7D5T

Cryo-EM structure of 90S preribosome with inactive Utp24 (state F1)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 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 preribosome with inactive Utp24 (state F1)

Ye, K.

To be published.

Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S1-AD [auth SC]255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1A, PLC1, RPS10A, YLR441C, L9753.9
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Entity ID: 5
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40S ribosomal protein S4-AE [auth SF]261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4A, RPS7B, YJR145C, J2186
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Entity ID: 6
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40S ribosomal protein S5F [auth SG]225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5, RPS2, YJR123W, J2045
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Entity ID: 7
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40S ribosomal protein S6-AG [auth SH]236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6A, RPS101, RPS10B, YPL090C, LPG18C
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Entity ID: 8
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40S ribosomal protein S7-AH [auth SI]190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7A, RPS30, YOR096W, YOR3177W
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Entity ID: 9
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40S ribosomal protein S8-AI [auth SJ]200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8A, RPS14A, YBL072C, YBL06.05, YBL0613
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Entity ID: 10
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40S ribosomal protein S9-AJ [auth SK]197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9A, RPS13A, YS11A, YPL081W
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Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
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40S ribosomal protein S11-AK [auth SM]156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11A, RPS18A, YDR025W, YD9813.03
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Entity ID: 12
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40S ribosomal protein S13L [auth SO]151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13, RPS13C, YDR064W, D4252, YD9609.18
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Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
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40S ribosomal protein S14-AM [auth SP]137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14A, CRY1, RPL59, YCR031C, YCR31C
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Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
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40S ribosomal protein S16-AN [auth SR]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16A, RP61R, YMR143W, YM9375.12
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Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
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40S ribosomal protein S22-BO [auth SX]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22B, RPS24B, YLR367W, L8039.6
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Entity ID: 16
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40S ribosomal protein S23-AP [auth SY]145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23A, RPS28A, YGR118W, G6178
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Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
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40S ribosomal protein S24-AQ [auth SZ]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24A, RPS24EA, YER074W
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Entity ID: 18
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40S ribosomal protein S27-AR [auth Sc]82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27A, YKL156W
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Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
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40S ribosomal protein S28-AS [auth Sd]67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28A, RPS33, RPS33A, YOR167C, O3600
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
rRNA 2'-O-methyltransferase fibrillarinT [auth 3B],
U [auth 3C]		327Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP1, LOT3, YDL014W, D2870
EC: 2.1.1
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Find proteins for P15646 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleolar protein 56V [auth 3D]504Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP56, SIK1, YLR197W, L8167.9
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Find proteins for Q12460 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
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Nucleolar protein 58W [auth 3E]511Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP58, NOP5, YOR310C, O6108
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Find proteins for Q12499 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
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Ribosomal RNA-processing protein 9X [auth 3F]573Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP9, YPR137W
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Find proteins for Q06506 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinY [auth 3G],
Z [auth 3H]		126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU13, YEL026W
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Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 25
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U3 small nucleolar RNA-associated protein 5AA [auth A5]643Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP5, YDR398W, D9509.17
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Find proteins for Q04177 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
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U3 small nucleolar RNA-associated protein 10BA [auth AE]1,769Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP10, YJL109C, J0808
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Entity ID: 27
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NET1-associated nuclear protein 1CA [auth AG]896Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NAN1, UTP17, YPL126W
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Find proteins for Q02931 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
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Periodic tryptophan protein 2DA [auth B1]900Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PWP2, UTP1, YCR057C, YCR55C/YCR57C/YCR58C
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Find proteins for P25635 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
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U3 small nucleolar RNA-associated protein 12EA [auth B2]943Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIP2, UTP12, YLR129W, L3116, L9233.1
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Find proteins for Q12220 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
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U3 small nucleolar RNA-associated protein 13FA [auth B3]817Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP13, YLR222C
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Find proteins for Q05946 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
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U3 small nucleolar RNA-associated protein 18GA [auth B8]594Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP18, YJL069C, HRE594, J1098
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Find proteins for P40362 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
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U3 small nucleolar RNA-associated protein 21HA [auth BE]939Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP21, YLR409C, L8084.22
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Find proteins for Q06078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
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U3 small nucleolar RNA-associated protein 6IA [auth B6]440Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP6, YDR449C, D9461.34
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Find proteins for Q02354 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
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U3 small nucleolar RNA-associated protein 7JA [auth 5C]554Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP7, KRE31, YER082C
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Entity ID: 35
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U3 small nucleolar RNA-associated protein 11KA [auth 5D]250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP11, YKL099C, YKL449
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Find proteins for P34247 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 36
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U3 small nucleolar RNA-associated protein MPP10LA [auth 5E]593Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MPP10, YJR002W, J1411, YJR83.5
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Entity ID: 37
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U3 small nucleolar ribonucleoprotein protein IMP3MA [auth 5F]183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP3, YHR148W
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Entity ID: 38
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U3 small nucleolar ribonucleoprotein protein IMP4NA [auth 5G]290Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP4, YNL075W, N2353
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Something about silencing protein 10OA [auth 5H]610Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SAS10, UTP3, YDL153C, D1545
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Entity ID: 40
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Protein SOF1PA [auth 5I]489Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SOF1, YLL011W, L1339
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Entity ID: 41
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rRNA-processing protein FCF2QA [auth 5J]217Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FCF2, YLR051C, L2128
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rRNA-processing protein FCF1RA [auth 5K]189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FCF1, YDR339C, D9651.9
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Find proteins for Q05498 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 43
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rRNA biogenesis protein RRP5SA [auth RD]1,729Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP5, FMI1, YMR229C, YM9959.11C
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Find proteins for Q05022 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 44
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U3 small nucleolar RNA-associated protein 22TA [auth RE]1,237Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP22, YGR090W
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Find proteins for P53254 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 7UA [auth RF]297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP7, YCL031C, YCL184, YCL31C
UniProt
Find proteins for P25368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 46
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Ribosome biogenesis protein BMS1VA [auth RJ]1,183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BMS1, YPL217C
UniProt
Find proteins for Q08965 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 47
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RNA 3'-terminal phosphate cyclase-like proteinWA [auth RK]367Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RCL1, RTC1, YOL010W
UniProt
Find proteins for Q08096 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
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Nucleolar complex protein 14XA [auth RN]810Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP14, UTP2, YDL148C, D1566
UniProt
Find proteins for Q99207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
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U3 small nucleolar RNA-associated protein 20YA [auth RP]2,493Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP20, YBL004W, YBL0101
UniProt
Find proteins for P35194 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
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U3 small nucleolar RNA-associated protein 14ZA [auth RQ]899Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP14, YML093W
UniProt
Find proteins for Q04500 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
Pno1AB [auth RT]326Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 52
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Probable ATP-dependent RNA helicase DHR1BB [auth RZ]1,267Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ECM16, DHR1, YMR128W, YM9553.04
EC: 3.6.4.13
UniProt
Find proteins for Q04217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
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Unassigned peptides 1CB [auth X1]300Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 1
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U3 snoRNAA [auth 3A]333Saccharomyces cerevisiae S288C
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Entity ID: 2
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5' ETSB [auth 5A]700Saccharomyces cerevisiae S288C
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Entity ID: 3
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18S rRNAC [auth SA]1,812Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download Ideal Coordinates CCD File 
FB [auth RJ]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
ADP
Query on ADP
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HB [auth RZ]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
ZN
Query on ZN
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DB [auth Sc],
EB [auth 5K]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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GB [auth RJ]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



View more in-depth experimental data
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