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
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
M, NCPF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17- Domain
M, NCPF16205Ribosomal_S17 N-terminal (Ribosomal_S17_N)Ribosomal_S17 N-terminal- Family
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
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
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
CA, DDPF01667Ribosomal protein S27 (Ribosomal_S27e)Ribosomal protein S27- Family
DA, EDPF01200Ribosomal protein S28e (Ribosomal_S28e)Ribosomal protein S28e- 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
NA, ODPF00297Ribosomal protein L3 (Ribosomal_L3)Ribosomal protein L3- 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
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
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
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
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
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
QB, SEPF01247Ribosomal protein L35Ae (Ribosomal_L35Ae)Ribosomal protein L35Ae- Domain
RB, TEPF01199Ribosomal protein L34e (Ribosomal_L34e)Ribosomal protein L34e- 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
BF, ZBPF00935Ribosomal protein L44 (Ribosomal_L44)Ribosomal protein L44- Family
AC, CFPF01780Ribosomal L37ae protein family (Ribosomal_L37ae)Ribosomal L37ae protein family- Family
J, KCPF01201Ribosomal protein S8e (Ribosomal_S8e)Ribosomal protein S8e- Family
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
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
P, QCPF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
T, UCPF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
AA, BDPF03297S25 ribosomal protein (Ribosomal_S25)S25 ribosomal protein- Family
BA, CDPF01283Ribosomal protein S26e (Ribosomal_S26e)Ribosomal protein S26e- Family
EA, FDPF00253Ribosomal protein S14p/S29e (Ribosomal_S14)Ribosomal protein S14p/S29e- 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
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
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
TA, UDPF00347Ribosomal protein L6 (Ribosomal_L6)Ribosomal protein L6- Domain
UA, VDPF00252Ribosomal protein L16p/L10e (Ribosomal_L16)Ribosomal protein L16p/L10e- Family
WA, YDPF01294Ribosomal protein L13e (Ribosomal_L13e)Ribosomal protein L13e- Family
XA, ZDPF01929Ribosomal protein L14 (Ribosomal_L14e)Ribosomal protein L14- 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
HB, JEPF01246Ribosomal protein L24e (Ribosomal_L24e)Ribosomal protein L24e- Domain
MB, OEPF01779Ribosomal L29e protein family (Ribosomal_L29e)Ribosomal L29e protein family- Family
PB, REPF01655Ribosomal protein L32 (Ribosomal_L32e)Ribosomal protein L32- Family
G, HCPF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.Domain
SB, UEPF00831Ribosomal L29 protein (Ribosomal_L29)Ribosomal L29 protein- Family
AF, YBPF05162Ribosomal protein L41 (Ribosomal_L41)Ribosomal protein L41- Family
H, ICPF01092Ribosomal protein S6e (Ribosomal_S6e)Ribosomal protein S6e- 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
I, JCPF01251Ribosomal protein S7e (Ribosomal_S7e)Ribosomal protein S7e- Family

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
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
S9, s940S ribosomal protein S9-A
C1, c140S ribosomal protein S11-A
C3, c340S ribosomal protein S13
C5, c540S ribosomal protein S15
C6, c640S ribosomal protein S16-A
C7, c740S ribosomal protein S17-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
D7, d740S ribosomal protein S27-A
D8, d840S ribosomal protein S28-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
L3, l360S ribosomal protein L3
L5, l560S ribosomal protein L5
L6, l660S ribosomal protein L6-A
L8, l860S ribosomal protein L8-A
M1, m160S ribosomal protein L11-B
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
N5, n560S ribosomal protein L25
N6, n660S ribosomal protein L26-A
N7, n760S ribosomal protein L27-A
N8, n860S ribosomal protein L28
O0, o060S ribosomal protein L30
O1, o160S ribosomal protein L31-A
O3, o360S ribosomal protein L33-A
O4, o460S ribosomal protein L34-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
Q2, q260S ribosomal protein L42-A
Q3, q360S ribosomal protein L43-A
p2Unknown protein p2none none none
2, 618S ribosomal RNAnone none none
S8, s840S ribosomal protein S8-A
C0, c040S ribosomal protein S10-A
C2, c240S ribosomal protein S12
C4, c440S ribosomal protein S14-A
C8, c840S ribosomal protein S18-A
D5, d540S ribosomal protein S25-A
D6, d640S ribosomal protein S26-B
D9, d940S ribosomal protein S29-A
L2, l260S ribosomal protein L2-A
L4, l460S ribosomal protein L4-A
L7, l760S ribosomal protein L7-A
L9, l960S ribosomal protein L9-A
M0, m060S ribosomal protein L10
M3, m360S ribosomal protein L13-A
M4, m460S ribosomal protein L14-A
N0, n060S ribosomal protein L20-A
N4, n460S ribosomal protein L24-A
N9, n960S ribosomal protein L29
O2, o260S ribosomal protein L32
S5, s540S ribosomal protein S5
O5, o560S ribosomal protein L35-A
Q1, q160S ribosomal protein L41-A
S6, s640S ribosomal protein S6-A
e040S ribosomal protein S30-A
m2Unknown protein m2none none none
p060S acidic ribosomal protein P0
p1Unknown protein p1none none none
S7, s740S ribosomal protein S7-A