6FT6

Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure of the nuclear exosome captured on a maturing preribosome.

Schuller, J.M., Falk, S., Fromm, L., Hurt, E., Conti, E.

(2018) Science 360: 219-222

  • DOI: 10.1126/science.aar5428
  • Primary Citation of Related Structures:  
    6FT6, 6FSZ

  • PubMed Abstract: 

    • The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex captured on a precursor large ribosomal subunit (pre-60 S ) during 7 S -to-5 ...

    The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex captured on a precursor large ribosomal subunit (pre-60 S ) during 7 S -to-5.8 S rRNA processing. The cofactors of the nuclear exosome are sandwiched between the ribonuclease core complex (Exo-10) and the remodeled "foot" structure of the pre-60 S particle, which harbors the 5.8 S rRNA precursor. The exosome-associated helicase Mtr4 recognizes the preribosomal substrate by docking to specific sites on the 25 S rRNA, captures the 3' extension of the 5.8 S rRNA, and channels it toward Exo-10. The structure elucidates how the exosome forms a structural and functional unit together with its massive pre-60 S substrate to process rRNA during ribosome maturation.

    Organizational Affiliation: 

    Department of Structural Cell Biology, Max Planck Institute (MPI) for Biochemistry, Munich, Germany. conti@biochem.mpg.de ed.hurt@bzh.uni-heidelberg.de.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L2-AB [auth A]254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2A, RPL5B, YFR031C-A, YFR031BC
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Entity ID: 3
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60S ribosomal protein L3C [auth B]387Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3, MAK8, TCM1, YOR063W, YOR29-14
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Entity ID: 4
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60S ribosomal protein L4-AD [auth C]362Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4A, RPL2, RPL2A, YBR031W, YBR0315
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Entity ID: 5
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60S ribosomal protein L5E [auth D]297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5, RPL1, RPL1A, YPL131W, LPI14W
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Entity ID: 6
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60S ribosomal protein L6-AF [auth E]176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6A, RPL17A, YL16A, YML073C
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Entity ID: 7
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60S ribosomal protein L7-AG [auth F]244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7A, RPL6A, RPL8A, YL8A, YGL076C
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Entity ID: 8
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60S ribosomal protein L8-AH [auth G]256Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8A, MAK7, RPL4A, YHL033C
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Entity ID: 9
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60S ribosomal protein L9-AI [auth H]191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9A, RPL8A, RPL9, YGL147C
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Entity ID: 10
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Bud site selection protein 20J [auth I]166Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD20, YLR074C
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Entity ID: 11
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60S ribosomal protein L11-AK [auth J]174Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11A, RP39A, RPL16A, YPR102C, P8283.14
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Entity ID: 12
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60S ribosomal protein L13-AL199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13A, YDL082W
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Entity ID: 13
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60S ribosomal protein L14-AM138Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14A, YKL006W, YKL153
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Entity ID: 14
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60S ribosomal protein L15-AN204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15A, RPL10A, RPL13A, YL10A, YLR029C
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Entity ID: 15
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60S ribosomal protein L16-AO199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16A, RPL13, RPL21A, YIL133C
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Entity ID: 16
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60S ribosomal protein L17-AP184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17A, RPL17, RPL20A, YKL180W
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Entity ID: 17
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60S ribosomal protein L18-AQ186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18A, RP28A, YOL120C
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Entity ID: 18
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60S ribosomal protein L19-AR189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19A, RPL23A, YL14A, YBR084C-A, YBR084BC
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Entity ID: 19
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60S ribosomal protein L20-AS172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20A, RPL18A, RPL18A2, YMR242C, YM9408.04C
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Entity ID: 20
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60S ribosomal protein L21-AT160Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21A, URP1, YBR191W, YBR1401
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Entity ID: 21
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60S ribosomal protein L22-AU121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22A, YLR061W, L2168
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Entity ID: 22
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60S ribosomal protein L23-AV137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23A, RPL17A, RPL17AA, YBL087C, YBL0713
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Entity ID: 23
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Ribosome assembly factor MRT4W236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MRT4, YKL009W, YKL160
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Entity ID: 24
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60S ribosomal protein L25X142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25, YOL127W
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Entity ID: 25
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60S ribosomal protein L26-AY127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26A, RPL26, RPL33A, YLR344W, L8300.4
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Entity ID: 26
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60S ribosomal protein L27-AZ136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27A, RPL27, YHR010W
