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- PDB-5wlc: The complete structure of the small subunit processome -

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Basic information

Entry
Database: PDB / ID: 5wlc
TitleThe complete structure of the small subunit processome
Components
  • 18S pre-rRNA
  • 5' ETS
  • Bms1
  • Bud21
  • Emg1
  • Enp1
  • Enp2
  • Faf1
  • Fcf2
  • Imp3
  • Imp4
  • Kre33
  • Krr1
  • Lcp5
  • Mpp10
  • Noc4
  • Nop1
  • Nop14
  • Nop56
  • Nop58
  • Pno1
  • Rcl1
  • Rrp5
  • Rrp7
  • Rrp9
  • Rrt14
  • Sas10
  • Snu13
  • Sof1
  • U3 snoRNA
  • Unassigned peptides
  • Utp1
  • Utp10
  • Utp11
  • Utp12
  • Utp13
  • Utp14
  • Utp15
  • Utp17
  • Utp18
  • Utp20
  • Utp21
  • Utp22
  • Utp24
  • Utp30
  • Utp4
  • Utp5
  • Utp6
  • Utp7
  • Utp8
  • Utp9
  • rpS11_uS17
  • rpS13_uS15
  • rpS14_uS11
  • rpS16_uS9
  • rpS18_uS13
  • rpS22_uS8
  • rpS23_uS12
  • rpS24_eS24
  • rpS28_eS28
  • rpS4_eS4
  • rpS5_uS7
  • rpS6_eS6
  • rpS7_eS7
  • rpS8_eS8
  • rpS9_uS4
KeywordsRIBOSOME / Ribosome assembly
Function / homologytRNA methyltransferase complex GCD14 subunit / WD40-repeat-containing domain superfamily / Ribosome biogenesis protein Bms1, N-terminal / rRNA-processing protein Fcf1, PIN domain / RNA 3'-terminal phosphate cyclase domain superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S7 domain superfamily / K Homology domain, type 1 superfamily / RNA 3'-terminal phosphate cyclase, insert domain superfamily ...tRNA methyltransferase complex GCD14 subunit / WD40-repeat-containing domain superfamily / Ribosome biogenesis protein Bms1, N-terminal / rRNA-processing protein Fcf1, PIN domain / RNA 3'-terminal phosphate cyclase domain superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S7 domain superfamily / K Homology domain, type 1 superfamily / RNA 3'-terminal phosphate cyclase, insert domain superfamily / Nop domain superfamily / ATPase family associated with various cellular activities (AAA) / Ribosomal protein S8 superfamily / Nrap protein, domain 6 / Nrap protein, domain 5 / Nrap protein, domain 4 / Nrap protein, domain 3 / Nrap protein, domain 2 / Nrap protein domain 1 / RNA cytidine acetyltransferase NAT10 / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S4/S9 N-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein L1p/L10e family / Fibrillarin / Ribosomal protein S7e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S8e / Ribosomal protein S28e / RNA 3'-terminal phosphate cyclase / Ribosomal protein S6e / Ribosomal family S4e / S1 RNA binding domain / Ribosomal protein S12/S23 / KOW motif / Ribosomal protein S13/S18 / Ribosomal protein S11 / Ribosomal protein S8 / WD domain, G-beta repeat / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal protein S7p/S5e / TmcA/NAT10/Kre33 / 40S ribosomal protein S4, C-terminal domain / S4 domain / G-protein beta WD-40 repeat / Ribosomal protein S8e/ribosomal biogenesis NSA2 / U3 small nucleolar RNA-associated protein 10 / HEAT, type 2 / Fibrillarin, conserved site / RNA 3'-terminal phosphate cyclase-like, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S17, conserved site / RNA-binding domain, S1 / WD40 repeat, conserved site / U3 small nucleolar RNA-associated protein 15, C-terminal / Sas10 C-terminal domain / U3 small nucleolar RNA-associated protein 8 / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein S8e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S4/S9 / Ribosomal protein S15P / Regulator of rDNA transcription 14 / Ribosomal protein L1/ribosomal biogenesis protein / Bms1/Tsr1-type G domain / 50S ribosomal protein L30e-like / S-adenosyl-L-methionine-dependent methyltransferase / PIN-like domain superfamily / Alpha/beta knot methyltransferases / tRNA (guanine-N1-)-methyltransferase, N-terminal / Helix hairpin bin domain superfamily / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1-like / Possible tRNA binding domain / P-loop containing nucleoside triphosphate hydrolase / Nucleolar complex protein 4 / Periodic tryptophan protein 2 / Anaphase-promoting complex subunit 4, WD40 domain / Ribosomal RNA-processing protein 7 / Ribosomal RNA assembly KRR1 / Ribosomal protein S7 domain / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S24e / snoRNA binding domain, fibrillarin / Ribosomal S11, conserved site / Ribosomal protein S4 signature. / HEAT repeat profile. / RNA 3'-terminal phosphate cyclase signature. / Ribosomal protein S8e signature. / Ribosomal protein L7Ae signature. / Ribosomal protein S28e signature. / Ribosomal protein S7e signature. / Trp-Asp (WD) repeats signature. / Ribosomal protein S13 signature.
Function and homology information
Specimen sourceSaccharomyces cerevisiae BY4741 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsBarandun, J. / Chaker-Margot, M. / Hunziker, M. / Klinge, S.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: The complete structure of the small-subunit processome.
Authors: Jonas Barandun / Malik Chaker-Margot / Mirjam Hunziker / Kelly R Molloy / Brian T Chait / Sebastian Klinge
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 26, 2017 / Release: Sep 27, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 27, 2017Structure modelrepositoryInitial release
1.1Oct 11, 2017Structure modelDatabase referencescitation_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
1.2Oct 18, 2017Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization
1.3Nov 22, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
L0: 5' ETS
L1: 18S pre-rRNA
L2: U3 snoRNA
L3: rpS18_uS13
L4: rpS4_eS4
L5: rpS5_uS7
L6: rpS6_eS6
L7: rpS7_eS7
L8: rpS8_eS8
L9: rpS9_uS4
LC: rpS16_uS9
LD: rpS11_uS17
LE: rpS22_uS8
LF: rpS24_eS24
LG: rpS28_eS28
LH: Utp17
LI: Utp8
LJ: Utp15
LK: Utp9
LL: Utp5
LM: Utp10
LN: Utp4
LO: Utp1
LP: Utp6
LQ: Utp12
LR: Utp13
LS: Utp18
LT: Utp21
LU: Sof1
LV: Enp2
LW: Utp7
LX: Kre33
LY: Kre33
LZ: Imp3
NA: Mpp10
NB: Sas10
NC: Lcp5
ND: Bud21
NE: Faf1
NF: rpS13_uS15
NG: rpS14_uS11
NH: Utp22
NI: Rrp7
NJ: Rrp5
NK: Krr1
SA: Nop56
SB: Nop58
SC: Nop1
SD: Nop1
SE: Snu13
SF: Snu13
SG: Rrp9
SH: Rcl1
SI: Bms1
SJ: Emg1
SK: Emg1
SL: Utp24
SM: Imp4
SN: Utp30
SO: Pno1
SP: Utp20
SQ: Fcf2
SR: rpS23_uS12
SS: Utp14
ST: Nop14
SU: Noc4
SV: Rrt14
SX: Unassigned peptides
SY: Utp11
SZ: Enp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,499,17571
Polyers4,499,11070
Non-polymers651
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules L0L1L2

