7AM2 | pdb_00007am2

Intermediate assembly of the Large subunit from Leishmania major mitochondrial ribosome


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
HB [auth CC]SCOP2B SuperfamilyACP-like 8074650 3001805 SCOP2B (2022-06-29)
BB [auth Bl]SCOP2B SuperfamilyCyclophilin-like 8103168 3000168 SCOP2B (2022-06-29)
TA [auth BH]SCOP2B SuperfamilyCyclophilin-like 8103170 3000168 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
MB [auth BV]MnmE_helical_2nde7am2BV1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: MnmE_helical_2ndECOD (1.6)
KB [auth BU]KH_dom-likee7am2BU2 A: a+b two layersX: Alpha-lytic protease prodomain-likeH: Probable GTPase Der, C-terminal domain (From Topology)T: Probable GTPase Der, C-terminal domainF: KH_dom-likeECOD (1.6)
KB [auth BU]MnmE_helical_2nde7am2BU3 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: MnmE_helical_2ndECOD (1.6)
JB [auth BT]MnmE_helical_2nde7am2BT1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: MnmE_helical_2ndECOD (1.6)
IB [auth CD]F_UNCLASSIFIEDe7am2CD1 A: alpha bundlesX: LYR protein (From Topology)H: LYR protein (From Topology)T: LYR proteinF: F_UNCLASSIFIEDECOD (1.6)
HB [auth CC]PP-bindinge7am2CC1 A: alpha bundlesX: ACP-likeH: Acyl-carrier protein (ACP) (From Topology)T: Acyl-carrier protein (ACP)F: PP-bindingECOD (1.6)
GB [auth BZ]F_UNCLASSIFIEDe7am2BZ2 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Alpha-L RNA-binding motifF: F_UNCLASSIFIEDECOD (1.6)
GB [auth BZ]PseudoU_synth_2e7am2BZ1 A: a+b two layersX: Alpha-beta plaitsH: Pseudouridine synthase (From Topology)T: Pseudouridine synthaseF: PseudoU_synth_2ECOD (1.6)
FB [auth BX]SpoU_sub_bind_1e7am2BX2 A: a+b three layersX: Bacillus chorismate mutase-likeH: L30e-like (From Topology)T: L30e-likeF: SpoU_sub_bind_1ECOD (1.6)
FB [auth BX]SpoU_methylasee7am2BX1 A: a/b three-layered sandwichesX: alpha/beta knot (From Topology)H: alpha/beta knot (From Topology)T: alpha/beta knotF: SpoU_methylaseECOD (1.6)
EB [auth BY]SpoU_sub_bind_1e7am2BY2 A: a+b three layersX: Bacillus chorismate mutase-likeH: L30e-like (From Topology)T: L30e-likeF: SpoU_sub_bind_1ECOD (1.6)
EB [auth BY]SpoU_methylasee7am2BY1 A: a/b three-layered sandwichesX: alpha/beta knot (From Topology)H: alpha/beta knot (From Topology)T: alpha/beta knotF: SpoU_methylaseECOD (1.6)
BB [auth Bl]Pro_isomerasee7am2Bl1 A: beta barrelsX: Cyclophilin-like (From Topology)H: Cyclophilin-like (From Topology)T: Cyclophilin-likeF: Pro_isomeraseECOD (1.6)
E [auth F]Ribosomal_L13e7am2F1 A: a/b three-layered sandwichesX: Ribosomal protein L13/L15p/L18e/L32eH: Ribosomal protein L13 and L16-A (From Topology)T: Ribosomal protein L13 and L16-AF: Ribosomal_L13ECOD (1.6)
TA [auth BH]Pro_isomerasee7am2BH1 A: beta barrelsX: Cyclophilin-like (From Topology)H: Cyclophilin-like (From Topology)T: Cyclophilin-likeF: Pro_isomeraseECOD (1.6)
RA [auth Ad]Img2e7am2Ad1 A: a+b two layersX: Glucose permease domain IIB-likeH: eIF1-like (From Topology)T: eIF1-likeF: Img2ECOD (1.6)
QA [auth BG]F_UNCLASSIFIEDe7am2BG1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: F_UNCLASSIFIEDECOD (1.6)
OA [auth Am]PPR_longe7am2Am1 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: PPR_longECOD (1.6)
CA [auth BO]Ribosomal_L14e7am2BO1 A: beta barrelsX: Ribosomal protein L14-likeH: Ribosomal protein L14-related (From Topology)T: Ribosomal protein L14-relatedF: Ribosomal_L14ECOD (1.6)
X [auth CB]RsfSe7am2CB1 A: a+b three layersX: Nucleotidyltransferase-likeH: Nucleotidyltransferase (From Topology)T: NucleotidyltransferaseF: RsfSECOD (1.6)
T [auth BA]F_UNCLASSIFIEDe7am2BA1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Flavoproteins/Phosphotyrosine protein phosphatases-likeT: Rhodanese/Cell cycle control phosphataseF: F_UNCLASSIFIEDECOD (1.6)
