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- PDB-6hd7: Cryo-EM structure of the ribosome-NatA complex -

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Entry
Database: PDB / ID: 6hd7
TitleCryo-EM structure of the ribosome-NatA complex
Components
  • (60S ribosomal protein ...) x 40
  • (N-terminal acetyltransferase A complex ...) x 2
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • N-alpha-acetyltransferase NAT5
  • P-site tRNA
  • Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA
  • Ubiquitin-60S ribosomal protein L40
  • nascent polypeptide chain
  • ribosomal protein RPL1
  • tRNATransfer RNA
KeywordsTRANSLATION / N-terminal acetylation / protein modification / ribosome / expansion segments
Function / homologyRibosomal protein L7A/L8 superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L32e superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L21 superfamily ...Ribosomal protein L7A/L8 superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L32e superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L38e superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein L40e superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein L35A superfamily / Ribosomal protein L30/YlxQ / 60S ribosomal protein L19 / Ribosomal protein L14 / Ribosomal protein L7/L30 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L14p/L23e / Ubiquitin family / Ribosomal protein L16p/L10e / Ribosomal protein L23 / Ribosomal protein L5 / Ribosomal protein L3 / Ribosomal protein L30p/L7e / Ribosomal L18e/L15P superfamily / Ribosomal protein L19/L19e superfamily / KOW motif / Ribosomal protein L13, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L18e, conserved site / 60S ribosomal protein L18a/ L20, eukaryotes / N-terminal acetyltransferase A, auxiliary subunit / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L30e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein L24e, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L4 domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein L19/L19e conserved site / Ribosomal protein L15e core domain superfamily / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / 60S ribosomal protein L4, C-terminal domain / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L19, eukaryotic / Ribosomal protein L6 / Ribosomal protein L13 / Ribosomal protein L31e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein 60S L18 and 50S L18e / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L14 signature. / Ribosomal protein L23 signature. / Ribosomal protein L39e signature. / Ubiquitin domain signature. / Ribosomal protein L5 signature. / Ribosomal protein L22 signature. / Ribosomal protein L2 signature. / Ribosomal protein L3 signature. / Ribosomal protein L15 signature. / Ribosomal protein L19e signature. / Ribosomal protein L29 signature. / Ribosomal protein L30 signature. / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L6 signature 2. / Ribosomal protein L30e signature 1. / Ribosomal protein L13 signature. / Ribosomal protein L1e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L24e signature. / Ribosomal protein L37e signature. / Ribosomal protein L7Ae signature. / Ribosomal protein L13e signature. / Ribosomal protein L35Ae signature. / Ribosomal protein L18e signature. / Ribosomal protein L27e signature. / Ribosomal protein L24 signature. / Ribosomal protein L31e signature. / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal L18 C-terminal region / Ribosomal protein L4/L1 family
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.4 Å resolution
AuthorsKnorr, A.G. / Becker, T. / Beckmann, R.
Funding supportGermany , 2 items
OrganizationGrant numberCountry
German Research FoundationGRK1721Germany
German Research FoundationFOR1805Germany
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: Ribosome-NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation.
Authors: Alexandra G Knorr / Christian Schmidt / Petr Tesina / Otto Berninghausen / Thomas Becker / Birgitta Beatrix / Roland Beckmann
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 17, 2018 / Release: Dec 19, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 19, 2018Structure modelrepositoryInitial release
1.1Dec 26, 2018Structure modelAdvisory / Data collection / Database references / Derived calculationscitation / citation_author / database_PDB_rev / database_PDB_rev_record / em_admin / pdbx_data_processing_status / pdbx_database_proc / pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type_citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code_mod
1.2Jan 16, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
1: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA
3: 5S rRNA
4: 5.8S rRNA
A: tRNA
B: P-site tRNA
C: 60S ribosomal protein L42-A
D: 60S ribosomal protein L43-A
E: 60S ribosomal protein L2-A
F: 60S ribosomal protein L3
G: 60S ribosomal protein L4-A
H: 60S ribosomal protein L5
I: 60S ribosomal protein L6-A
J: 60S ribosomal protein L7-A
K: 60S ribosomal protein L8-A
L: 60S ribosomal protein L9-A
M: 60S ribosomal protein L11-A
N: 60S ribosomal protein L13-A
O: 60S ribosomal protein L14-A
P: 60S ribosomal protein L15-A
Q: 60S ribosomal protein L16-A
R: 60S ribosomal protein L17-A
S: 60S ribosomal protein L18-A
T: 60S ribosomal protein L19-A
U: 60S ribosomal protein L20-A
V: 60S ribosomal protein L21-A
W: 60S ribosomal protein L22-A
X: 60S ribosomal protein L23-A
Y: 60S ribosomal protein L24-A
Z: 60S ribosomal protein L25
a: 60S ribosomal protein L26-A
b: 60S ribosomal protein L27-A
c: 60S ribosomal protein L28
d: 60S ribosomal protein L29
e: 60S ribosomal protein L30
f: 60S ribosomal protein L31-A
g: 60S ribosomal protein L32
h: 60S ribosomal protein L33-A
i: 60S ribosomal protein L34-A
j: 60S ribosomal protein L35-A
k: 60S ribosomal protein L36-A
l: 60S ribosomal protein L37-A
m: 60S ribosomal protein L38
n: 60S ribosomal protein L39
o: Ubiquitin-60S ribosomal protein L40
p: 60S ribosomal protein L41-A
r: ribosomal protein RPL1
s: 60S ribosomal protein L10
t: N-terminal acetyltransferase A complex subunit NAT1
u: N-terminal acetyltransferase A complex catalytic subunit ARD1
v: N-alpha-acetyltransferase NAT5
z: nascent polypeptide chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,146,18352
Polyers2,145,90151
Non-polymers2811
Water0
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

