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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

5WYJ

Cryo-EM structure of the 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP, state 1)

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
13AU3 RNApolymer333106503.31Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
23B, 3CrRNA 2'-O-methyltransferase fibrillarinpolymer32734525.42UniProt (P15646)
Pfam (PF01269)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Histone-glutamine methyltransferase,U3 small nucleolar RNA-associated protein NOP1,U3 snoRNA-associated protein NOP1
33DNucleolar protein 56polymer50456961.21UniProt (Q12460)
Pfam (PF08156)
Pfam (PF01798)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Ribosome biosynthesis protein SIK1,Suppressor of I kappa b protein 1
43ENucleolar protein 58polymer51157060.31UniProt (Q12499)
Pfam (PF08156)
Pfam (PF01798)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nucleolar protein 5
53FRibosomal RNA-processing protein 9polymer57365147.01UniProt (Q06506)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
63G, 3H13 kDa ribonucleoprotein-associated proteinpolymer12613582.92UniProt (P39990)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Small nuclear ribonucleoprotein-associated protein 1
75A5ETS RNApolymer700225543.11GenBank (1262303)Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
8AAUtp4polymer77666059.21Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
9ABUtp5polymer64354740.61Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
10ACUtp8polymer71360697.81Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
11ADUtp9polymer57548953.41Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
12AEU3 small nucleolar RNA-associated protein 10,Utp10polymer1769173592.41UniProt (P42945)
Pfam (PF12397)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)U3 snoRNA-associated protein 10,U three protein 10,U3 protein 10 required for transcription,t-UTP10
13AFUtp15polymer51343676.91Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
14AGUtp17polymer89676271.41Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
15B1Ribosome biogenesis protein BMS1polymer1183135792.31UniProt (Q08965)
Pfam (PF00004)
Pfam (PF08142)
Pfam (PF04950)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
16BAPeriodic tryptophan protein 2polymer923104097.01UniProt (P25635)
Pfam (PF00400)
Pfam (PF04003)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)U three protein 1,U3 small nucleolar RNA-associated protein 1,U3 snoRNA-associated protein 1
17BBU3 small nucleolar RNA-associated protein 12polymer943106481.11UniProt (Q12220)
Pfam (PF00400)
Pfam (PF04003)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)U3 snoRNA-associated protein 12,DOM34-interacting protein 2,U three protein 12
18BCU3 small nucleolar RNA-associated protein 13polymer81791132.61UniProt (Q05946)
Pfam (PF00400)
Pfam (PF08625)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)U3 snoRNA-associated protein 13,U three protein 13
19BDU3 small nucleolar RNA-associated protein 18polymer59466494.31UniProt (P40362)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)U3 snoRNA-associated protein 18,U three protein 18
20BEU3 small nucleolar RNA-associated protein 21polymer939104927.81UniProt (Q06078)
Pfam (PF00400)
Pfam (PF04192)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)U3 snoRNA-associated protein 21,U three protein 21
21CARibosomal RNA-processing protein 7polymer29734526.41UniProt (P25368)
Pfam (PF17799)
Pfam (PF12923)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
22CBU3 small nucleolar RNA-associated protein 22polymer1237140660.11UniProt (P53254)
Pfam (PF03813)
Pfam (PF17403)
Pfam (PF17404)
Pfam (PF17405)
Pfam (PF17406)
Pfam (PF17407)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)U3 snoRNA-associated protein 22,U three protein 22
23E1, E2Ribosomal RNA small subunit methyltransferase NEP1polymer25227936.52UniProt (Q06287)
Pfam (PF03587)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)18S rRNA (pseudouridine(1189)-N1)-methyltransferase,18S rRNA Psi1189 methyltransferase,Essential for mitotic growth protein 1,Nucleolar essential protein 1
24E3Essential nuclear protein 1polymer48355207.41UniProt (P38333)
Pfam (PF05291)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
25E4Enp2polymer70760187.11Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
26K1KRR1 small subunit processome componentpolymer31637226.31UniProt (P25586)
Pfam (PF17903)
Pfam (PF21800)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)KRR-R motif-containing protein 1,Ribosomal RNA assembly protein KRR1
27MAU3 small nucleolar ribonucleoprotein protein IMP3polymer18321928.51UniProt (P32899)
Pfam (PF00163)
Pfam (PF01479)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)U3 snoRNP protein IMP3,Interacting with MPP10 protein 3
28MBU3 small nucleolar ribonucleoprotein protein IMP4polymer29033536.21UniProt (P53941)