Q [auth T]F_UNCLASSIFIEDe7am2T1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: F_UNCLASSIFIEDECOD (1.6)
N [auth Q]Ribosomal_L28_1,Methyltransf_5_2nde7am2Q1 A: few secondary structure elementsX: Ribosomal protein bL28-related (From Homology)H: Ribosomal protein bL28-relatedT: Mitoribosomal protein bL28mF: Ribosomal_L28_1,Methyltransf_5_2ndECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
G [auth I]PF01196Ribosomal protein L17 (Ribosomal_L17)Ribosomal protein L17- Family
MB [auth BV]PF0192650S ribosome-binding GTPase (MMR_HSR1)50S ribosome-binding GTPase- Family
LB [auth BW]PF00270DEAD/DEAH box helicase (DEAD)DEAD/DEAH box helicaseMembers of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ...Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Domain
KB [auth BU]PF14714KH-domain-like of EngA bacterial GTPase enzymes, C-terminal (KH_dom-like)KH-domain-like of EngA bacterial GTPase enzymes, C-terminalThe KH-like domain at the C-terminus of the EngA subfamily of essential bacterial GTPases has a unique domain structure position. The two adjacent GTPase domains (GD1 and GD2), two domains of family MMR_HSR1, Pfam:PF01926, pack at either side of the ...The KH-like domain at the C-terminus of the EngA subfamily of essential bacterial GTPases has a unique domain structure position. The two adjacent GTPase domains (GD1 and GD2), two domains of family MMR_HSR1, Pfam:PF01926, pack at either side of the C-terminal domain. This C-terminal domain resembles a KH domain but is missing the distinctive RNA recognition elements. Conserved motifs of the nucleotide binding site of GD1 are integral parts of the GD1-KH domain interface, suggesting the interactions between these two domains are directly influenced by the GTP/GDP cycling of the protein. In contrast, the GD2-KH domain interface is distal to the GDP binding site of GD2. This family has not been added to the KH clan since SCOP classifies it separately due to its missing the key KH motif/fold.
Domain
KB [auth BU]PF0192650S ribosome-binding GTPase (MMR_HSR1)50S ribosome-binding GTPase- Family
JB [auth BT]PF0192650S ribosome-binding GTPase (MMR_HSR1)50S ribosome-binding GTPase- Family
F [auth G]PF00828Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A (Ribosomal_L27A)Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27AThis family includes higher eukaryotic ribosomal 60S L27A, archaeal 50S L18e, prokaryotic 50S L15, fungal mitochondrial L10, plant L27A, mitochondrial L15 and chloroplast L18-3 proteins. Domain
HB [auth CC]PF00550Phosphopantetheine attachment site (PP-binding)Phosphopantetheine attachment siteA 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes memb ...A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Swiss:P19828 has the attachment serine replaced by an alanine.
Domain
GB [auth BZ]PF00849RNA pseudouridylate synthase (PseudoU_synth_2)RNA pseudouridylate synthase- Family
EB [auth BY],
FB [auth BX]
PF00588SpoU rRNA Methylase family (SpoU_methylase)SpoU rRNA Methylase family- Family
E [auth F]PF00572Ribosomal protein L13 (Ribosomal_L13)Ribosomal protein L13- Family
TA [auth BH]PF00160Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD (Pro_isomerase)Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLDThe peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond pr ...The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilised in the cis conformation. Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA). Other roles for cyclophilins may include chaperone and cell signalling function [1].