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RNA chain , 5 types, 5 molecules 134AB

#1: RNA chain Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: REF: 831416132
#2: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38951.105 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#3: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1398978137
#4: RNA chain tRNA / Transfer RNA


Mass: 24378.408 Da / Num. of mol.: 1
Details: The A-site tRNA was modeled based on an E. coli tRNA-Lys
Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#5: RNA chain P-site tRNA


Mass: 24815.684 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)

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60S ribosomal protein ... , 40 types, 40 molecules CDEFGHIJKLMNOPQRSTUVWXYZabcdef...

#6: Protein/peptide 60S ribosomal protein L42-A / Ribosome / L41 / Large ribosomal subunit protein eL42-A / YL27 / YP44


Mass: 12246.658 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX27
#7: Protein/peptide 60S ribosomal protein L43-A / Ribosome / L37a / Large ribosomal subunit protein eL43-A / YL35


Mass: 10112.952 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX25
#8: Protein/peptide 60S ribosomal protein L2-A / Ribosome / L5 / Large ribosomal subunit protein uL2-A / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX45
#9: Protein/peptide 60S ribosomal protein L3 / / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43850.793 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14126
#10: Protein/peptide 60S ribosomal protein L4-A / Ribosome / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P10664
#11: Protein/peptide 60S ribosomal protein L5 / / L1 / L1a / Large ribosomal subunit protein uL18 / Ribosomal 5S RNA-binding protein / YL3


Mass: 33764.828 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26321
#12: Protein/peptide 60S ribosomal protein L6-A / Ribosome / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02326
#13: Protein/peptide 60S ribosomal protein L7-A / Ribosome / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05737
#14: Protein/peptide 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: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P17076
#15: Protein/peptide 60S ribosomal protein L9-A / Ribosome / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05738
#16: Protein/peptide 60S ribosomal protein L11-A / Ribosome / L16 / Large ribosomal subunit protein uL5-A / RP39 / YL22


Mass: 19755.691 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C0W9
#17: Protein/peptide 60S ribosomal protein L13-A / Ribosome / Large ribosomal subunit protein eL13-A


Mass: 22604.164 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q12690
#18: Protein/peptide 60S ribosomal protein L14-A / Ribosome / Large ribosomal subunit protein eL14-A


Mass: 15195.066 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36105
#19: Protein/peptide 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: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05748
#20: Protein/peptide 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: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26784
#21: Protein/peptide 60S ribosomal protein L17-A / Ribosome / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20589.518 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05740
#22: Protein/peptide 60S ribosomal protein L18-A / Ribosome / Large ribosomal subunit protein eL18-A / RP28


Mass: 20609.252 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX49
#23: Protein/peptide 60S ribosomal protein L19-A / Ribosome / L23 / Large ribosomal subunit protein eL19-A / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX82
#24: Protein/peptide 60S ribosomal protein L20-A / Ribosome / L18a / Large ribosomal subunit protein eL20-A


Mass: 20478.852 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX23
#25: Protein/peptide 60S ribosomal protein L21-A / Ribosome / Large ribosomal subunit protein eL21-A


Mass: 18279.266 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02753
#26: Protein/peptide 60S ribosomal protein L22-A / Ribosome / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31


Mass: 13711.359 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05749
#27: Protein/peptide 60S ribosomal protein L23-A / Ribosome / L17a / Large ribosomal subunit protein uL14-A / YL32