#1: RNA chain 5' ETS


Mass: 225543.094 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: GenBank: 1262303
#2: RNA chain 18S pre-rRNA


Mass: 582052.438 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: GenBank: 874346701
#3: RNA chain U3 snoRNA


Mass: 106503.258 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: GenBank: 176452

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Protein/peptide , 63 types, 67 molecules L3L4L5L6L7L8L9LCLDLELFLGLHLILJLKLLLMLNLOLPLQLRLSLTLULVLWLXLY...

#4: Protein/peptide rpS18_uS13


Mass: 16773.332 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0CX55
#5: Protein/peptide rpS4_eS4


Mass: 29469.330 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0CX35
#6: Protein/peptide rpS5_uS7


Mass: 25072.600 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: A0A1L4AA68
#7: Protein/peptide rpS6_eS6


Mass: 27054.486 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0CX37
#8: Protein/peptide rpS7_eS7


Mass: 21658.209 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P26786
#9: Protein/peptide rpS8_eS8


Mass: 22537.803 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0CX39
#10: Protein/peptide rpS9_uS4


Mass: 22487.893 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: O13516
#11: Protein/peptide rpS16_uS9


Mass: 15877.490 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0CX51
#12: Protein/peptide rpS11_uS17


Mass: 17785.934 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0CX47
#13: Protein/peptide rpS22_uS8


Mass: 14650.062 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0C0W1
#14: Protein/peptide rpS24_eS24


Mass: 15362.848 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0CX31
#15: Protein/peptide rpS28_eS28


Mass: 7605.847 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q3E7X9
#16: Protein/peptide Utp17


Mass: 100960.445 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q02931
#17: Protein/peptide Utp8


Mass: 65572.977 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P53276
#18: Protein/peptide Utp15 /


Mass: 57765.289 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q04305
#19: Protein/peptide Utp9


Mass: 64378.512 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P38882
#20: Protein/peptide Utp5


Mass: 72079.445 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q04177
#21: Protein/peptide Utp10


Mass: 200020.719 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P42945
#22: Protein/peptide Utp4


