4U4R

Crystal structure of Lactimidomycin bound to the yeast 80S ribosome


Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
B, CCPF00318Ribosomal protein S2 (Ribosomal_S2)Ribosomal protein S2- Family
C, DCPF01015Ribosomal S3Ae family (Ribosomal_S3Ae)Ribosomal S3Ae family- Family
D, ECPF03719Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)Ribosomal protein S5, C-terminal domain- Domain
D, ECPF00333Ribosomal protein S5, N-terminal domain (Ribosomal_S5)Ribosomal protein S5, N-terminal domain- Domain
E, FCPF07650KH domain (KH_2)KH domain- Domain
E, FCPF00189Ribosomal 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
F, GCPF00900Ribosomal family S4e (Ribosomal_S4e)Ribosomal family S4e- Family
F, GCPF1612140S ribosomal protein S4 C-terminus (40S_S4_C)40S ribosomal protein S4 C-terminus- Family
F, GCPF08071RS4NT (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
F, GCPF01479S4 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
F, GCPF00467KOW motif (KOW)KOW motif- Family
G, HCPF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.Domain
H, ICPF01092Ribosomal protein S6e (Ribosomal_S6e)Ribosomal protein S6e- Family
I, JCPF01251Ribosomal protein S7e (Ribosomal_S7e)Ribosomal protein S7e- Family
J, KCPF01201Ribosomal protein S8e (Ribosomal_S8e)Ribosomal protein S8e- Family
K, LCPF01479S4 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
L, MCPF03501Plectin/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
M, NCPF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17- Domain
M, NCPF16205Ribosomal_S17 N-terminal (Ribosomal_S17_N)Ribosomal_S17 N-terminal- Family
N, OCPF01248Ribosomal 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
O, PCPF08069Ribosomal 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
O, PCPF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15- Domain
P, QCPF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
Q, RCPF00203Ribosomal protein S19 (Ribosomal_S19)Ribosomal protein S19- Domain
R, SCPF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
S, TCPF00833Ribosomal S17 (Ribosomal_S17e)Ribosomal S17- Family
T, UCPF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
U, VCPF01090Ribosomal protein S19e (Ribosomal_S19e)Ribosomal protein S19e- Family
V, WCPF00338Ribosomal protein S10p/S20e (Ribosomal_S10)Ribosomal protein S10p/S20e- Family
W, XCPF01249Ribosomal protein S21e (Ribosomal_S21e)Ribosomal protein S21e- Family
X, YCPF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8- Domain
Y, ZCPF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
AD, ZPF01282Ribosomal protein S24e (Ribosomal_S24e)Ribosomal protein S24e- Family
AA, BDPF03297S25 ribosomal protein (Ribosomal_S25)S25 ribosomal protein- Family
BA, CDPF01283Ribosomal protein S26e (Ribosomal_S26e)Ribosomal protein S26e- Family
CA, DDPF01667Ribosomal protein S27 (Ribosomal_S27e)Ribosomal protein S27- Family
DA, EDPF01200Ribosomal protein S28e (Ribosomal_S28e)Ribosomal protein S28e- Family
EA, FDPF00253Ribosomal protein S14p/S29e (Ribosomal_S14)Ribosomal protein S14p/S29e- Family
FAPF04758Ribosomal protein S30 (Ribosomal_S30)Ribosomal protein S30- Family
GA, HDPF00240Ubiquitin family (ubiquitin)Ubiquitin familyThis family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].
Domain
GA, HDPF01599Ribosomal 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
HA, IDPF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
IA, JDPF09598Stm1 (Stm1_N)Stm1- Family
MA, NDPF03947Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C)Ribosomal Proteins L2, C-terminal domain- Domain
MA, NDPF00181Ribosomal Proteins L2, RNA binding domain (Ribosomal_L2)Ribosomal Proteins L2, RNA binding domain- Domain
NA, ODPF00297Ribosomal protein L3 (Ribosomal_L3)Ribosomal protein L3- Family
OA, PDPF1437460S ribosomal protein L4 C-terminal domain (Ribos_L4_asso_C)60S ribosomal protein L4 C-terminal domainThis family is found at the very C-terminal of 60 ribosomal L4 proteins.Domain
OA, PDPF00573Ribosomal protein L4/L1 family (Ribosomal_L4)Ribosomal protein L4/L1 family- Family
PA, QDPF17144Ribosomal large subunit proteins 60S L5, and 50S L18 (Ribosomal_L5e)Ribosomal large subunit proteins 60S L5, and 50S L18- Family
PA, QDPF14204Ribosomal L18 C-terminal region (Ribosomal_L18_c)Ribosomal L18 C-terminal regionThis domain is the C-terminal end of ribosomal L18/L5 proteins.Domain
QA, RDPF01159Ribosomal protein L6e (Ribosomal_L6e)Ribosomal protein L6e- Family
RA, SDPF08079Ribosomal L30 N-terminal domain (Ribosomal_L30_N)Ribosomal L30 N-terminal domainThis presumed domain is found at the N-terminus of Ribosomal L30 proteins and has been termed RL30NT or NUC018 [1].Domain
RA, SDPF00327Ribosomal protein L30p/L7e (Ribosomal_L30)Ribosomal protein L30p/L7eThis family includes prokaryotic L30 and eukaryotic L7.Domain
SA, TDPF01248Ribosomal 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
TA, UDPF00347Ribosomal protein L6 (Ribosomal_L6)Ribosomal protein L6- Domain
UA, VDPF00252Ribosomal protein L16p/L10e (Ribosomal_L16)Ribosomal protein L16p/L10e- Family
VA, WDPF00281Ribosomal protein L5 (Ribosomal_L5)Ribosomal protein L5- Domain
VA, WDPF00673ribosomal L5P family C-terminus (Ribosomal_L5_C)ribosomal L5P family C-terminusThis region is found associated with Pfam:PF00281.Domain
WA, YDPF01294Ribosomal protein L13e (Ribosomal_L13e)Ribosomal protein L13e- Family
XA, ZDPF01929Ribosomal protein L14 (Ribosomal_L14e)Ribosomal protein L14- Family
AE, YAPF00827Ribosomal L15 (Ribosomal_L15e)Ribosomal L15- Family
BE, ZAPF00572Ribosomal protein L13 (Ribosomal_L13)Ribosomal protein L13- Family
AB, CEPF00237Ribosomal protein L22p/L17e (Ribosomal_L22)Ribosomal protein L22p/L17eThis family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes.Domain
BB, DEPF17135Ribosomal protein 60S L18 and 50S L18e (Ribosomal_L18)Ribosomal protein 60S L18 and 50S L18e- Family
CB, EEPF01280Ribosomal protein L19e (Ribosomal_L19e)Ribosomal protein L19e- Family
EB, GEPF01157Ribosomal protein L21e (Ribosomal_L21e)Ribosomal protein L21e- Family
FB, HEPF01776Ribosomal L22e protein family (Ribosomal_L22e)Ribosomal L22e protein family- Family
GB, IEPF00238Ribosomal protein L14p/L23e (Ribosomal_L14)Ribosomal protein L14p/L23e- Domain
HB, JEPF01246Ribosomal protein L24e (Ribosomal_L24e)Ribosomal protein L24e- Domain
IB, KEPF03939Ribosomal protein L23, N-terminal domain (Ribosomal_L23eN)Ribosomal protein L23, N-terminal domain- Family
IB, KEPF00276Ribosomal protein L23 (Ribosomal_L23)Ribosomal protein L23- Family
JB, LEPF16906Ribosomal proteins L26 eukaryotic, L24P archaeal (Ribosomal_L26)Ribosomal proteins L26 eukaryotic, L24P archaeal- Family
JB, LEPF00467KOW motif (KOW)KOW motif- Family
KB, MEPF01777Ribosomal L27e protein family (Ribosomal_L27e)Ribosomal L27e protein family- Family
LB, NEPF00828Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A (Ribosomal_L27A)Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A- Family
MB, OEPF01779Ribosomal L29e protein family (Ribosomal_L29e)Ribosomal L29e protein family- Family
NB, PEPF01248Ribosomal 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
OB, QEPF01198Ribosomal protein L31e (Ribosomal_L31e)Ribosomal protein L31e- Family
PB, REPF01655Ribosomal protein L32 (Ribosomal_L32e)Ribosomal protein L32- Family
QB, SEPF01247Ribosomal protein L35Ae (Ribosomal_L35Ae)Ribosomal protein L35Ae- Domain
RB, TEPF01199Ribosomal protein L34e (Ribosomal_L34e)Ribosomal protein L34e- Family
SB, UEPF00831Ribosomal L29 protein (Ribosomal_L29)Ribosomal L29 protein- Family
TB, VEPF01158Ribosomal protein L36e (Ribosomal_L36e)Ribosomal protein L36e- Family
UB, WEPF01907Ribosomal protein L37e (Ribosomal_L37e)Ribosomal protein L37e- Family
VB, XEPF01781Ribosomal L38e protein family (Ribosomal_L38e)Ribosomal L38e protein family- Family
WB, YEPF00832Ribosomal L39 protein (Ribosomal_L39)Ribosomal L39 protein- Family
XB, ZEPF01020Ribosomal L40e family (Ribosomal_L40e)Ribosomal L40e family- Family
XB, ZEPF00240Ubiquitin family (ubiquitin)Ubiquitin familyThis family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].
Domain
AF, YBPF05162Ribosomal protein L41 (Ribosomal_L41)Ribosomal protein L41- Family
BF, ZBPF00935Ribosomal protein L44 (Ribosomal_L44)Ribosomal protein L44- Family
AC, CFPF01780Ribosomal L37ae protein family (Ribosomal_L37ae)Ribosomal L37ae protein family- Family
GDPF04758Ribosomal protein S30 (Ribosomal_S30)Ribosomal protein S30- Family
DFPF17777Insertion domain in 60S ribosomal protein L10P (RL10P_insert)Insertion domain in 60S ribosomal protein L10PThis domain is found in prokaryotic and archaeal ribosomal L10 protein [1].Domain
DFPF00466Ribosomal protein L10 (Ribosomal_L10)Ribosomal protein L10- Family
DB, FEPF01775Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A (Ribosomal_L18A)Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18AThis family includes: archaeal 50S ribosomal protein L18Ae, often referred to as L20e or LX; fungal 60S ribosomal protein L20; and higher eukaryote 60S ribosomal protein L18A.Domain

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
2, 618S ribosomal RNAnone none none
S0, s040S ribosomal protein S0-A
S1, s140S ribosomal protein S1-A
S2, s240S ribosomal protein S2
S3, s340S ribosomal protein S3
S4, s440S ribosomal protein S4-A
S5, s540S ribosomal protein S5
S6, s640S ribosomal protein S6-A
S7, s740S ribosomal protein S7-A
S8, s840S ribosomal protein S8-A
S9, s940S ribosomal protein S9-A
C0, c040S ribosomal protein S10-A
C1, c140S ribosomal protein S11-A
C2, c240S ribosomal protein S12
C3, c340S ribosomal protein S13
C4, c440S ribosomal protein S14-A
C5, c540S ribosomal protein S15
C6, c640S ribosomal protein S16-A
C7, c740S ribosomal protein S17-A
C8, c840S ribosomal protein S18-A
C9, c940S ribosomal protein S19-A
D0, d040S ribosomal protein S20
D1, d140S ribosomal protein S21-A
D2, d240S ribosomal protein S22-A
D3, d340S ribosomal protein S23-A
D4, d440S ribosomal protein S24-A
D5, d540S ribosomal protein S25-A
D6, d640S ribosomal protein S26-B
D7, d740S ribosomal protein S27-A
D8, d840S ribosomal protein S28-A
D9, d940S ribosomal protein S29-A
E040S ribosomal protein S30-A
E1, e1Ubiquitin-40S ribosomal protein S31
SR, sRGuanine nucleotide-binding protein subunit beta-like protein
SM, sMSuppressor protein STM1
1, 525S ribosomal RNAnone none none
3, 75S ribosomal RNAnone none none
4, 85.8S ribosomal RNAnone none none
L2, l260S ribosomal protein L2-A
L3, l360S ribosomal protein L3
L4, l460S ribosomal protein L4-A
L5, l560S ribosomal protein L5
L6, l660S ribosomal protein L6-A
L7, l760S ribosomal protein L7-A
L8, l860S ribosomal protein L8-A
L9, l960S ribosomal protein L9-A
M0, m060S ribosomal protein L10
M1, m160S ribosomal protein L11-B
M3, m360S ribosomal protein L13-A
M4, m460S ribosomal protein L14-A
M5, m560S ribosomal protein L15-A
M6, m660S ribosomal protein L16-A
M7, m760S ribosomal protein L17-A
M8, m860S ribosomal protein L18-A
M9, m960S ribosomal protein L19-A
N1, n160S ribosomal protein L21-A
N2, n260S ribosomal protein L22-A
N3, n360S ribosomal protein L23-A
N4, n460S ribosomal protein L24-A
N5, n560S ribosomal protein L25
N6, n660S ribosomal protein L26-A
N7, n760S ribosomal protein L27-A
N8, n860S ribosomal protein L28
N9, n960S ribosomal protein L29
O0, o060S ribosomal protein L30
O1, o160S ribosomal protein L31-A
O2, o260S ribosomal protein L32
O3, o360S ribosomal protein L33-A
O4, o460S ribosomal protein L34-A
O5, o560S ribosomal protein L35-A
O6, o660S ribosomal protein L36-A
O7, o760S ribosomal protein L37-A
O8, o860S ribosomal protein L38
O9, o960S ribosomal protein L39
Q0, q0Ubiquitin-60S ribosomal protein L40
Q1, q160S ribosomal protein L41-A
Q2, q260S ribosomal protein L42-A
Q3, q360S ribosomal protein L43-A
e040S ribosomal protein S30-A
m2Unknown protein m2none none none
p060S acidic ribosomal protein P0
p1Unknown protein p1none none none
p2Unknown protein p2none none none
N0, n060S ribosomal protein L20-A