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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

6LQS

Cryo-EM structure of 90S small subunit preribosomes in transition states (State D)

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
13AU3 snoRNApolymer333106503.31Saccharomyces cerevisiae S288C (Baker's yeast)
25A5' ETSpolymer700225543.11Saccharomyces cerevisiae S288C (Baker's yeast)
3SA18S pre-rRNApolymer1809582710.91Saccharomyces cerevisiae S288C (Baker's yeast)
4SC40S ribosomal protein S1-Apolymer25528798.51UniProt (P33442)
Pfam (PF01015)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps1, RP10A
5SF40S 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)Rps4, RP5,S7,YS6
6SG40S ribosomal protein S5polymer22525072.61UniProt (P26783)
Pfam (PF00177)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps5, RP14,S2,YS8
7SH40S ribosomal protein S6-Apolymer23627054.51UniProt (P0CX37)
Pfam (PF01092)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps6, RP9,S10,YS4
8SI40S ribosomal protein S7-Apolymer19021658.21UniProt (P26786)
Pfam (PF01251)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps7, RP30,RP40
9SJ40S ribosomal protein S8-Apolymer20022537.81UniProt (P0CX39)
Pfam (PF01201)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps8, RP19,S14,YS9
10SK40S ribosomal protein S9-Apolymer19722487.91UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps9, RP21,S13,YP28,YS11
11SM40S ribosomal protein S11-Apolymer15617785.91UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps11, RP41,S18,YS12
12SO40S ribosomal protein S13polymer15117059.91UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps13, S27a,YS15
13SP40S ribosomal protein S14-Apolymer13714562.71UniProt (P06367)
Pfam (PF00411)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps14, RP59A
14SR40S ribosomal protein S16-Apolymer14315877.51UniProt (P0CX51)
Pfam (PF00380)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps16, RP61R
15SX40S ribosomal protein S22-Bpolymer13014650.11UniProt (Q3E7Y3)
Pfam (PF00410)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps22, RP50,S24,Small ribosomal subunit protein uS8-B,YP58,YS22
16SY40S ribosomal protein S23-Apolymer14516073.91UniProt (P0CX29)
Pfam (PF00164)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps23, RP37,S28,YS14
17SZ40S ribosomal protein S24-Apolymer13515362.81UniProt (P0CX31)
Pfam (PF01282)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps24,RP50
18Sc40S ribosomal protein S27-Apolymer828893.41UniProt (P35997)
Pfam (PF01667)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps27, RP61,YS20
19Sd40S ribosomal protein S28-Apolymer677605.81UniProt (Q3E7X9)
Pfam (PF01200)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps28, S33,YS27
203B, 3CrRNA 2'-O-methyltransferase fibrillarinpolymer32734525.42UniProt (P15646)
Pfam (PF01269)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nop1, Histone-glutamine methyltransferase,U3 small nucleolar RNA-associated protein NOP1,U3 snoRNA-associated protein NOP1
213DNucleolar protein 56polymer50456961.21UniProt (Q12460)
Pfam (PF08156)
Pfam (PF01798)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nop56, Ribosome biosynthesis protein SIK1,Suppressor of I kappa b protein 1
223ENucleolar protein 58polymer51157060.31UniProt (Q12499)
Pfam (PF08156)
Pfam (PF01798)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nucleolar protein 5
233FRibosomal RNA-processing protein 9polymer57365147.01UniProt (Q06506)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rrp9
243G, 3H13 kDa ribonucleoprotein-associated proteinpolymer12613582.92UniProt (P39990)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Snu13, Small nuclear ribonucleoprotein-associated protein 1
25A4U3 small nucleolar RNA-associated protein 4polymer77687909.21UniProt (Q06679)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp4, U3 snoRNA-associated protein 4,U three protein 4,U3 protein 4 required for transcription,t-UTP4
26A5U3 small nucleolar RNA-associated protein 5polymer64372079.41UniProt (Q04177)
Pfam (PF04003)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp5, U3 snoRNA-associated protein 5,U three protein 5,U3 protein 5 required for transcription,t-UTP5
27A8U3 small nucleolar RNA-associated protein 8polymer71380269.61UniProt (P53276)
Pfam (PF10395)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp8, U3 snoRNA-associated protein 8,U three protein 8,U3 protein 8 required for transcription,t-UTP8
28A9U3 small nucleolar RNA-associated protein 9polymer57565347.31UniProt (P38882)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp9, U3 snoRNA-associated protein 9,U three protein 9,U3 protein 9 required for transcription,t-UTP9
29AEU3 small nucleolar RNA-associated protein 10polymer1769200299.01UniProt (P42945)
Pfam (PF12397)
Pfam (PF08146)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp10, U3 snoRNA-associated protein 10,U three protein 10,U3 protein 10 required for transcription,t-UTP10
