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- PDB-8hl4: Cryo-EM Structures and Translocation Mechanism of Crenarchaeota R... -

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Entry
Database: PDB / ID: 8hl4
TitleCryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Components
  • (30S ribosomal protein ...) x 24
  • (50S ribosomal protein ...) x 34
  • 16s rRNA (1493-MER)
  • 23s rRNA (3000-MER)
  • 5s rRNA (122-MER)
  • Conserved protein
  • DUF2280 domain-containing protein
  • Elongation factor 2
  • PHE-PHE-PHE-PHE-PHE-PHE
  • Small ribosomal subunit protein uS8
  • mRNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
  • tRNA (76-MER)
KeywordsRIBOSOME / Sulfolobus acidocaldarius ribosome small subunit
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / cytosolic ribosome / ribosomal large subunit biogenesis / large ribosomal subunit / ribosome biogenesis / regulation of translation / large ribosomal subunit rRNA binding / 5S rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / cytosolic ribosome / ribosomal large subunit biogenesis / large ribosomal subunit / ribosome biogenesis / regulation of translation / large ribosomal subunit rRNA binding / 5S rRNA binding / small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / GTP binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Translation elongation factor EFG/EF2, archaeal / Domain of unknown function DUF5622 / Domain of unknown function (DUF5622) / Ribosomal protein L1, archaea / Ribosomal protein L14e / : / Ribosomal protein S27ae / Ribosomal protein L40e, archaeal / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal ...Translation elongation factor EFG/EF2, archaeal / Domain of unknown function DUF5622 / Domain of unknown function (DUF5622) / Ribosomal protein L1, archaea / Ribosomal protein L14e / : / Ribosomal protein S27ae / Ribosomal protein L40e, archaeal / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / Ribosomal protein S3, archaeal / 30S ribosomal protein S3Ae / : / Ribosomal protein S7, archaeal / Ribosomal protein S19e, archaeal / Ribosomal protein S11, archaeal / Ribosomal protein S2, archaeal / Ribosomal protein S14, type Z, archaeal / Ribosomal protein S8e, archaeal / Ribosomal protein L15e, archaeal / Ribosomal protein L19e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L32e, archaeal / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L7Ae, archaea / Ribosomal protein L24e / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal protein L23 / : / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / metallochaperone-like domain / TRASH domain / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L1 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / : / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L44e / Ribosomal protein L24e, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L44 / Ribosomal protein L24e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L30e signature 1. / Translation elongation factor EFTu-like, domain 2 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L40e family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S27e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein S19A/S15e
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / UNKNOWN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / Large ribosomal subunit protein uL24 ...PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / UNKNOWN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Elongation factor 2 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL31 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL18 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS19 / Conserved protein / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein eL42 / Uncharacterized protein / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein eL14 / 50S ribosomal protein L40e / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein eL24 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16
Similarity search - Component
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.62 Å
AuthorsWang, Y.H. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971226 China
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome.
Authors: Ying-Hui Wang / Hong Dai / Ling Zhang / Yun Wu / Jingfen Wang / Chen Wang / Cai-Huang Xu / Hai Hou / Bing Yang / Yongqun Zhu / Xing Zhang / Jie Zhou /
Abstract: Archaeal ribosomes have many domain-specific features; however, our understanding of these structures is limited. We present 10 cryo-electron microscopy (cryo-EM) structures of the archaeal ribosome ...Archaeal ribosomes have many domain-specific features; however, our understanding of these structures is limited. We present 10 cryo-electron microscopy (cryo-EM) structures of the archaeal ribosome from crenarchaeota Sulfolobus acidocaldarius (Sac) at 2.7-5.7 Å resolution. We observed unstable conformations of H68 and h44 of ribosomal RNA (rRNA) in the subunit structures, which may interfere with subunit association. These subunit structures provided models for 12 rRNA expansion segments and 3 novel r-proteins. Furthermore, the 50S-aRF1 complex structure showed the unique domain orientation of aRF1, possibly explaining P-site transfer RNA (tRNA) release after translation termination. Sac 70S complexes were captured in seven distinct steps of the tRNA translocation reaction, confirming conserved structural features during archaeal ribosome translocation. In aEF2-engaged 70S ribosome complexes, 3D classification of cryo-EM data based on 30S head domain identified two new translocation intermediates with 30S head domain tilted 5-6° enabling its disengagement from the translocated tRNA and its release post-translocation. Additionally, we observed conformational changes to aEF2 during ribosome binding and switching from three different states. Our structural and biochemical data provide new insights into archaeal translation and ribosome translocation.
History
DepositionNov 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A23S: 23s rRNA (3000-MER)
A16S: 16s rRNA (1493-MER)
A5S: 5s rRNA (122-MER)
AL2P: 50S ribosomal protein L2
AL3P: 50S ribosomal protein L3
AL4P: 50S ribosomal protein L4
AL5P: 50S ribosomal protein L5
AL6P: 50S ribosomal protein L6
ALX0: 50S ribosomal protein L18Ae
L10E: 50S ribosomal protein L10e
L13P: 50S ribosomal protein L13
L141: 50S ribosomal protein L14e
L142: 50S ribosomal protein L14e
L14P: 50S ribosomal protein L14
L15E: 50S ribosomal protein L15e
L18E: 50S ribosomal protein L18e
L18P: 50S ribosomal protein L18
L19E: 50S ribosomal protein L19e
L22P: 50S ribosomal protein L22
L23P: 50S ribosomal protein L23
L24E: 50S ribosomal protein L24e
L24P: 50S ribosomal protein L24
L29P: 50S ribosomal protein L29
L30E: 50S ribosomal protein L30e
L30P: 50S ribosomal protein L30
L31E: 50S ribosomal protein L31e
L32E: 50S ribosomal protein L32e
L34E: 50S ribosomal protein L34e
L37A: 50S ribosomal protein L37Ae
L37E: 50S ribosomal protein L37e
L39E: 50S ribosomal protein L39e
L40E: 50S ribosomal protein L40E
L44E: 50S ribosomal protein L44e
L7A1: 50S ribosomal protein L7Ae
L7A2: 50S ribosomal protein L7Ae
L15P: 50S ribosomal protein L15
L21E: 50S ribosomal protein L21e
L45A: DUF2280 domain-containing protein
L46A: Conserved protein
L47A: 50S ribosomal protein L47A
AL1P: 50S ribosomal protein L1
AS2P: 30S ribosomal protein S2
AS4E: 30S ribosomal protein S4e
AS4P: 30S ribosomal protein S4
AS5P: 30S ribosomal protein S5
AS6E: 30S ribosomal protein S6e
AS8E: 30S ribosomal protein S8e
AS8P: Small ribosomal subunit protein uS8
S11P: 30S ribosomal protein S11
S12P: 30S ribosomal protein S12
S15P: 30S ribosomal protein S15
S17P: 30S ribosomal protein S17
S24E: 30S ribosomal protein S24e
S27E: 30S ribosomal protein S27e
S3AE: 30S ribosomal protein S3Ae
AS3P: 30S ribosomal protein S3
AS7P: 30S ribosomal protein S7
S10P: 30S ribosomal protein S10
S13P: 30S ribosomal protein S13
S14P: 30S ribosomal protein S14 type Z
S17E: 30S ribosomal protein S17e
S19P: 30S ribosomal protein S19
AS9P: 30S ribosomal protein S9
S28E: 30S ribosomal protein S28e
S27A: 30S ribosomal protein S27ae
SL7A: 50S ribosomal protein L7Ae
AMRN: mRNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
APTN: tRNA (76-MER)
APTP: PHE-PHE-PHE-PHE-PHE-PHE
S19E: 30S ribosomal protein S19e
AEFG: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,553,030129
Polymers2,546,63071
Non-polymers6,40058
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 5 types, 5 molecules A23SA16SA5SAMRNAPTN

