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 (2021-05-27)
L [auth LL]SCOP2 SuperfamilyNucleic acid-binding proteins8101687 3000135 SCOP2 (2021-05-27)
P [auth PP]SCOP2B SuperfamilyRibosomal protein S168101499 3000680 SCOP2B (2021-05-27)
S [auth SS]SCOP2 FamilyRibosomal protein S198101606 4001081 SCOP2 (2021-05-27)
S [auth SS]SCOP2 SuperfamilyRibosomal protein S198101607 3000686 SCOP2 (2021-05-27)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
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)
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)
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
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
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
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
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
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
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- -
DA [auth 44],
EA [auth 55]
Fe superoxide dismutase -
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
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
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
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