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- PDB-6c0f: Yeast nucleolar pre-60S ribosomal subunit (state 2) -

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Basic information

Entry
Database: PDB / ID: 6c0f
TitleYeast nucleolar pre-60S ribosomal subunit (state 2)
Components
  • (60S ribosomal protein ...) x 19
  • (Ribosomal RNA-processing protein ...) x 3
  • (Ribosome biogenesis protein ...) x 7
  • 5.8S rRNA5.8S ribosomal RNA
  • ATP-dependent RNA helicase HAS1
  • Brx1-associated peptide
  • Eukaryotic translation initiation factor 6
  • ITS2Internal transcribed spacer
  • Nucleolar GTP-binding protein 1
  • Nucleolar protein 16Nucleolus
  • Pescadillo homolog
  • Proteasome-interacting protein CIC1
  • Protein MAK11
  • Protein MAK16
  • Ribosome production factor 1
  • Saccharomyces cerevisiae S288c 35S pre-ribosomal RNA miscRNA
  • rRNA-processing protein EBP2
KeywordsRIBOSOME / Pre-60S / ribosome biogenesis / LSU processome
Function / homology
Function and homology information


snoRNA release from pre-rRNA / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor ...snoRNA release from pre-rRNA / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / regulation of cell size / maturation of 5.8S rRNA / proteasome binding / ribosomal subunit export from nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / ATPase activator activity / Formation of a pool of free 40S subunits / ribosomal large subunit binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / ribonucleoprotein complex binding / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation initiation factor activity / small-subunit processome / proteasome complex / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / maintenance of translational fidelity / macroautophagy / protein catabolic process / ribosomal small subunit biogenesis / rRNA processing / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / protein-macromolecule adaptor activity / nuclear envelope / 5S rRNA binding / cytoplasmic translation / ATPase binding / cytosolic large ribosomal subunit / negative regulation of translation / RNA helicase activity / rRNA binding / RNA helicase / ribosome / structural constituent of ribosome / cell cycle / translation / mRNA binding / GTPase activity / GTP binding / nucleolus / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L36 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4280 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3450 / translation elongation factor selb, chain A, domain 4 / Ribosomal RNA-processing protein 14, N-terminal / 60S ribosome biogenesis protein Rrp14 / Ribosomal RNA-processing protein 15 / Rrp15p / Surfeit locus 6 / Ribosomal RNA-processing protein 14/surfeit locus protein 6, C-terminal domain ...Ribosomal protein L36 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4280 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3450 / translation elongation factor selb, chain A, domain 4 / Ribosomal RNA-processing protein 14, N-terminal / 60S ribosome biogenesis protein Rrp14 / Ribosomal RNA-processing protein 15 / Rrp15p / Surfeit locus 6 / Ribosomal RNA-processing protein 14/surfeit locus protein 6, C-terminal domain / Surfeit locus protein 6 / WDR74/Nsa1 / Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / Mak16 protein / Mak16 protein C-terminal region / Ribosome biogenesis protein 15, RNA recognition motif / Ribosomal protein L15e / Ribosomal protein L15 / Ribosomal Protein L15; Chain: K; domain 2 - #10 / Ribosomal Protein L3; Chain: B; domain 2, / Ribosomal Protein L3; Chain: B; domain 2, - #10 / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosome biogenesis protein BRX1 / DDX18/Has1, DEAD-box helicase domain / Ribosome biogenesis protein Nop16 / Ribosome biogenesis protein Nop16 / Domain of unknown function DUF4217 / Domain of unknown function (DUF4217) / DUF4217 / BOP1, N-terminal domain / WD repeat BOP1/Erb1 / BOP1NT (NUC169) domain / BOP1NT (NUC169) domain / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / U3 snoRNP protein/Ribosome production factor 1 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ubiquitin-like (UB roll) - #10 / Pescadillo / Pescadillo N-terminus / SH3 type barrels. - #30 / BRCT domain, a BRCA1 C-terminus domain / Ribosomal protein L30/S12 / NOG, C-terminal / Nucleolar GTP-binding protein 1 / NOGCT (NUC087) domain / Nucleolar GTP-binding protein 1, Rossman-fold domain / NOG1, N-terminal helical domain / Nucleolar GTP-binding protein 1 (NOG1) / NOG1 N-terminal helical domain / Brix domain / Brix domain / Brix domain profile. / Brix / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / : / DEAD-box RNA helicase Q motif profile. / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / GTP binding domain / Translation factors / metallochaperone-like domain / TRASH domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / breast cancer carboxy-terminal domain / 60S ribosomal protein L35 / Ribosomal protein L35Ae, conserved site / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L35A / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L35A superfamily / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L35Ae / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L6e signature. / Ribosomal protein L15e, conserved site / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L37e, conserved site / Ribosomal protein L3, domain 3, archaeal type superfamily
