7D4I

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structure of 90S small ribosomal precursors complex with Dhr1

Ye, K.

To be published.

Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-AD [auth SC]255Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AE [auth SF]261Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5F [auth SG]225Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AG [auth SH]236Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AH [auth SI]190Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AI [auth SJ]200Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AJ [auth SK]197Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AK [auth SM]156Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13L [auth SO]151Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AM [auth SP]137Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AN [auth SR]143Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AO [auth ST]146Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-AP [auth SU]144Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-BQ [auth SX]130Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AR [auth SY]145Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AS [auth SZ]135Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AT [auth Sc]82Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-AU [auth Sd]67Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA 2'-O-methyltransferase fibrillarinV [auth 3B],
W [auth 3C]
327Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1
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Find proteins for P15646 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 56X [auth 3D]504Saccharomyces cerevisiae S288CMutation(s): 0 
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Find proteins for Q12460 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 58Y [auth 3E]511Saccharomyces cerevisiae S288CMutation(s): 0 
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Find proteins for Q12499 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 9Z [auth 3F]573Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinAA [auth 3G],
BA [auth 3H]
126Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 4CA [auth A4]776Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q06679 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 5DA [auth A5]643Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 8EA [auth A8]713Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P53276 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 9FA [auth A9]575Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38882 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 10GA [auth AE]1,769Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 15HA [auth AF]513Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NET1-associated nuclear protein 1IA [auth AG]896Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q02931 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Periodic tryptophan protein 2JA [auth B1]900Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P25635 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 12KA [auth B2]943Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12220 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 13LA [auth B3]817Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 18MA [auth B8]594Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 21NA [auth BE]939Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q06078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 6OA [auth B6]440Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Bud site selection protein 21PA [auth 5B]214Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q08492 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 7QA [auth 5C]554Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40055 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 11RA [auth 5D]250Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P34247 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein MPP10SA [auth 5E]593Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P47083 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP3TA [auth 5F]183Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP4UA [auth 5G]290Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P53941 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Something about silencing protein 10VA [auth 5H]610Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12136 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SOF1WA [auth 5I]489Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P33750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF2XA [auth 5J]217Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12035 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF1YA [auth 5K]189Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q05498 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA biogenesis protein RRP5ZA [auth RD]1,729Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q05022 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 22AB [auth RE]1,237Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P53254 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 7BB [auth RF]297Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P25368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA small subunit methyltransferase NEP1CB [auth RG],
DB [auth RH]
252Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1.260
UniProt
Find proteins for Q06287 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BMS1EB [auth RJ]1,183Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q08965 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like proteinFB [auth RK]367Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q08096 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 14GB [auth RN]810Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q99207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 4HB [auth RO]552Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q06512 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 20IB [auth RP]2,493Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P35194 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 14JB [auth RQ]899Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q04500 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Essential nuclear protein 1KB [auth RS]480Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38333 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Pno1LB [auth RT]326Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Regulator of rDNA transcription protein 14MB [auth RW]206Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40470 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DHR1NB [auth RZ]1,267Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.13
UniProt
Find proteins for Q04217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned peptides 1OB [auth X1]611Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned peptides 2PB [auth X2]694Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP45QB [auth R5]305Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component SKI6RB [auth R1]246Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP43SB [auth R3]394Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P25359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP46TB [auth R6]223Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P53256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP42UB [auth R2]265Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component MTR3VB [auth M3]250Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P48240 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP40WB [auth R0]240Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q08285 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP4XB [auth r4]359Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component CSL4YB [auth C4]292Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P53859 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex exonuclease DIS3ZB [auth R4]1,001Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
UniProt
Find proteins for Q08162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP6AC [auth r6]733Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.1.13
UniProt
Find proteins for Q12149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex protein LRP1BC [auth R7]184Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38801 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DOB1CC [auth M4]1,073Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.13
UniProt
Find proteins for P47047 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
M-phase phosphoprotein 6 homologDC [auth M6]186Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P53725 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
MoleculeChains LengthOrganismImage
U3 snoRNAA [auth 3A]333Saccharomyces cerevisiae S288C
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Entity ID: 2
MoleculeChains LengthOrganismImage
5' ETSB [auth 5A]700Saccharomyces cerevisiae S288C
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Entity ID: 3
MoleculeChains LengthOrganismImage
18S rRNAC [auth SA]1,812Saccharomyces cerevisiae S288C
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China91940302, 91540201, 31430024, 31325007
Chinese Academy of SciencesChinaXDB08010203

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release