6FYX

Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C1)


Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
DPF00318Ribosomal protein S2 (Ribosomal_S2)Ribosomal protein S2- Family
EPF01015Ribosomal S3Ae family (Ribosomal_S3Ae)Ribosomal S3Ae family- Family
FPF03719Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)Ribosomal protein S5, C-terminal domain- Domain
FPF00333Ribosomal protein S5, N-terminal domain (Ribosomal_S5)Ribosomal protein S5, N-terminal domain- Domain
GPF07650KH domain (KH_2)KH domain- Domain
GPF00189Ribosomal 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
HPF00900Ribosomal family S4e (Ribosomal_S4e)Ribosomal family S4e- Family
HPF1612140S ribosomal protein S4 C-terminus (40S_S4_C)40S ribosomal protein S4 C-terminus- Family
HPF08071RS4NT (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
HPF01479S4 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
HPF00467KOW motif (KOW)KOW motif- Family
IPF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.Domain
JPF01092Ribosomal protein S6e (Ribosomal_S6e)Ribosomal protein S6e- Family
KPF01251Ribosomal protein S7e (Ribosomal_S7e)Ribosomal protein S7e- Family
LPF01201Ribosomal protein S8e (Ribosomal_S8e)Ribosomal protein S8e- Family
MPF00163Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4)Ribosomal protein S4/S9 N-terminal domain- Family
MPF01479S4 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
NPF03501Plectin/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
OPF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17- Domain
OPF16205Ribosomal_S17 N-terminal (Ribosomal_S17_N)Ribosomal_S17 N-terminal- Family
PPF01248Ribosomal 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
QPF08069Ribosomal 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
QPF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15- Domain
RPF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
SPF00203Ribosomal protein S19 (Ribosomal_S19)Ribosomal protein S19- Domain
TPF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
UPF00833Ribosomal S17 (Ribosomal_S17e)Ribosomal S17- Family
WPF01090Ribosomal protein S19e (Ribosomal_S19e)Ribosomal protein S19e- Family
XPF00338Ribosomal protein S10p/S20e (Ribosomal_S10)Ribosomal protein S10p/S20e- Family
YPF01249Ribosomal protein S21e (Ribosomal_S21e)Ribosomal protein S21e- Family
ZPF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8- Domain
AAPF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
BAPF01282Ribosomal protein S24e (Ribosomal_S24e)Ribosomal protein S24e- Family
CAPF03297S25 ribosomal protein (Ribosomal_S25)S25 ribosomal protein- Family
DAPF01283Ribosomal protein S26e (Ribosomal_S26e)Ribosomal protein S26e- Family
EAPF01667Ribosomal protein S27 (Ribosomal_S27e)Ribosomal protein S27- Family
FAPF01200Ribosomal protein S28e (Ribosomal_S28e)Ribosomal protein S28e- Family
GAPF00253Ribosomal protein S14p/S29e (Ribosomal_S14)Ribosomal protein S14p/S29e- Family
HAPF04758Ribosomal protein S30 (Ribosomal_S30)Ribosomal protein S30- Family
IAPF00240Ubiquitin 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
IAPF01599Ribosomal 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
JAPF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
KAPF05162Ribosomal protein L41 (Ribosomal_L41)Ribosomal protein L41- Family
LAPF01176Translation initiation factor 1A / IF-1 (eIF-1a)Translation initiation factor 1A / IF-1This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1.Domain
MAPF07541Eukaryotic translation initiation factor 2 alpha subunit (EIF_2_alpha)Eukaryotic translation initiation factor 2 alpha subunit- Family
MAPF00575S1 RNA binding domain (S1)S1 RNA binding domainThe S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.Domain
NAPF00009Elongation factor Tu GTP binding domain (GTP_EFTU)Elongation factor Tu GTP binding domainThis domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.Domain
NAPF09173Initiation factor eIF2 gamma, C terminal (eIF2_C)Initiation factor eIF2 gamma, C terminalMembers of this family, which are found in the initiation factors eIF2 and EF-Tu, adopt a structure consisting of a beta barrel with Greek key topology. They are required for formation of the ternary complex with GTP and initiator tRNA [1].Domain
NAPF03144Elongation factor Tu domain 2 (GTP_EFTU_D2)Elongation factor Tu domain 2Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ...Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to Pfam:PF03143, and in fact has weak sequence matches to this domain.
Domain
OAPF01873Domain found in IF2B/IF5 (eIF-5_eIF-2B)Domain found in IF2B/IF5- Family
PAPF02020eIF4-gamma/eIF5/eIF2-epsilon (W2)eIF4-gamma/eIF5/eIF2-epsilon- Family
PAPF01873Domain found in IF2B/IF5 (eIF-5_eIF-2B)Domain found in IF2B/IF5- Family
RAPF08662Eukaryotic translation initiation factor eIF2A (eIF2A)Eukaryotic translation initiation factor eIF2A- Family
RAPF00076RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) (RRM_1)RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The mo ...The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.
Domain
SAPF05470Eukaryotic translation initiation factor 3 subunit 8 N-terminus (eIF-3c_N)Eukaryotic translation initiation factor 3 subunit 8 N-terminus- Family
SAPF01399PCI domain (PCI)PCI domainThis domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) [1].Domain
TAPF12353Eukaryotic translation initiation factor 3 subunit G (eIF3g)Eukaryotic translation initiation factor 3 subunit G- Family
TAPF00076RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) (RRM_1)RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The mo ...The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.
Domain
UAPF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
VPF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
1tRNAinone none none
218S ribosomal RNAnone none none
3mRNA (31-MER)none none none
A40S ribosomal protein S0
B40S ribosomal protein S1
CKLLA0F09812p
DKLLA0D08305p
E40S ribosomal protein S4
FKLLA0D10659p
G40S ribosomal protein S6
H40S ribosomal protein S7
I40S ribosomal protein S8
JKLLA0E23673p
KKLLA0B08173p
LKLLA0A10483p
M40S ribosomal protein S12
NKLLA0F18040p
O40S ribosomal protein S14
PKLLA0F07843p
Q40S ribosomal protein S16
RKLLA0B01474p
TKLLA0A07194p
UKLLA0F25542p
V40S ribosomal protein S21
W40S ribosomal protein S22
XKLLA0B11231p
Y40S ribosomal protein S24
ZKLLA0B06182p
a40S ribosomal protein S26
b40S ribosomal protein S27
c40S ribosomal protein S28
d40S ribosomal protein S29
e40S ribosomal protein S30
fUbiquitin-40S ribosomal protein S27a
gKLLA0E12277p
h60S ribosomal protein L41-A
iEukaryotic translation initiation factor 1A
jEukaryotic translation initiation factor 2 subunit alpha
kEukaryotic translation initiation factor 2 subunit gamma
lEukaryotic translation initiation factor 2 subunit beta
mEukaryotic translation initiation factor 5
oEukaryotic translation initiation factor 3 subunit A
pEukaryotic translation initiation factor 3 subunit B
qeIF3c,eIF3c
rEukaryotic translation initiation factor 3 subunit G
sEukaryotic translation initiation factor 3 subunit I
SKLLA0B01562p