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein eL18A / Large ribosomal subunit protein uL29A / Large ribosomal subunit protein uL4A / Protein MAK16 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / Large ribosomal subunit protein uL13A / Ribosomal RNA-processing protein 1 / Ribosomal RNA-processing protein 14 / Large ribosomal subunit protein eL14A / Large ribosomal subunit protein eL32 / Proteasome-interacting protein CIC1 / Ribosome biogenesis protein SSF1 / Ribosome production factor 1 / Nucleolar protein 16 / Ribosome biogenesis protein RLP7 / Large ribosomal subunit protein eL37A / Ribosome biogenesis protein NSA1 / Pescadillo homolog / Ribosome biogenesis protein 15 / Large ribosomal subunit protein eL6A / Nucleolar GTP-binding protein 1 / ATP-dependent RNA helicase HAS1 / Ribosome biogenesis protein ERB1 / Ribosomal RNA-processing protein 15 / Ribosome biogenesis protein RLP24 / Ribosome biogenesis protein BRX1 / Eukaryotic translation initiation factor 6 / Large ribosomal subunit protein eL13A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae BY4741 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsSanghai, Z.A. / Miller, L. / Barandun, J. / Hunziker, M. / Chaker-Margot, M. / Klinge, S.
Funding support United States, Switzerland, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM123459 United States
Swiss National Science Foundation155515 Switzerland
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115327-Tan United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103314 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM109824 United States
CitationJournal: Nature / Year: 2018
Title: Modular assembly of the nucleolar pre-60S ribosomal subunit.
Authors: Zahra Assur Sanghai / Linamarie Miller / Kelly R Molloy / Jonas Barandun / Mirjam Hunziker / Malik Chaker-Margot / Junjie Wang / Brian T Chait / Sebastian Klinge /
Abstract: Early co-transcriptional events during eukaryotic ribosome assembly result in the formation of precursors of the small (40S) and large (60S) ribosomal subunits. A multitude of transient assembly ...Early co-transcriptional events during eukaryotic ribosome assembly result in the formation of precursors of the small (40S) and large (60S) ribosomal subunits. A multitude of transient assembly factors regulate and chaperone the systematic folding of pre-ribosomal RNA subdomains. However, owing to a lack of structural information, the role of these factors during early nucleolar 60S assembly is not fully understood. Here we report cryo-electron microscopy (cryo-EM) reconstructions of the nucleolar pre-60S ribosomal subunit in different conformational states at resolutions of up to 3.4 Å. These reconstructions reveal how steric hindrance and molecular mimicry are used to prevent both premature folding states and binding of later factors. This is accomplished by the concerted activity of 21 ribosome assembly factors that stabilize and remodel pre-ribosomal RNA and ribosomal proteins. Among these factors, three Brix-domain proteins and their binding partners form a ring-like structure at ribosomal RNA (rRNA) domain boundaries to support the architecture of the maturing particle. The existence of mutually exclusive conformations of these pre-60S particles suggests that the formation of the polypeptide exit tunnel is achieved through different folding pathways during subsequent stages of ribosome assembly. These structures rationalize previous genetic and biochemical data and highlight the mechanisms that drive eukaryotic ribosome assembly in a unidirectional manner.
History
DepositionDec 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
1: Saccharomyces cerevisiae S288c 35S pre-ribosomal RNA miscRNA
2: 5.8S rRNA
6: ITS2
A: Ribosome biogenesis protein NSA1
B: 60S ribosomal protein L3
C: 60S ribosomal protein L4-A
D: Protein MAK16
E: 60S ribosomal protein L6-A
F: 60S ribosomal protein L7-A
G: 60S ribosomal protein L8-A
I: Ribosome production factor 1
K: Proteasome-interacting protein CIC1
L: 60S ribosomal protein L13-A
M: 60S ribosomal protein L14-A
N: 60S ribosomal protein L15-A
O: 60S ribosomal protein L16-A
P: 60S ribosomal protein L17-A
Q: 60S ribosomal protein L18-A
S: 60S ribosomal protein L20-A
V: 60S ribosomal protein L23-A
W: Nucleolar GTP-binding protein 1
Y: 60S ribosomal protein L26-A
7: Nucleolar protein 16
8: Ribosomal RNA-processing protein 14
b: Ribosome biogenesis protein BRX1
e: 60S ribosomal protein L32
f: 60S ribosomal protein L33-A
h: 60S ribosomal protein L35-A
i: 60S ribosomal protein L36-A
j: 60S ribosomal protein L37-A
x: Brx1-associated peptide
m: rRNA-processing protein EBP2
n: Pescadillo homolog
o: Ribosome biogenesis protein 15
p: ATP-dependent RNA helicase HAS1
q: Protein MAK11
s: Ribosome biogenesis protein ERB1
t: Ribosome biogenesis protein RLP7
u: Ribosome biogenesis protein RLP24
v: Ribosome biogenesis protein SSF1
w: Ribosomal RNA-processing protein 15
y: Eukaryotic translation initiation factor 6
z: Ribosomal RNA-processing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,443,79446
Polymers2,443,59843
Non-polymers1963
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules 126