#1: RNA chain 23s rRNA (3000-MER)


Mass: 980552.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
#2: RNA chain 16s rRNA (1493-MER)


Mass: 487531.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
#3: RNA chain 5s rRNA (122-MER)


Mass: 39440.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: GenBank: 68566501
#64: RNA chain mRNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 2710.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
#65: RNA chain tRNA (76-MER)


Mass: 24485.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: GenBank: 1850337400

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50S ribosomal protein ... , 34 types, 37 molecules AL2PAL3PAL4PAL5PAL6PALX0L10EL13PL141L142L14PL15EL18EL18PL19EL22PL23PL24EL24PL29PL30EL30PL31EL32EL34EL37AL37EL39EL40EL44E...

#4: Protein 50S ribosomal protein L2


Mass: 24881.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB43
#5: Protein 50S ribosomal protein L3


Mass: 38186.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB40
#6: Protein 50S ribosomal protein L4


Mass: 27357.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB41
#7: Protein 50S ribosomal protein L5


Mass: 19095.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P41202
#8: Protein 50S ribosomal protein L6


Mass: 20305.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05637
#9: Protein 50S ribosomal protein L18Ae / 50S ribosomal protein L20e / 50S ribosomal protein LX


Mass: 8926.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P38613
#10: Protein 50S ribosomal protein L10e


Mass: 18670.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JC84
#11: Protein 50S ribosomal protein L13


Mass: 15808.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39473
#12: Protein 50S ribosomal protein L14e


Mass: 9559.101 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAJ9
#13: Protein 50S ribosomal protein L14


Mass: 14707.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB50
#14: Protein 50S ribosomal protein L15e


Mass: 20179.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB20
#15: Protein 50S ribosomal protein L18e / HL29e


Mass: 12747.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39474
#16: Protein 50S ribosomal protein L18


Mass: 21766.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05640
#17: Protein 50S ribosomal protein L19e


Mass: 17108.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05639
#18: Protein 50S ribosomal protein L22


Mass: 17360.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB45
#19: Protein 50S ribosomal protein L23