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Entity ID: 27
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60S ribosomal protein L28AA [auth a]149Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28, CYH2, YGL103W
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Entity ID: 28
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Nucleolar GTP-binding protein 1BA [auth b]647Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOG1, YPL093W, LPG15W
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Entity ID: 29
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60S ribosomal protein L30CA [auth c]105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30, RPL32, YGL030W
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Entity ID: 30
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60S ribosomal protein L31-ADA [auth d]113Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31A, RPL34, RPL34A, YDL075W, D2478
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Entity ID: 31
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60S ribosomal protein L32EA [auth e]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32, YBL092W, YBL0838
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Entity ID: 32
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60S ribosomal protein L33-AFA [auth f]107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33A, RPL37A, YPL143W, LPI4W, P2625
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Entity ID: 33
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60S ribosomal protein L34-AGA [auth g]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34A, YER056C-A, YER056BC
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Entity ID: 34
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60S ribosomal protein L35-AHA [auth h]120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35A, SOS1, YDL191W, D1249
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Entity ID: 35
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60S ribosomal protein L36-AIA [auth i]100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36A, RPL39A, YMR194W, YM9646.06
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Entity ID: 36
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60S ribosomal protein L37-AJA [auth j]88Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37A, RPL35A, YLR185W, L9470.6
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Entity ID: 37
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60S ribosomal protein L38KA [auth k]78Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38, YLR325C, L8543.2
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Entity ID: 38
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60S ribosomal protein L39LA [auth l]51Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39, RPL46, SPB2, YJL189W, J0360
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Entity ID: 39
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Nucleolar GTP-binding protein 2MA [auth m]486Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOG2, YNR053C, N3484
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Entity ID: 40
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Pescadillo homologNA [auth n]605Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP7, RRP13, YPH1, YGR103W
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Entity ID: 41
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60S ribosomal protein L43-AOA [auth p]92Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43A, YPR043W, YP9499.02
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Entity ID: 42
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Ribosome biogenesis protein NSA2PA [auth r]261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NSA2, YER126C, SYGP-ORF47
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Entity ID: 43
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Nuclear GTP-binding protein NUG1QA [auth s]520Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUG1, YER006W
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Entity ID: 44
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Ribosome biogenesis protein RLP24RA [auth u]199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RLP24, YLR009W
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Entity ID: 45
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Ribosome biogenesis protein RPF2SA [auth v]344Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPF2, YKR081C, YKR401
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Entity ID: 46
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Regulator of ribosome biosynthesisTA [auth w]203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRS1, YOR294W
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Entity ID: 47
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Ribosome assembly protein 4UA [auth x]515Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSA4, YCR072C, YCR72C
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Entity ID: 48
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Eukaryotic translation initiation factor 6VA [auth y]245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF6, CDC95, YPR016C, LPZ15C
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Entity ID: 49
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UPF0642 protein YBL028CWA [auth z]106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YBL028C, YBL0423
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Entity ID: 52
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Probable metalloprotease ARX1ZA [auth 4]593Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARX1, YDR101C, YD8557.10c
EC: 3
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
rRNA-processing protein CGR1AB [auth 5]120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CGR1, YGL029W
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP6BB [auth KK]733Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP6, UNC733, YOR001W
EC: 3.1.13
UniProt
Find proteins for Q12149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex protein LRP1CB [auth LL]184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LRP1, RRP47, YC1D, YHR081W
UniProt
Find proteins for P38801 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DOB1DB [auth MM]1011Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTR4, DOB1, YJL050W, J1158
EC: 3.6.4.13
UniProt
Find proteins for P47047 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
MPP6EB [auth NN]11Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
7S ribosomal RNAA [auth 2]162Saccharomyces cerevisiae S288C
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Entity ID: 50
MoleculeChainsLengthOrganismImage
25S ribosomal RNAXA [auth 1]3396Saccharomyces cerevisiae S288C
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Entity ID: 51
MoleculeChainsLengthOrganismImage
5S ribosomal RNAYA [auth 3]121Saccharomyces cerevisiae S288C
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
ERCBelgiumEXORICO

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-11
    Changes: Other