#1: RNA chain Saccharomyces cerevisiae S288c 35S pre-ribosomal RNA miscRNA


Mass: 1097172.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: GenBank: 259147931
#2: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: GenBank: 1267176496
#3: RNA chain ITS2 / Internal transcribed spacer


Mass: 74308.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: GenBank: 1104417410

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Ribosome biogenesis protein ... , 7 types, 7 molecules Abostuv

#4: Protein Ribosome biogenesis protein NSA1 / / NOP7-associated protein 1


Mass: 51982.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P53136
#25: Protein Ribosome biogenesis protein BRX1 /


Mass: 33079.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q08235*PLUS
#34: Protein Ribosome biogenesis protein 15 / / Nucleolar protein 15


Mass: 25499.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P53927
#37: Protein Ribosome biogenesis protein ERB1 / / Eukaryotic ribosome biogenesis protein 1


Mass: 89176.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q04660*PLUS
#38: Protein Ribosome biogenesis protein RLP7 / / Ribosomal protein L7-like


Mass: 36621.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P40693
#39: Protein Ribosome biogenesis protein RLP24 / / Ribosomal protein L24-like


Mass: 24027.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q07915
#40: Protein Ribosome biogenesis protein SSF1 /


Mass: 51861.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P38789

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60S ribosomal protein ... , 19 types, 19 molecules BCEFGLMNOPQSVYefhij

#5: Protein 60S ribosomal protein L3 / / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin ...Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43850.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P14126
#6: Protein 60S ribosomal protein L4-A / Ribosome / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P10664
#8: Protein 60S ribosomal protein L6-A / Ribosome / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q02326
#9: Protein 60S ribosomal protein L7-A / Ribosome / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P05737
#10: Protein 60S ribosomal protein L8-A / Ribosome / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P17076
#13: Protein 60S ribosomal protein L13-A / Ribosome / Large ribosomal subunit protein eL13-A


Mass: 22604.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q12690
#14: Protein 60S ribosomal protein L14-A / Ribosome / Large ribosomal subunit protein eL14-A


Mass: 15195.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P36105
#15: Protein 60S ribosomal protein L15-A / Ribosome / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P05748
#16: Protein 60S ribosomal protein L16-A / Ribosome / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P26784
#17: Protein 60S ribosomal protein L17-A / Ribosome / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20589.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P05740
#18: Protein 60S ribosomal protein L18-A / Ribosome / Large ribosomal subunit protein eL18-A / RP28