Mass: 9261.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB42
#20: Protein 50S ribosomal protein L24e


Mass: 6338.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAV2
#21: Protein 50S ribosomal protein L24


Mass: 14130.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05633
#22: Protein 50S ribosomal protein L29


Mass: 7378.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB47
#23: Protein 50S ribosomal protein L30e


Mass: 10391.282 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P11522
#24: Protein 50S ribosomal protein L30


Mass: 17819.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05642
#25: Protein 50S ribosomal protein L31e


Mass: 8935.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P38618
#26: Protein 50S ribosomal protein L32e


Mass: 14328.114 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05638
#27: Protein 50S ribosomal protein L34e


Mass: 8993.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05981
#28: Protein 50S ribosomal protein L37Ae / Ribosomal protein L43e


Mass: 7536.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB29
#29: Protein 50S ribosomal protein L37e


Mass: 6274.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAZ9
#30: Protein/peptide 50S ribosomal protein L39e / L46e


Mass: 5861.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P13005
#31: Protein 50S ribosomal protein L40E


Mass: 6336.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAP0
#32: Protein 50S ribosomal protein L44e


Mass: 10805.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J9B2
#33: Protein 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 13351.481 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J8P1
#34: Protein 50S ribosomal protein L15


Mass: 16476.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05643
#35: Protein 50S ribosomal protein L21e


Mass: 11155.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB11
#38: Protein 50S ribosomal protein L47A


Mass: 9276.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: F2Z6C4
#39: Protein 50S ribosomal protein L1


Mass: 24416.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P35024

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Protein , 4 types, 4 molecules L45AL46AAS8PAEFG

#36: Protein DUF2280 domain-containing protein


Mass: 11662.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J9G6
#37: Protein Conserved protein


Mass: 8320.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J953
#46: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14624.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05636
#68: Protein Elongation factor 2 / EF-2


Mass: 81106.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P23112

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30S ribosomal protein ... , 24 types, 24 molecules AS2PAS4EAS4PAS5PAS6EAS8ES11PS12PS15PS17PS24ES27ES3AEAS3PAS7PS10PS13PS14PS17ES19PAS9PS28ES27AS19E

#40: Protein 30S ribosomal protein S2


Mass: 22474.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39478
#41: Protein 30S ribosomal protein S4e


Mass: 27339.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05634
#42: Protein 30S ribosomal protein S4


Mass: 19440.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39467
#43: Protein 30S ribosomal protein S5


Mass: 22782.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05641
#44: Protein 30S ribosomal protein S6e


Mass: 11479.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAI1
#45: Protein 30S ribosomal protein S8e


Mass: 14113.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAP5
#47: Protein 30S ribosomal protein S11


Mass: 13652.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39469
#48: Protein 30S ribosomal protein S12


Mass: 15703.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P11524
#49: Protein 30S ribosomal protein S15


Mass: 17438.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAI3
#50: Protein 30S ribosomal protein S17


Mass: 12602.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB49
#51: Protein 30S ribosomal protein S24e


Mass: 10765.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAF9
#52: Protein 30S ribosomal protein S27e


Mass: 6576.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J9B1
#53: Protein 30S ribosomal protein S3Ae / Ribosomal protein S1e


Mass: 21876.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB17
#54: Protein 30S ribosomal protein S3


Mass: 22396.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB46
#55: Protein 30S ribosomal protein S7


Mass: 21862.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P17198
#56: Protein 30S ribosomal protein S10


Mass: 11775.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P17199
#57: Protein 30S ribosomal protein S13


Mass: 17140.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39470
#58: Protein 30S ribosomal protein S14 type Z


Mass: 6190.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05635
#59: Protein 30S ribosomal protein S17e


Mass: 7336.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAX5
#60: Protein 30S ribosomal protein S19


Mass: 13800.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB44
#61: Protein 30S ribosomal protein S9


Mass: 15638.136 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39468
#62: Protein 30S ribosomal protein S28e


Mass: 7094.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAV1
#63: Protein 30S ribosomal protein S27ae


Mass: 6261.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAG0
#67: Protein 30S ribosomal protein S19e


Mass: 17559.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J8U1

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Protein/peptide , 1 types, 1 molecules APTP

#66: Protein/peptide PHE-PHE-PHE-PHE-PHE-PHE


Mass: 901.058 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)

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Non-polymers , 2 types, 58 molecules

#69: Chemical...
ChemComp-UNK / UNKNOWN


Type: L-peptide linking / Mass: 103.120 Da / Num. of mol.: 57 / Source method: obtained synthetically / Formula: C4H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#70: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Sulfolobus acidocaldarius ribosome small sbunit / Type: RIBOSOME / Entity ID: #1, #3-#37 / Source: NATURAL
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 26.7 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5357 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 261.02 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0056185125
ELECTRON MICROSCOPYf_angle_d0.7147273214
ELECTRON MICROSCOPYf_chiral_restr0.038334331
ELECTRON MICROSCOPYf_plane_restr0.00517014
ELECTRON MICROSCOPYf_dihedral_angle_d16.296666640

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