Pfam (PF04427)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)U3 snoRNP protein IMP4,Interacting with MPP10 protein 4
29MCMpp10,U3 small nucleolar RNA-associated protein MPP10polymer59354937.01UniProt (P47083)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)U3 snoRNA-associated protein MPP10,M phase phosphoprotein 10
30P1Pre-rRNA-processing protein PNO1polymer27430380.61UniProt (Q99216)
Pfam (PF17903)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Partner of NOB1,Ribosomal RNA-processing protein 20
31R1RNA 3'-terminal phosphate cyclase-like proteinpolymer36740220.61UniProt (Q08096)
Pfam (PF01137)
Pfam (PF05189)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
32R2rRNA biogenesis protein RRP5polymer1729193411.41UniProt (Q05022)
Pfam (PF00575)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Ribosomal RNA-processing protein 5,U3 small nucleolar RNA-associated protein RRP5,U3 snoRNA-associated protein RRP5
33S1Sof1polymer48941634.31Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
34SA18S ribosomal RNApolymer1812583636.61GenBank (874346701)Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
35SC40S ribosomal protein S1-Apolymer25528798.51UniProt (P33442)
Pfam (PF01015)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP10A
36SF40S ribosomal protein S4-Apolymer26129469.31UniProt (P0CX35)
Pfam (PF08071)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP5,S7,YS6
37SG40S ribosomal protein S5polymer22525072.61UniProt (P26783)
Pfam (PF00177)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP14,S2,YS8
38SH40S ribosomal protein S6-Apolymer23627054.51UniProt (P0CX37)
Pfam (PF01092)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP9,S10,YS4
39SI40S ribosomal protein S7-Apolymer19021658.21UniProt (P26786)
Pfam (PF01251)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP30,RP40
40SJ40S ribosomal protein S8-Apolymer20022537.81UniProt (P0CX39)
Pfam (PF01201)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP19,S14,YS9
41SK40S ribosomal protein S9-Apolymer19722487.91UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP21,S13,YP28,YS11
42SM40S ribosomal protein S11-Apolymer15617785.91UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP41,S18,YS12
43SN40S ribosomal protein S12polymer14315488.61UniProt (P48589)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
44SO40S ribosomal protein S13polymer15117059.91UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S27a,YS15
45SP40S ribosomal protein S14-Apolymer13714562.71UniProt (P06367)
Pfam (PF00411)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP59A
46SR40S ribosomal protein S16-Apolymer14315877.51UniProt (P0CX51)
Pfam (PF00380)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP61R
47SX40S ribosomal protein S22-Apolymer13014650.11UniProt (P0C0W1)
Pfam (PF00410)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP50,S24,YP58,YS22
48SY40S ribosomal protein S23-Apolymer14516073.91UniProt (P0CX29)
Pfam (PF00164)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP37,S28,YS14
49SZ40S ribosomal protein S24-Apolymer13515362.81UniProt (P0CX31)
Pfam (PF01282)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP50
50Sc40S ribosomal protein S27-Apolymer828893.41UniProt (P35997)
Pfam (PF01667)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP61,YS20
51Sd40S ribosomal protein S28-Apolymer677605.81UniProt (Q3E7X9)
Pfam (PF01200)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S33,YS27
52Sf40S ribosomal protein S30-Apolymer637137.51UniProt (P0CX33)
Pfam (PF04758)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
53SgUbiquitin-40S ribosomal protein S31polymer15217254.21UniProt (P05759)
Pfam (PF00240)
Pfam (PF01599)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
54U1Utp7polymer55447166.21Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
55U2Utp11polymer25021294.21Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
56U3Utp20polymer2493212188.81Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
57U4rRNA-processing protein FCF1polymer18921650.71UniProt (Q05498)
Pfam (PF04900)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)FAF1-copurifying factor 1
58U5Ribosome biogenesis protein UTP30polymer27431668.91UniProt (P36144)
Pfam (PF00687)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)U3 snoRNP-associated protein UTP30
59UAHelical domain proteinpolymer1615137462.41Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
60UBHelical domain proteinpolymer98784015.71Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
61UCUnassigned helicespolymer103387930.41Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Sequence modifications
AE: 1 - 808 (UniProt: P42945)
AE: 809 - 1769 (PDB: 5WYJ)
MC: 1 - 428 (PDB: 5WYJ)
MC: 429 - 593 (UniProt: P47083)
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains64
Total formula weight4111922.2
All*Total formula weight4111922.2
*Water molecules are not included.

218853

PDB entries from 2024-04-24

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