Mass: 20609.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P0CX49
#19: Protein 60S ribosomal protein L20-A / Ribosome / L18a / Large ribosomal subunit protein eL20-A


Mass: 20478.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P0CX23
#20: Protein 60S ribosomal protein L23-A / Ribosome / L17a / Large ribosomal subunit protein uL14-A / YL32


Mass: 14493.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P0CX41
#22: Protein 60S ribosomal protein L26-A / Ribosome / L33 / Large ribosomal subunit protein uL24-A / YL33


Mass: 14265.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P05743
#26: Protein 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32


Mass: 14809.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P38061
#27: Protein 60S ribosomal protein L33-A / Ribosome / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P05744
#28: Protein 60S ribosomal protein L35-A / Ribosome / Large ribosomal subunit protein uL29-A


Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P0CX84
#29: Protein 60S ribosomal protein L36-A / Ribosome / L39 / Large ribosomal subunit protein eL36-A / YL39


Mass: 11151.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P05745
#30: Protein 60S ribosomal protein L37-A / Ribosome / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P49166

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Protein , 10 types, 10 molecules DIKW7mnpqy

#7: Protein Protein MAK16 / Maintenance of killer protein 16


Mass: 35754.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P10962
#11: Protein Ribosome production factor 1 / Ribosome biogenesis protein RPF1


Mass: 35184.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P38805
#12: Protein Proteasome-interacting protein CIC1 / Core interacting component 1


Mass: 42596.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P38779
#21: Protein Nucleolar GTP-binding protein 1


Mass: 74531.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q02892
#23: Protein Nucleolar protein 16 / Nucleolus


Mass: 26954.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P40007
#32: Protein rRNA-processing protein EBP2 / EBNA1-binding protein homolog


Mass: 6315.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast)
#33: Protein Pescadillo homolog / Nucleolar protein 7 / Ribosomal RNA-processing protein 13


Mass: 69984.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P53261
#35: Protein ATP-dependent RNA helicase HAS1 / Helicase associated with SET1 protein 1


Mass: 56798.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q03532, RNA helicase
#36: Protein Protein MAK11 / Maintenance of killer protein 11


Mass: 24272.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast)
#42: Protein Eukaryotic translation initiation factor 6 / eIF-6


Mass: 26476.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q12522

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Ribosomal RNA-processing protein ... , 3 types, 3 molecules 8wz

#24: Protein Ribosomal RNA-processing protein 14 / Ribosome biogenesis protein RRP14


Mass: 50599.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P36080
#41: Protein Ribosomal RNA-processing protein 15


Mass: 28268.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q06511
#43: Protein Ribosomal RNA-processing protein 1


Mass: 33250.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P35178

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Protein/peptide / Non-polymers , 2 types, 4 molecules x