Domain
D [auth E]PF03946Ribosomal protein L11, N-terminal domain (Ribosomal_L11_N)Ribosomal protein L11, N-terminal domainThe N-terminal domain of Ribosomal protein L11 adopts an alpha/beta fold and is followed by the RNA binding C-terminal domain. Domain
D [auth E]PF00298Ribosomal protein L11, RNA binding domain (Ribosomal_L11)Ribosomal protein L11, RNA binding domainDomain
PF01281Ribosomal protein L9, N-terminal domain (Ribosomal_L9_N)Ribosomal protein L9, N-terminal domainDomain
CA [auth BO]PF00238Ribosomal protein L14p/L23e (Ribosomal_L14)Ribosomal protein L14p/L23eDomain
X [auth CB]PF02410Ribosomal silencing factor during starvation (RsfS)Ribosomal silencing factor during starvation- Family
PF00573Ribosomal protein L4/L1 family (Ribosomal_L4)Ribosomal protein L4/L1 family- Family
O [auth R]PF06984Mitochondrial 39-S ribosomal protein L47 (MRP-L47) (MRP-L47)Mitochondrial 39-S ribosomal protein L47 (MRP-L47)- Family
K [auth M]PF00237Ribosomal protein L22p/L17e (Ribosomal_L22)Ribosomal protein L22p/L17eThis family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. Domain
J [auth L]PF00829Ribosomal prokaryotic L21 protein (Ribosomal_L21p)Ribosomal prokaryotic L21 protein- Family
PF00297Ribosomal protein L3 (Ribosomal_L3)Ribosomal protein L3- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
I [auth K]bL20m
H [auth J]bL19m- -
ZB [auth U8]U8---
YB [auth R5]R5---
XB [auth R2]R2---
WB [auth R1]R1---
VB [auth 1]Ribosomal RNA---
UB [auth U2]U2---
TB [auth BR]mL78- - -
SB [auth U5]U5---
G [auth I]Putative 50S ribosomal protein L17
RB [auth U4]U4---
QB [auth U3]U3---
PB [auth U1]U1---
OB [auth U6]U6---
NB [auth U7]mL78---
MB [auth BV]G domain-containing protein - -
LB [auth BW]DEAD/DEAH box helicase-like protein -
KB [auth BU]GTPase Der
JB [auth BT]G domain-containing protein -
IB [auth CD]L0R8F8- - -
F [auth G]Ribosomal_L18e/L15P domain-containing protein
HB [auth CC]Acyl carrier protein
GB [auth BZ]Pseudouridylate synthase-like protein -
EB [auth BY],
FB [auth BX]
SpoU_methylase domain-containing protein -
DB [auth BS]DNAj-like protein -
CB [auth Ax]LIM zinc-binding domain-containing protein - -
BB [auth Bl]Peptidyl-prolyl cis-trans isomerase
AB [auth Ag]mL59/64- - -
ZA [auth BM]mL70- -
YA [auth Av]mL88- - -
XA [auth BF]mL99- - -
E [auth F]50S ribosomal protein L13-like protein
WA [auth An]mL76- - -
VA [auth Ar]mL84- - -
UA [auth Aj]mL72- - -
TA [auth BH]Peptidyl-prolyl cis-trans isomerase
SA [auth Aw]mL89- - -
RA [auth Ad]mL49- - -
QA [auth BG]mL100- - -
PA [auth As]mL85- - -
OA [auth Am]mL75 -
NA [auth Az]mL93- - -
D [auth E]Putative ribosomal protein L11
MA [auth BP]mL52,mL52- - -
LA [auth Aa]mL42- - -
KA [auth Ab]L51_S25_CI-B8 domain-containing protein
JA [auth Al]mL74- - -
IA [auth Ap]mL80- - -
HA [auth Ah]mL68- - -
GA [auth Af]mL63- - -
FA [auth Ae]mL53- - -
EA [auth Au]mL87- - -
DA [auth At]mL86- -
RIBOSOMAL_L9 domain-containing protein- -
CA [auth BO]Putative ribosomal protein L14
BA [auth BE]mL98- -
AA [auth BN]mL81- - -
Z [auth BQ]mL71- - -
Y [auth BK]mL67- - -
X [auth CB]RNA uridylyltransferase -
W [auth BB]mL95- - -
V [auth UA]UA---
U [auth CA]TRUD domain-containing protein
T [auth BA]mL94- - -
uL4m
S [auth Z]mL41- - -
R [auth V]bL35m- - -
Q [auth T]bL32m- -
P [auth S]uL30m- -
O [auth R]uL29m
N [auth Q]bL28m -
M [auth O]uL24m
L [auth N]uL23m
K [auth M]uL22m
J [auth L]bL21m
Ribosomal protein L3-like protein

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
I [auth K]IPR035566Ribosomal protein bL20, C-terminalHomologous Superfamily
I [auth K]IPR005813Large ribosomal subunit protein bL20Family
G [auth I]IPR036373Large ribosomal subunit protein bL17 superfamilyHomologous Superfamily
G [auth I]IPR000456Large ribosomal subunit protein bL17Family
MB [auth BV]IPR030393EngB-type guanine nucleotide-binding (G) domainDomain
MB [auth BV]IPR006073GTP binding domainDomain
MB [auth BV]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
LB [auth BW]IPR001650Helicase, C-terminal domain-likeDomain
LB [auth BW]IPR050079DEAD box RNA helicaseFamily
LB [auth BW]IPR014001Helicase superfamily 1/2, ATP-binding domainDomain
LB [auth BW]IPR014014RNA helicase, DEAD-box type, Q motifDomain
LB [auth BW]IPR011545DEAD/DEAH-box helicase domainDomain
LB [auth BW]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
KB [auth BU]IPR005225Small GTP-binding domainDomain
KB [auth BU]IPR015946K homology domain-like, alpha/betaHomologous Superfamily
KB [auth BU]IPR016484GTPase DerFamily
KB [auth BU]IPR032859GTPase Der, C-terminal KH-domain-likeDomain
KB [auth BU]IPR006073GTP binding domainDomain
KB [auth BU]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
JB [auth BT]IPR006073GTP binding domainDomain
JB [auth BT]IPR023179GTP-binding protein, orthogonal bundle domain superfamilyHomologous Superfamily
JB [auth BT]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
F [auth G]IPR021131Large ribosomal subunit protein uL15/eL18Domain
F [auth G]IPR036227Large ribosomal subunit protein uL15/eL18 superfamilyHomologous Superfamily
F [auth G]IPR005749Large ribosomal subunit protein uL15, bacteriaFamily
HB [auth CC]IPR006162Phosphopantetheine attachment sitePTM
HB [auth CC]IPR009081Phosphopantetheine binding ACP domainDomain
HB [auth CC]IPR036736ACP-like superfamilyHomologous Superfamily
HB [auth CC]IPR003231Acyl carrier proteinFamily
GB [auth BZ]IPR020103Pseudouridine synthase, catalytic domain superfamilyHomologous Superfamily
GB [auth BZ]IPR050188RluA Pseudouridine SynthaseFamily
GB [auth BZ]IPR006145Pseudouridine synthase, RsuA/RluA-likeDomain
EB [auth BY],
FB [auth BX]
IPR001537tRNA/rRNA methyltransferase, SpoU typeDomain
EB [auth BY],
FB [auth BX]
IPR029026tRNA (guanine-N1-)-methyltransferase, N-terminalHomologous Superfamily
EB [auth BY],
FB [auth BX]
IPR051259Ribosomal RNA MethyltransferaseFamily
EB [auth BY],
FB [auth BX]
IPR029028Alpha/beta knot methyltransferasesHomologous Superfamily
EB [auth BY],
FB [auth BX]
IPR029064Ribosomal protein eL30-like superfamilyHomologous Superfamily
DB [auth BS]IPR053232Chloroplastic DnaJ C/III subfamily chaperoneFamily
DB [auth BS]IPR001623DnaJ domainDomain
DB [auth BS]IPR036869Chaperone J-domain superfamilyHomologous Superfamily
CB [auth Ax]IPR001781Zinc finger, LIM-typeDomain
BB [auth Bl]IPR029000Cyclophilin-like domain superfamilyHomologous Superfamily
BB [auth Bl]IPR002130Cyclophilin-type peptidyl-prolyl cis-trans isomerase domainDomain
E [auth F]IPR005822Large ribosomal subunit protein uL13Family
E [auth F]IPR036899Large ribosomal subunit protein uL13 superfamilyHomologous Superfamily
UA [auth Aj]IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
TA [auth BH]IPR029000Cyclophilin-like domain superfamilyHomologous Superfamily
TA [auth BH]IPR002130Cyclophilin-type peptidyl-prolyl cis-trans isomerase domainDomain
TA [auth BH]IPR020892Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved siteConserved Site
OA [auth Am]IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
OA [auth Am]IPR002885Pentatricopeptide repeatRepeat
D [auth E]IPR020783Large ribosomal subunit protein uL11, C-terminalDomain
D [auth E]IPR000911Ribosomal protein uL11Family
D [auth E]IPR036769Large ribosomal subunit protein uL11, C-terminal domain superfamilyHomologous Superfamily
D [auth E]IPR020784Large ribosomal subunit protein uL11, N-terminalDomain
D [auth E]IPR036796Large ribosomal subunit protein uL11, N-terminal domain superfamilyHomologous Superfamily
KA [auth Ab]IPR007741Ribosomal protein/NADH dehydrogenase domainDomain
KA [auth Ab]IPR036249Thioredoxin-like superfamilyHomologous Superfamily
KA [auth Ab]IPR039927Large ribosomal subunit protein mL43Family
IPR020070Large ribosomal subunit protein bL9, N-terminalDomain
CA [auth BO]IPR036853Large ribosomal subunit protein uL14 superfamilyHomologous Superfamily
CA [auth BO]IPR000218Large ribosomal subunit protein uL14Family
Z [auth BQ]IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
X [auth CB]IPR043519Nucleotidyltransferase superfamilyHomologous Superfamily
X [auth CB]IPR004394Protein Iojap/ribosomal silencing factor RsfSFamily
U [auth CA]IPR020103Pseudouridine synthase, catalytic domain superfamilyHomologous Superfamily
U [auth CA]IPR042214Pseudouridine synthase, TruD, catalytic domainHomologous Superfamily
U [auth CA]IPR001656Pseudouridine synthase, TruDFamily
U [auth CA]IPR011760Pseudouridine synthase, TruD, insertion domainDomain
IPR013005Large ribosomal subunit protein uL4-likeFamily
IPR002136Large ribosomal subunit protein uL4Family
IPR023574Large ribosomal subunit protein uL4 domain superfamilyHomologous Superfamily
P [auth S]IPR036919Large ribosomal subunit protein uL30, ferredoxin-like fold domain superfamilyHomologous Superfamily
O [auth R]IPR038340MRP-L47 superfamily, mitochondrialHomologous Superfamily
O [auth R]IPR010729Large ribosomal subunit protein uL29m, mitochondrialFamily
N [auth Q]IPR026569Large ribosomal subunit protein bL28Family
M [auth O]IPR003256Large ribosomal subunit protein uL24Family
M [auth O]IPR041988Large ribosomal subunit protein uL24, KOW domainDomain
M [auth O]IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
M [auth O]IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
M [auth O]IPR005825Large ribosomal subunit protein uL24, conserved siteConserved Site
L [auth N]IPR012678Ribosomal protein uL23/eL15/eS24 core domain superfamilyHomologous Superfamily
L [auth N]IPR012677Nucleotide-binding alpha-beta plait domain superfamilyHomologous Superfamily
L [auth N]IPR013025Large ribosomal subunit protein uL23-likeFamily
K [auth M]IPR036394Ribosomal protein uL22 superfamilyHomologous Superfamily
K [auth M]IPR001063Large ribosomal subunit protein uL22Family
K [auth M]IPR047867Large ribosomal subunit protein uL22, bacteria/organellaFamily
J [auth L]IPR028909Large ribosomal subunit protein bL21-likeFamily
J [auth L]IPR001787Large ribosomal subunit protein bL21Family
J [auth L]IPR036164Large ribosomal subunit protein bL21-like superfamilyHomologous Superfamily
IPR019927Large ribosomal subunit protein uL3, bacteria/organellaFamily
IPR009000Translation protein, beta-barrel domain superfamilyHomologous Superfamily
IPR000597Large ribosomal subunit protein uL3Family