Loading
PDBj
English日本語简体中文繁體中文한국어
✖
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help
SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

7D4I

Cryo-EM structure of 90S small ribosomal precursors complex with the DEAH-box RNA helicase Dhr1 (State F)

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
13AU3 snoRNApolymer333106487.31Saccharomyces cerevisiae S288C (Baker's yeast)
25A5' ETSpolymer700225543.11Saccharomyces cerevisiae S288C (Baker's yeast)
3SA18S rRNApolymer1812583714.61Saccharomyces 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)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)RP5,S7,YS6
6SG40S ribosomal protein S5polymer22525072.61UniProt (P26783)
Pfam (PF00177)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP14,S2,YS8
7SH40S ribosomal protein S6-Apolymer23627054.51UniProt (P0CX37)
Pfam (PF01092)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP9,S10,YS4
8SI40S ribosomal protein S7-Apolymer19021658.21UniProt (P26786)
Pfam (PF01251)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP30,RP40
9SJ40S ribosomal protein S8-Apolymer20022537.81UniProt (P0CX39)
Pfam (PF01201)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)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)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)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
15ST40S ribosomal protein S18-Apolymer14617071.61UniProt (P0CX55)
Pfam (PF00416)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps18, Small ribosomal subunit protein uS13-A
16SU40S ribosomal protein S19-Apolymer14415942.11UniProt (P07280)
Pfam (PF01090)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP55A,S16a,Small ribosomal subunit protein eS19-A,YP45,YS16A
17SX40S 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
18SY40S ribosomal protein S23-Apolymer14516073.91UniProt (P0CX29)
Pfam (PF00164)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps23, RP37,S28,YS14
19SZ40S ribosomal protein S24-Apolymer13515362.81UniProt (P0CX31)
Pfam (PF01282)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps24,RP50
20Sc40S ribosomal protein S27-Apolymer828893.41UniProt (P35997)
Pfam (PF01667)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps27, RP61,YS20
21Sd40S ribosomal protein S28-Apolymer677605.81UniProt (Q3E7X9)
Pfam (PF01200)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rps28, S33,YS27
223B, 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
233DNucleolar 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
243ENucleolar protein 58polymer51157060.31UniProt (Q12499)
Pfam (PF01798)
Pfam (PF08156)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nucleolar protein 5
253FRibosomal RNA-processing protein 9polymer57365147.01UniProt (Q06506)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rrp9
263G, 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
27A4U3 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
28A5U3 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
29A8U3 small nucleolar RNA-associated protein 8polymer71380269.61UniProt (P53276)
Pfam (PF10395)
Pfam (PF22542)
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
30A9U3 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
31AEU3 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
32AFU3 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
33AGNET1-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
34B1Periodic 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
35B2U3 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
36B3U3 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
37B8U3 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
38BEU3 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
39B6U3 small nucleolar RNA-associated protein 6polymer44052495.31UniProt (Q02354)
Pfam (PF08640)
Pfam (PF05843)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp6, U3 snoRNA-associated protein 6,U three protein 6
405BBud 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
415CU3 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
425DU3 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
435EU3 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
445FU3 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
455GU3 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
465HSomething 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
475IProtein 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
485JrRNA-processing protein FCF2polymer21725689.21UniProt (Q12035)
Pfam (PF08698)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)FAF1 copurifying factor 2
495KrRNA-processing protein FCF1polymer18921649.71UniProt (Q05498)
Pfam (PF04900)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp24, FAF1-copurifying factor 1
50RDrRNA biogenesis protein RRP5polymer1729193411.41UniProt (Q05022)
Pfam (PF00575)
Pfam (PF05843)
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
51REU3 small nucleolar RNA-associated protein 22polymer1237140660.11UniProt (P53254)
Pfam (PF17403)
Pfam (PF17404)
Pfam (PF17405)
Pfam (PF17406)
Pfam (PF17407)
Pfam (PF03813)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Utp22, U3 snoRNA-associated protein 22,U three protein 22
52RFRibosomal RNA-processing protein 7polymer29734526.41UniProt (P25368)
Pfam (PF17799)
Pfam (PF12923)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rrp7
53RG, 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
54RJRibosome biogenesis protein BMS1polymer1183135792.31UniProt (Q08965)
Pfam (PF00004)
Pfam (PF08142)
Pfam (PF04950)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Bms1
55RKRNA 3'-terminal phosphate cyclase-like proteinpolymer36740220.61UniProt (Q08096)
Pfam (PF01137)
Pfam (PF05189)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rcl1
56RNNucleolar 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
57RONucleolar 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
58RPU3 small nucleolar RNA-associated protein 20polymer2493287915.51UniProt (P35194)
Pfam (PF20416)
Pfam (PF07539)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)U3 snoRNA-associated protein 20,U three protein 20
59RQU3 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
60RSEssential nuclear protein 1polymer48054879.11UniProt (P38333)
Pfam (PF05291)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
61RTPno1polymer32636356.51Saccharomyces cerevisiae S288C (Baker's yeast)
62RWRegulator of rDNA transcription protein 14polymer20623898.31UniProt (P40470)
Pfam (PF17075)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Rrt14
63RZProbable ATP-dependent RNA helicase DHR1polymer1267145171.41UniProt (Q04217)
Pfam (PF00270)
Pfam (PF00271)
Pfam (PF04408)
Pfam (PF21010)
Pfam (PF07717)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)DEAH box RNA helicase DHR1,Extracellular mutant protein 16
64X1Unassigned peptides 1polymer61152017.21Saccharomyces cerevisiae S288C (Baker's yeast)
65X2Unassigned peptides 2polymer69459080.81Saccharomyces cerevisiae S288C (Baker's yeast)
66R5Exosome 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
67R1Exosome 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
68R3Exosome complex component RRP43polymer39444060.91UniProt (P25359)
Pfam (PF01138)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Ribosomal RNA-processing protein 43
69R6Exosome 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
70R2Exosome complex component RRP42polymer26529085.21UniProt (Q12277)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Ribosomal RNA-processing protein 42
71M3Exosome complex component MTR3polymer25027604.01UniProt (P48240)
Pfam (PF01138)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)mRNA transport regulator 3
72R0Exosome 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
73r4Exosome 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
74C4Exosome 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
75R4Exosome 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
76r6Exosome 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
77R7Exosome 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
78M4ATP-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
79M6M-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
80Sc, 5KZINC IONnon-polymer65.42Chemie (ZN)
81RJGUANOSINE-5'-TRIPHOSPHATEnon-polymer523.21Chemie (GTP)
82RJMAGNESIUM IONnon-polymer24.31Chemie (MG)
83RZADENOSINE-5'-DIPHOSPHATEnon-polymer427.21Chemie (ADP)
Sequence modifications
5K: 1 - 189 (UniProt: Q05498)
PDBExternal DatabaseDetails
Asn 138Asp 138variant
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains82
Total formula weight5298996.3
Non-Polymers*Number of molecules5
Total formula weight1105.5
All*Total formula weight5300101.8
*Water molecules are not included.

222624

PDB entries from 2024-07-17

PDB statisticsPDBj update infoContact PDBjnumon