30AFU3 small nucleolar RNA-associated protein 15polymer51357765.31UniProt (Q04305)
Pfam (PF00400)
Pfam (PF09384)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp15, U3 snoRNA-associated protein 15,U three protein 15,U3 protein 15 required for transcription,t-UTP15
31AGNET1-associated nuclear protein 1polymer896101341.71UniProt (Q02931)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp17, U three protein 17,t-17,U3 protein 17 required for transcription,U3 small nucleolar RNA-associated protein 17,U3 snoRNA-associated protein 17
32B1Periodic tryptophan protein 2polymer900101467.41UniProt (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
33B2U3 small nucleolar RNA-associated protein 12polymer943106481.11UniProt (Q12220)
Pfam (PF00400)
Pfam (PF04003)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp12, U3 snoRNA-associated protein 12,DOM34-interacting protein 2,U three protein 12
34B3U3 small nucleolar RNA-associated protein 13polymer81791132.61UniProt (Q05946)
Pfam (PF00400)
Pfam (PF08625)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp13, U3 snoRNA-associated protein 13,U three protein 13
35B8U3 small nucleolar RNA-associated protein 18polymer59466494.31UniProt (P40362)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp18, U3 snoRNA-associated protein 18,U three protein 18
36BEU3 small nucleolar RNA-associated protein 21polymer939104927.81UniProt (Q06078)
Pfam (PF00400)
Pfam (PF04192)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp21, U3 snoRNA-associated protein 21,U three protein 21
37B6U3 small nucleolar RNA-associated protein 6polymer44052495.31UniProt (Q02354)
Pfam (PF08640)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp6, U3 snoRNA-associated protein 6,U three protein 6
385BBud site selection protein 21polymer21424431.01UniProt (Q08492)
Pfam (PF08297)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Bud21, U three protein 16,U3 small nucleolar RNA-associated protein 16,U3 snoRNA-associated protein 16
395CU3 small nucleolar RNA-associated protein 7polymer55462418.61UniProt (P40055)
Pfam (PF00400)
Pfam (PF08149)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp7, U3 snoRNA-associated protein 7,U three protein 7
405DU3 small nucleolar RNA-associated protein 11polymer25029806.31UniProt (P34247)
Pfam (PF03998)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp11, U3 snoRNA-associated protein 11,U three protein 11
415EU3 small nucleolar RNA-associated protein MPP10polymer59367042.51UniProt (P47083)
Pfam (PF04006)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Mpp10, U3 snoRNA-associated protein MPP10,M phase phosphoprotein 10
425FU3 small nucleolar ribonucleoprotein protein IMP3polymer18321928.51UniProt (P32899)
Pfam (PF00163)
Pfam (PF01479)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Imp3, U3 snoRNP protein IMP3,Interacting with MPP10 protein 3
435GU3 small nucleolar ribonucleoprotein protein IMP4polymer29033536.21UniProt (P53941)
Pfam (PF04427)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Imp4, U3 snoRNP protein IMP4,Interacting with MPP10 protein 4
445HSomething about silencing protein 10polymer61070364.41UniProt (Q12136)
Pfam (PF04000)
Pfam (PF09368)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Sas10, U three protein 3,U3 small nucleolar RNA-associated protein 3,U3 snoRNA-associated protein 11
455IProtein SOF1polymer48956888.91UniProt (P33750)
Pfam (PF00400)
Pfam (PF04158)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Sof1, U3 small nucleolar RNA-associated protein SOF1,U3 snoRNA-associated protein SOF1
465JrRNA-processing protein FCF2polymer21725689.21UniProt (Q12035)
Pfam (PF08698)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)FAF1 copurifying factor 2
475KrRNA-processing protein FCF1polymer18921650.71UniProt (Q05498)
Pfam (PF04900)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp24, FAF1-copurifying factor 1
48RDrRNA 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
49REU3 small nucleolar RNA-associated protein 22polymer1237140660.11UniProt (P53254)
Pfam (PF17406)
Pfam (PF17407)
Pfam (PF03813)
Pfam (PF17403)
Pfam (PF17404)
Pfam (PF17405)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp22, U3 snoRNA-associated protein 22,U three protein 22
50RFRibosomal RNA-processing protein 7polymer29734526.41UniProt (P25368)
Pfam (PF17799)
Pfam (PF12923)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rrp7
51RG, RHRibosomal RNA small subunit methyltransferase NEP1polymer25227936.52UniProt (Q06287)
Pfam (PF03587)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Emg1, 18S rRNA (pseudouridine(1189)-N1)-methyltransferase,18S rRNA Psi1189 methyltransferase,Essential for mitotic growth protein 1,Nucleolar essential protein 1
52RJRibosome biogenesis protein BMS1polymer1183135792.31UniProt (Q08965)
Pfam (PF00004)
Pfam (PF08142)
Pfam (PF04950)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Bms1
