit protein uS4Family
E [auth EE]IPR000851Small ribosomal subunit protein uS5Family
E [auth EE]IPR005324Small ribosomal subunit protein uS5, C-terminalDomain
E [auth EE]IPR013810Small ribosomal subunit protein uS5, N-terminalDomain
E [auth EE]IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
E [auth EE]IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
F [auth FF]IPR000529Small ribosomal subunit protein bS6Family
F [auth FF]IPR035980Small ribosomal subunit protein bS6 superfamilyHomologous Superfamily
F [auth FF]IPR014717Translation elongation factor EF1B/small ribosomal subunit protein bS6Homologous Superfamily
G [auth GG]IPR047988Small ribosomal subunit protein uS7m, fungiDomain
G [auth GG]IPR000235Small ribosomal subunit protein uS7Family
G [auth GG]IPR036823Small ribosomal subunit protein uS7 domain superfamilyHomologous Superfamily
G [auth GG]IPR023798Small ribosomal subunit protein uS7 domainDomain
H [auth HH]IPR000630Small ribosomal subunit protein uS8Family
H [auth HH]IPR035987Small ribosomal subunit protein uS8 superfamilyHomologous Superfamily
I [auth II]IPR020574Small ribosomal subunit protein uS9, conserved siteConserved Site
I [auth II]IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
I [auth II]IPR000754Small ribosomal subunit protein uS9Family
I [auth II]IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily