4D5Y

Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state

External Resource: Annotation


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ARibosomal_L2_1e4d5yA1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: Ribosomal_L2_1ECOD (1.6)
ARibosomal_L2_C_2e4d5yA2 A: beta barrelsX: SH3H: SH3T: SH3F: Ribosomal_L2_C_2ECOD (1.6)
BRibosomal_L3e4d5yB1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Alanine racemase-CF: Ribosomal_L3ECOD (1.6)
CRibosomal_L4e4d5yC1 A: a/b three-layered sandwichesX: Ribosomal protein L4 (From Topology)H: Ribosomal protein L4 (From Topology)T: Ribosomal protein L4F: Ribosomal_L4ECOD (1.6)
CRibos_L4_asso_Ce4d5yC2 A: extended segmentsX: C-terminal helical region in 60S ribosomal protein L4 (L4p) (From Topology)H: C-terminal helical region in 60S ribosomal protein L4 (L4p) (From Topology)T: C-terminal helical region in 60S ribosomal protein L4 (L4p)F: Ribos_L4_asso_CECOD (1.6)
DRibosomal_L5ee4d5yD1 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: Ribosomal_L5eECOD (1.6)
ERibosomal_L6ee4d5yE1 A: beta barrelsX: SH3H: SH3T: SH3F: Ribosomal_L6eECOD (1.6)
FRibosomal_L30_1e4d5yF1 A: a+b two layersX: Ribosomal protein L30p/L7e (From Topology)H: Ribosomal protein L30p/L7e (From Topology)T: Ribosomal protein L30p/L7eF: Ribosomal_L30_1ECOD (1.6)
GRibosomal_L7Ae_1e4d5yG1 A: a+b three layersX: Bacillus chorismate mutase-likeH: L30e-like (From Topology)T: L30e-likeF: Ribosomal_L7Ae_1ECOD (1.6)
HRibosomal_L6_2e4d5yH2 A: a+b two layersX: Ribosomal protein L6 (From Topology)H: Ribosomal protein L6 (From Topology)T: Ribosomal protein L6F: Ribosomal_L6_2ECOD (1.6)
HRibosomal_L6e4d5yH1 A: a+b two layersX: Ribosomal protein L6 (From Topology)H: Ribosomal protein L6 (From Topology)T: Ribosomal protein L6F: Ribosomal_L6ECOD (1.6)
IRibosomal_L16e4d5yI1 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Ribosomal protein L10eF: Ribosomal_L16ECOD (1.6)
JRibosomal_L5_Ce4d5yJ1 A: a+b two layersX: Ribosomal protein L5 (From Topology)H: Ribosomal protein L5 (From Topology)T: Ribosomal protein L5F: Ribosomal_L5_CECOD (1.6)
K [auth L]Ribosomal_L13ee4d5yL1 A: extended segmentsX: RPL13 (From Topology)H: RPL13 (From Topology)T: RPL13F: Ribosomal_L13eECOD (1.6)
L [auth M]Ribosomal_L14ee4d5yM1 A: beta barrelsX: SH3H: SH3T: SH3F: Ribosomal_L14eECOD (1.6)
M [auth N]Ribosomal_L15ee4d5yN1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal proteins S24e, L23 and L15e (From Topology)T: Ribosomal proteins S24e, L23 and L15eF: Ribosomal_L15eECOD (1.6)
N [auth O]Ribosomal_L13e4d5yO1 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)
O [auth P]Ribosomal_L22e4d5yP1 A: a+b two layersX: Enolase-N/ribosomal proteinH: Ribosomal protein L22 (From Topology)T: Ribosomal protein L22F: Ribosomal_L22ECOD (1.6)
P [auth Q]Ribosomal_L18e4d5yQ1 A: a/b three-layered sandwichesX: Ribosomal protein L13/L15p/L18e/L32eH: Ribosomal proteins L15p and L18e (From Topology)T: Ribosomal proteins L15p and L18eF: Ribosomal_L18ECOD (1.6)
Q [auth R]Ribosomal_L19e_Ne4d5yR1 A: alpha arraysX: Ribosomal protein L19 (L19e) N-terminal domain (From Topology)H: Ribosomal protein L19 (L19e) N-terminal domain (From Topology)T: Ribosomal protein L19 (L19e) N-terminal domainF: Ribosomal_L19e_NECOD (1.6)
Q [auth R]Ribosomal_L19e_Ce4d5yR2 A: alpha bundlesX: Ribosomal protein L19 (L19e) C-terminal domain (From Topology)H: Ribosomal protein L19 (L19e) C-terminal domain (From Topology)T: Ribosomal protein L19 (L19e) C-terminal domainF: Ribosomal_L19e_CECOD (1.6)