#31: Protein/peptide Brx1-associated peptide


Mass: 2400.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast)
#44: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Sequence detailsThe full sample sequence of entity 22, chain m is ...The full sample sequence of entity 22, chain m is MAKGFKLKELLSHQKEIEKAEKLENDLKKKKSQELKKEEPTIVTASNLKKLEKKEKKADV KKEVAADTEEYQSQALSKKEKRKLKKELKKMQEQDATEAQKHMSGDEDESGDDREEEEEE EEEEEGRLDLEKLAKSDSESEDDSESENDSEEDEDVVAKEESEEKEEQEEEQDVPLSDVE FDSDADVVPHHKLTVNNTKAMKHALERVQLPWKKHSFQEHQSVTSETNTDEHIKDIYDDT ERELAFYKQSLDAVLVARDELKRLKVPFKRPLDYFAEMVKSDEHMDKIKGKLIEEASDKK AREEARRQRQLKKFGKQVQNATLQKRQLEKRETLEKIKSLKNKRKHNEIDHSEFNVGVEE EVEGKRFDRGRPNGKRAAKNAKYGQGGMKRFKRKNDATSSADVSGFSSRKMKGKTNRPGK SRRARRF The full sample sequence of entity 25, chain b is MSSIYKALAGKSKDNKSEKKQGNVKQFMNKQRTLLISSRGVNYRHRHLIQDLSGLLPHSR KEPKLDTKKDLQQLNEIAELYNCNNVLFFEARKHQDLYLWLSKPPNGPTIKFYIQNLHTM DELNFTGNCLKGSRPVLSFDQRFESSPHYQLIKELLVHNFGVPPNARKSKPFIDHVMSFS IVDDKIWVRTYEISHSTKNKEEYEDGEEDISLVEIGPRFVMTVILILEGSFGGPKIYENK QYVSPNVVRAQIKQQAAEEAKSRAEAAVERKIKRRENVLAADPLSNDALFK The full sample sequence of entity 35, chain q is MSAIGDKNQFRIIVGSYEHNILCLSLDIPNQKENDAAKTPHFMPIFHFQAHSLSIKCLAV SRRYLVSGSNDEHIRIYDLQKRKELGTLLSHQGSITALQFSHPASSSEDAAVSKGSKNSK WLLSASEDHKIMVWRVKDWETVGTLKGHTARVNDVDIHPTNRIAISVSDDHSIRLWNLMT LRNAAVLKLRKYNTNGTCVRWLGAKGDYFAVGLRDRVLIYETGSAKVFKEIVFQRKTLMH IETHILPFDNKEYLSVGISDGNVHFYPCEELFEKVEENEKQEDDDDKEDISPAFSLLGHT NRIKDFKFYTNEFGTYLVTIGSDGKIVVWDMSTKEQVAVYDCGERLNCLTLCDESIEKYN TMKKRDAETADIGDQSEVESDTEELKKIMFGEKKKLNKKKRKQLKKSKVSVELE The full sample sequence of entity 37, chain s is MMAKNNKTTEAKMSKKRAASEESDVEEDEDKLLSVDGLIDAEASESDEDDDEYESAVEEK ESSSDKEAQDDSDDDSDAELNKLLAEEEGDGEEDYDSSEFSDDTTSLTDRLSGVKLQTIV DPNIYSKYADGSDRIIKPEINPVYDSDDSDAETQNTIGNIPLSAYDEMPHIGYDINGKRI MRPAKGSALDQLLDSIELPEGWTGLLDKNSGSSLNLTKEELELISKIQRNEQTDDSINPY EPLIDWFTRHEEVMPLTAVPEPKRRFVPSKNEAKRVMKIVRAIREGRIIPPKKLKEMKEK EKIENYQYDLWGDSTETNDHVMHLRAPKLPPPTNEESYNPPEEYLLSPEEKEAWENTEYS ERERNFIPQKYSALRKVPGYGESIRERFERSLDLYLAPRVRKNKLNIDPNSLIPELPSPK DLRPFPIRCSTIYAGHKGKVRTLSIDPSGLWLATGSDDGTVRVWEILTGREVYRTTLIDD EENPDYHIECIEWNPDANNGILAVAVGENIHLIVPPIFGYDIENNGKTKIEDGFGYDTFG TVKKSNLEVNENGDGDEDGENESAKNAVKKQVAQWNKPSQKQLEKDICITISCKKTVKKL SWHRKGDYFVTVQPDSGNTSVLIHQVSKHLTQSPFKKSKGIIMDAKFHPFKPQLFVCSQR YVRIYDLSQQILVKKLLPGARWLSKIDIHPRGDNLIASSFDKRVLWHDLDLASTPYKTLR YHEKAVRSVNFHKKLPLFSSAADDGTIHVFHATVYDDMMKNPMIVPLKKLTGHKVINSLG VLDAIWHPREAWLFSAGADNTARLWTT

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Yeast large subunit processome / Type: COMPLEX
Entity ID: #4, #6-#15, #18-#19, #22-#23, #25-#30, #33-#35, #37-#38, #43, #5, #16-#17, #20-#21, #24, #36, #39-#42, #1-#3
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.56 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4.1CTF correction
7Coot0.8.8model fitting
12RELION2.13D reconstruction
19PHENIX1.13rc1-2961model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 201114 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL

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