Mass: 87316.500 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q06679
#23: Protein/peptide Utp1


Mass: 104097.039 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P25635
#24: Protein/peptide Utp6 /


Mass: 48437.402 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q02354
#25: Protein/peptide Utp12


Mass: 105037.648 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q12220
#26: Protein/peptide Utp13


Mass: 75035.867 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q05946
#27: Protein/peptide Utp18 /


Mass: 66494.250 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P40362
#28: Protein/peptide Utp21


Mass: 104927.844 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q06078
#29: Protein/peptide Sof1


Mass: 56888.918 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P33750
#30: Protein/peptide Enp2


Mass: 81864.172 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P48234
#31: Protein/peptide Utp7


Mass: 62418.570 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P40055
#32: Protein/peptide Kre33


Mass: 95337.062 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
References: UniProt: P53914, Transferring groups other than amino-acyl groups
#33: Protein/peptide Imp3 /


Mass: 21928.529 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P32899
#34: Protein/peptide Mpp10


Mass: 67042.492 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P47083
#35: Protein/peptide Sas10


Mass: 69705.703 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q12136
#36: Protein/peptide Lcp5


Mass: 40864.391 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P40079
#37: Protein/peptide Bud21


Mass: 23835.627 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q08492
#38: Protein/peptide Faf1 /


Mass: 38173.699 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P40546
#39: Protein/peptide rpS13_uS15


Mass: 17059.945 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P05756
#40: Protein/peptide rpS14_uS11


Mass: 14562.655 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P06367
#41: Protein/peptide Utp22


Mass: 140660.141 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P53254
#42: Protein/peptide Rrp7


Mass: 34526.441 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P25368
#43: Protein/peptide Rrp5


Mass: 193411.422 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q05022
#44: Protein/peptide Krr1 /


Mass: 37226.254 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: B3LU25
#45: Protein/peptide Nop56


Mass: 56394.863 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q12460
#46: Protein/peptide Nop58 /


Mass: 53814.520 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q12499
#47: Protein/peptide Nop1


Mass: 34525.418 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P15646, Methyltransferases
#48: Protein/peptide Snu13


Mass: 13582.855 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P39990
#49: Protein/peptide Rrp9 /


Mass: 65146.969 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q06506
#50: Protein/peptide Rcl1 /


Mass: 40220.559 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q08096
#51: Protein/peptide Bms1


Mass: 135152.938 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q08965
#52: Protein/peptide Emg1 /


Mass: 27936.461 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
References: UniProt: Q06287, rRNA small subunit pseudouridine methyltransferase Nep1
#53: Protein/peptide Utp24


Mass: 21650.729 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q05498
#54: Protein/peptide Imp4 /


Mass: 33536.168 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P53941
#55: Protein/peptide Utp30


Mass: 31668.939 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P36144
#56: Protein/peptide Pno1


Mass: 30380.623 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q99216
#57: Protein/peptide Utp20 /


Mass: 83590.180 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
#58: Protein/peptide Fcf2


Mass: 25689.240 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q12035
#59: Protein/peptide rpS23_uS12


Mass: 16073.896 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0CY39
#60: Protein/peptide Utp14


Mass: 101101.461 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q04500
#61: Protein/peptide Nop14


Mass: 85993.961 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q99207
#62: Protein/peptide Noc4


Mass: 58369.125 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q06512
#63: Protein/peptide Rrt14


Mass: 21036.877 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: B5VKI1, UniProt: E9P9B2
#64: Protein/peptide Unassigned peptides


Mass: 8783.818 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
#65: Protein/peptide Utp11


Mass: 29806.348 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: B5VM59
#66: Protein/peptide Enp1


Mass: 55207.422 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P38333

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Non-polymers , 1 types, 1 molecules

#67: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Small subunit processome / Type: COMPLEX
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66
Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast)
Buffer solutionpH: 7.7
Buffer component
IDConc.NameFormulaBuffer ID
150 mMTris(HOCH2)3CNH21
2150 mMsodium chlorideNaCl1
31 mMEDTA(HO2CCH2)2NCH2CH2N(CH2CO2H)21
40.1 %Triton X-1001
55 mMbiotin1
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 50 mA / Grid material: COPPER / Grid mesh size: 400 / Grid type: Ted Pella Inc.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 / Nominal defocus max: 2600 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 1.56 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 4 / Number of real images: 10029
Image scansMovie frames/image: 32

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Processing

EM software
IDNameVersionCategory
1RELION2particle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
7Coot0.8.9model fitting
9RELION2initial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION23D reconstruction
13PHENIX1.12rc1model refinement
CTF correctionType: NONE
Particle selectionNumber of particles selected: 772120
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 284213 / Number of class averages: 2 / Symmetry type: POINT
Atomic model buildingOverall b value: 338.9 / Ref protocol: OTHER / Ref space: REAL

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EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

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Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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