R [auth S]Ribosomal_L18Ae4d5yS1 A: a+b two layersX: GP2-likeH: RplX-like (From Topology)T: RplX-likeF: Ribosomal_L18AECOD (1.6)
S [auth T]Ribosomal_L21ee4d5yT1 A: beta barrelsX: SH3H: SH3T: SH3F: Ribosomal_L21eECOD (1.6)
U [auth V]Ribosomal_L14e4d5yV1 A: beta barrelsX: Ribosomal protein L14-likeH: Ribosomal protein L14-related (From Topology)T: Ribosomal protein L14-relatedF: Ribosomal_L14ECOD (1.6)
V [auth W]Ribosomal_L24ee4d5yW1 A: few secondary structure elementsX: Glucocorticoid receptor-likeH: LIM domain-likeT: LIM domain-likeF: Ribosomal_L24eECOD (1.6)
W [auth X]Ribosomal_L23_3e4d5yX1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal proteins S24e, L23 and L15e (From Topology)T: Ribosomal proteins S24e, L23 and L15eF: Ribosomal_L23_3ECOD (1.6)
Y [auth Z]Ribosomal_L27ee4d5yZ1 A: beta barrelsX: SH3H: SH3T: SH3F: Ribosomal_L27eECOD (1.6)
Z [auth a]Ribosomal_L18e4d5ya1 A: a/b three-layered sandwichesX: Ribosomal protein L13/L15p/L18e/L32eH: Ribosomal proteins L15p and L18e (From Topology)T: Ribosomal proteins L15p and L18eF: Ribosomal_L18ECOD (1.6)
AA [auth b]Ribosomal_L29ee4d5yb1 A: extended segmentsX: RPL29 (From Topology)H: RPL29 (From Topology)T: RPL29F: Ribosomal_L29eECOD (1.6)
BA [auth c]Ribosomal_L7Aee4d5yc1 A: a+b three layersX: Bacillus chorismate mutase-likeH: L30e-like (From Topology)T: L30e-likeF: Ribosomal_L7AeECOD (1.6)
CA [auth d]Ribosomal_L31ee4d5yd1 A: a+b two layersX: Ribosomal protein L31e-likeH: Ribosomal protein L31e/gp120 outer domain (From Topology)T: Ribosomal protein L31e/gp120 outer domainF: Ribosomal_L31eECOD (1.6)
DA [auth e]Ribosomal_L32ee4d5ye1 A: a/b three-layered sandwichesX: Ribosomal protein L13/L15p/L18e/L32eH: Ribosomal protein L32e (From Topology)T: Ribosomal protein L32eF: Ribosomal_L32eECOD (1.6)
EA [auth f]Ribosomal_L35Aee4d5yf1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Alanine racemase-CF: Ribosomal_L35AeECOD (1.6)
GA [auth h]Ribosomal_L29_2e4d5yh1 A: alpha bundlesX: Long alpha-hairpinH: Ribosomal protein L29 (L29p) (From Topology)T: Ribosomal protein L29 (L29p)F: Ribosomal_L29_2ECOD (1.6)
HA [auth i]Ribosomal_L36ee4d5yi1 A: alpha arraysX: 60S ribosomal protein rpL36 (L36e) (From Topology)H: 60S ribosomal protein rpL36 (L36e) (From Topology)T: 60S ribosomal protein rpL36 (L36e)F: Ribosomal_L36eECOD (1.6)
JA [auth k]Ribosomal_L38ee4d5yk1 A: a+b two layersX: SRP9/14-likeH: Signal recognition particle alu RNA binding heterodimer SRP9/14-related (From Topology)T: Signal recognition particle alu RNA binding heterodimer SRP9/14-relatedF: Ribosomal_L38eECOD (1.6)
KA [auth l]Ribosomal_L39e4d5yl1 A: extended segmentsX: Ribosomal protein L39e (From Topology)H: Ribosomal protein L39e (From Topology)T: Ribosomal protein L39eF: Ribosomal_L39ECOD (1.6)
LA [auth m]Ribosomal_L40ee4d5ym1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: Ribosomal_L40eECOD (1.6)
NA [auth o]Ribosomal_L44e4d5yo1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: Ribosomal_L44ECOD (1.6)
OA [auth p]Ribosomal_L37aee4d5yp1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: Ribosomal_L37aeECOD (1.6)
QA [auth u]Ribosomal_L1_2nd_1e4d5yu2 A: a+b two layersX: a+b domain in Ribosomal protein L1 (From Topology)H: a+b domain in Ribosomal protein L1 (From Topology)T: a+b domain in Ribosomal protein L1F: Ribosomal_L1_2nd_1ECOD (1.6)
QA [auth u]Ribosomal_L1_1st_1e4d5yu1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Rossmann-like domain in Ribosomal protein L1 (From Topology)T: Rossmann-like domain in Ribosomal protein L1F: Ribosomal_L1_1st_1ECOD (1.6)