53RKRNA 3'-terminal phosphate cyclase-like proteinpolymer36740220.61UniProt (Q08096)
Pfam (PF01137)
Pfam (PF05189)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rcl1
54RNNucleolar complex protein 14polymer81094463.21UniProt (Q99207)
Pfam (PF04147)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nop14, U three protein 2,U3 small nucleolar RNA-associated protein 2,U3 snoRNA-associated protein 2
55RONucleolar complex protein 4polymer55263707.81UniProt (Q06512)
Pfam (PF03914)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Noc4, U three protein 19,U3 small nucleolar RNA-associated protein 19,U3 snoRNA-associated protein 19
56RPU3 small nucleolar RNA-associated protein 20polymer2493287915.51UniProt (P35194)
Pfam (PF07539)
Pfam (PF20416)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)U3 snoRNA-associated protein 20,U three protein 20
57RQU3 small nucleolar RNA-associated protein 14polymer899103189.81UniProt (Q04500)
Pfam (PF04615)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp14, U3 snoRNA-associated protein 14,U three protein 14
58RSEssential nuclear protein 1polymer48054879.11UniProt (P38333)
Pfam (PF05291)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
59RTPno1polymer32636356.51Saccharomyces cerevisiae S288C (Baker's yeast)
60RWRegulator of rDNA transcription protein 14polymer20623898.31UniProt (P40470)
Pfam (PF17075)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rrt14
61X1Unassigned helices 1polymer34729549.31Saccharomyces cerevisiae S288C (Baker's yeast)
62X2Unassigned helices 2polymer69459080.81Saccharomyces cerevisiae S288C (Baker's yeast)
63R5Exosome complex component RRP45polymer30534001.91UniProt (Q05636)
Pfam (PF01138)
Pfam (PF03725)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Ribosomal RNA-processing protein 45
64R1Exosome complex component SKI6polymer24627599.71UniProt (P46948)
Pfam (PF01138)
Pfam (PF03725)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Extracellular mutant protein 20,Ribosomal RNA-processing protein 41,Superkiller protein 6
65R3Exosome complex component RRP43polymer39444060.91UniProt (P25359)
Pfam (PF01138)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Ribosomal RNA-processing protein 43
66R6Exosome complex component RRP46polymer22324430.21UniProt (P53256)
Pfam (PF01138)
Pfam (PF03725)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Ribosomal RNA-processing protein 46
67R2Exosome complex component RRP42polymer26529085.21UniProt (Q12277)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Ribosomal RNA-processing protein 42
68M3Exosome complex component MTR3polymer25027604.01UniProt (P48240)
Pfam (PF01138)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)mRNA transport regulator 3
69R0Exosome complex component RRP40polymer24026583.41UniProt (Q08285)
Pfam (PF18311)
Pfam (PF21262)
Pfam (PF15985)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Ribosomal RNA-processing protein 40
70r4Exosome complex component RRP4polymer35939470.21UniProt (P38792)
Pfam (PF14382)
Pfam (PF21266)
Pfam (PF15985)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Ribosomal RNA-processing protein 4
71C4Exosome complex component CSL4polymer29231619.31UniProt (P53859)
Pfam (PF21551)
Pfam (PF10447)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)CEP1 synthetic lethal protein 4
72R4Exosome complex exonuclease DIS3polymer1001113857.71UniProt (Q08162)
Pfam (PF13638)
Pfam (PF17216)
Pfam (PF17849)
Pfam (PF00773)
Pfam (PF17215)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Chromosome disjunction protein 3,Ribosomal RNA-processing protein 44
73r6Exosome complex exonuclease RRP6polymer73384160.61UniProt (Q12149)
Pfam (PF08066)
Pfam (PF01612)
Pfam (PF00570)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Ribosomal RNA-processing protein 6
74R7Exosome complex protein LRP1polymer18421086.31UniProt (P38801)
Pfam (PF04000)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Like an rRNA processing protein 1,Yeast C1D domain-containing protein,rRNA processing protein 47
75M4ATP-dependent RNA helicase DOB1polymer1073122228.01UniProt (P47047)
Pfam (PF00270)
Pfam (PF00271)
Pfam (PF21408)
Pfam (PF13234)
Pfam (PF08148)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)mRNA transport regulator MTR4
76M6M-phase phosphoprotein 6 homologpolymer18621185.51UniProt (P53725)
Pfam (PF10175)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Exosome-associated RNA-binding protein MPP6
77Sc, 5KZINC IONnon-polymer65.42Chemie (ZN)
78RJGUANOSINE-5'-TRIPHOSPHATEnon-polymer523.21Chemie (GTP)
79RJMAGNESIUM IONnon-polymer24.31Chemie (MG)
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains79
Total formula weight5097356.4
Non-Polymers*Number of molecules4
Total formula weight678.3
All*Total formula weight5098034.7
*Water molecules are not included.

218853

PDB entries from 2024-04-24

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