Mass: 14493.950 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX41
#28: Protein/peptide 60S ribosomal protein L24-A / Ribosome / L30 / Large ribosomal subunit protein eL24-A / RP29 / YL21


Mass: 17661.717 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04449
#29: Protein/peptide 60S ribosomal protein L25 / / Large ribosomal subunit protein uL23 / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04456
#30: Protein/peptide 60S ribosomal protein L26-A / Ribosome / L33 / Large ribosomal subunit protein uL24-A / YL33


Mass: 14265.784 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05743
#31: Protein/peptide 60S ribosomal protein L27-A / Ribosome / Large ribosomal subunit protein eL27-A


Mass: 15568.360 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H6
#32: Protein/peptide 60S ribosomal protein L28 / / L27a / L29 / Large ribosomal subunit protein uL15 / RP44 / RP62 / YL24


Mass: 16761.666 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P02406
#33: Protein/peptide 60S ribosomal protein L29 / / Large ribosomal subunit protein eL29 / YL43


Mass: 6691.884 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05747
#34: Protein/peptide 60S ribosomal protein L30 / / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14120
#35: Protein/peptide 60S ribosomal protein L31-A / Ribosome / L34 / Large ribosomal subunit protein eL31-A / YL28


Mass: 12649.754 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H8
#36: Protein/peptide 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32


Mass: 14809.441 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38061
#37: Protein/peptide 60S ribosomal protein L33-A / Ribosome / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05744
#38: Protein/peptide 60S ribosomal protein L34-A / Ribosome / Large ribosomal subunit protein eL34-A


Mass: 13673.196 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P87262
#39: Protein/peptide 60S ribosomal protein L35-A / Ribosome / Large ribosomal subunit protein uL29-A


Mass: 13942.640 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX84
#40: Protein/peptide 60S ribosomal protein L36-A / Ribosome / L39 / Large ribosomal subunit protein eL36-A / YL39


Mass: 11151.259 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05745
#41: Protein/peptide 60S ribosomal protein L37-A / Ribosome / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49166
#42: Protein/peptide 60S ribosomal protein L38 / / Large ribosomal subunit protein eL38


Mass: 8845.561 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49167
#43: Protein/peptide 60S ribosomal protein L39 / / L46 / Large ribosomal subunit protein eL39 / YL40


Mass: 6358.640 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04650
#45: Protein/peptide 60S ribosomal protein L41-A / Ribosome


Mass: 3354.243 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#47: Protein/peptide 60S ribosomal protein L10 / / L9 / Large ribosomal subunit protein uL16 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 25410.465 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P41805

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Protein/peptide , 4 types, 4 molecules orvz

#44: Protein/peptide Ubiquitin-60S ribosomal protein L40


Mass: 14583.077 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CH08
#46: Protein/peptide ribosomal protein RPL1 /


Mass: 17889.996 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#50: Protein/peptide N-alpha-acetyltransferase NAT5 / NatA complex subunit NAT5


Mass: 19753.727 Da / Num. of mol.: 1 / Details: ribosome binding subunit / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
References: UniProt: Q08689, N-terminal methionine Nalpha-acetyltransferase NatE
#51: Protein/peptide nascent polypeptide chain


Mass: 1975.426 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)

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N-terminal acetyltransferase A complex ... , 2 types, 2 molecules tu

#48: Protein/peptide N-terminal acetyltransferase A complex subunit NAT1 / NatA complex subunit NAT1 / Amino-terminal / alpha-amino / acetyltransferase 1


Mass: 99050.133 Da / Num. of mol.: 1 / Details: ribosome binding subunit / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P12945
#49: Protein/peptide N-terminal acetyltransferase A complex catalytic subunit ARD1 / NatA complex subunit ARD1 / Arrest-defective protein 1


Mass: 27635.168 Da / Num. of mol.: 1 / Details: catalytic subunit / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
References: UniProt: P07347, N-terminal amino-acid Nalpha-acetyltransferase NatA

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Non-polymers , 1 types, 1 molecules

#52: Chemical ChemComp-3HE / 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione


Mass: 281.347 Da / Num. of mol.: 1 / Formula: C15H23NO4

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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

Component

Source: NATURAL / Type: COMPLEX

IDNameDetailsEntity IDParent ID
1Ribosome-NatA complexCoordinates are only deposited for 60S subunit and NatA.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, 510
260S ribosomal subunit1, 2, 3, 4, 5, 6, 7, 8, 9, 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, 511
3N-terminal acetyl transferase A48, 49, 501
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
214932Saccharomyces cerevisiae (baker's yeast)
324932Saccharomyces cerevisiae (baker's yeast)
434932Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 2.5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 262507 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT

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