T [auth U]Ribosomal_L22ee4d5yU1 A: a+b two layersX: Ribosomal protein L22e (From Topology)H: Ribosomal protein L22e (From Topology)T: Ribosomal protein L22eF: Ribosomal_L22eECOD (1.6)
X [auth Y]Ribosomal_L26e4d5yY1 A: beta barrelsX: SH3H: SH3T: SH3F: Ribosomal_L26ECOD (1.6)
FA [auth g]Ribosomal_L34ee4d5yg1 A: few secondary structure elementsX: Glucocorticoid receptor-likeH: RPL34 (From Topology)T: RPL34F: Ribosomal_L34eECOD (1.6)
IA [auth j]Ribosomal_L37ee4d5yj1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: Ribosomal_L37eECOD (1.6)
MA [auth n]Ribosomal_L41e4d5yn1 A: extended segmentsX: Ribosomal protein L41-A (From Topology)H: Ribosomal protein L41-A (From Topology)T: Ribosomal protein L41-AF: Ribosomal_L41ECOD (1.6)
PA [auth t]Ribosomal_L28ee4d5yt1 A: a+b two layersX: RPL28 (From Topology)H: RPL28 (From Topology)T: RPL28F: Ribosomal_L28eECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF03947Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C)Ribosomal Proteins L2, C-terminal domain- Domain
PF00181Ribosomal Proteins L2, RNA binding domain (Ribosomal_L2)Ribosomal Proteins L2, RNA binding domain- Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
60S RIBOSOMAL PROTEIN UL2
60S RIBOSOMAL PROTEIN UL3---
60S RIBOSOMAL PROTEIN UL4---
60S RIBOSOMAL PROTEIN UL18---
60S RIBOSOMAL PROTEIN EL6---
60S RIBOSOMAL PROTEIN UL30---
60S RIBOSOMAL PROTEIN EL8---
60S RIBOSOMAL PROTEIN UL6---
60S RIBOSOMAL PROTEIN UL16---
60S RIBOSOMAL PROTEIN UL5---
K [auth L]60S RIBOSOMAL PROTEIN EL13---
L [auth M]60S RIBOSOMAL PROTEIN EL14---
M [auth N]60S RIBOSOMAL PROTEIN EL15---
N [auth O]60S RIBOSOMAL PROTEIN UL13---
O [auth P]60S RIBOSOMAL PROTEIN UL22---
P [auth Q]60S RIBOSOMAL PROTEIN EL18---
Q [auth R]60S RIBOSOMAL PROTEIN UL19---
R [auth S]60S RIBOSOMAL PROTEIN EL20---
S [auth T]60S RIBOSOMAL PROTEIN EL21---
U [auth V]60S RIBOSOMAL PROTEIN UL14---
V [auth W]60S RIBOSOMAL PROTEIN EL24---
W [auth X]60S RIBOSOMAL PROTEIN UL23---
Y [auth Z]60S RIBOSOMAL PROTEIN EL27---
Z [auth a]60S RIBOSOMAL PROTEIN UL15---
AA [auth b]60S RIBOSOMAL PROTEIN EL29---
BA [auth c]60S RIBOSOMAL PROTEIN EL30---
CA [auth d]60S RIBOSOMAL PROTEIN EL31---
DA [auth e]60S RIBOSOMAL PROTEIN EL32---
EA [auth f]60S RIBOSOMAL PROTEIN EL33---
GA [auth h]60S RIBOSOMAL PROTEIN UL29---
HA [auth i]60S RIBOSOMAL PROTEIN EL36---
JA [auth k]60S RIBOSOMAL PROTEIN EL38---
KA [auth l]60S RIBOSOMAL PROTEIN EL39---
LA [auth m]60S RIBOSOMAL PROTEIN EL40---
NA [auth o]60S RIBOSOMAL PROTEIN EL44---
OA [auth p]60S RIBOSOMAL PROTEIN EL43---
QA [auth u]60S RIBOSOMAL PROTEIN UL1---
SA [auth 3]5.8S Ribosomal RNA---
TA [auth 4]5S Ribosomal RNA---
T [auth U]60S RIBOSOMAL PROTEIN EL22---
X [auth Y]60S RIBOSOMAL PROTEIN UL24---
FA [auth g]60S RIBOSOMAL PROTEIN EL34---
IA [auth j]60S RIBOSOMAL PROTEIN EL37---
MA [auth n]60S RIBOSOMAL PROTEIN EL41---
PA [auth t]60S RIBOSOMAL PROTEIN EL28---
RA [auth 2]28S Ribosomal RNA---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR022669Large ribosomal subunit protein uL2, C-terminalDomain
IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
IPR023672Large ribosomal subunit protein uL2, archaeal-typeFamily
IPR022671Large ribosomal subunit protein uL2, conserved siteConserved Site
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR022666Large ribosomal subunit protein uL2, RNA-binding domainDomain
IPR014726Large ribosomal subunit protein uL2, domain 3Homologous Superfamily
IPR002171Large ribosomal subunit protein uL2Family