8HL4

Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.62 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome.

Wang, Y.H.Dai, H.Zhang, L.Wu, Y.Wang, J.Wang, C.Xu, C.H.Hou, H.Yang, B.Zhu, Y.Zhang, X.Zhou, J.

(2023) Nucleic Acids Res 51: 8909-8924

  • DOI: https://doi.org/10.1093/nar/gkad661
  • Primary Citation of Related Structures:  
    8HKU, 8HKV, 8HKX, 8HKY, 8HKZ, 8HL1, 8HL2, 8HL3, 8HL4, 8HL5

  • PubMed 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 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.


  • Organizational Affiliation

    Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2D [auth AL2P]234Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JB43 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth AL3P]339Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth AL4P]251Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5G [auth AL5P]168Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for P41202 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6H [auth AL6P]181Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for O05637 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18AeI [auth ALX0]76Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for P38613 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10eJ [auth L10E]164Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JC84 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13K [auth L13P]140Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14eL [auth L141],
M [auth L142]
86Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JAJ9 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14N [auth L14P]134Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JB50 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15eO [auth L15E]169Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18eP [auth L18E]112Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18Q [auth L18P]193Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19eR [auth L19E]144Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22S [auth L22P]150Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JB45 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23T [auth L23P]81Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24eU [auth L24E]54Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JAV2 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24V [auth L24P]122Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for O05633 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29W [auth L29P]63Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JB47 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30eX [auth L30E]94Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for P11522 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30Y [auth L30P]155Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for O05642 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31eZ [auth L31E]75Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for P38618 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32eAA [auth L32E]123Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34eBA [auth L34E]77Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L37AeCA [auth L37A]65Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L37eDA [auth L37E]54Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JAZ9 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L39eEA [auth L39E]49Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for P13005 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L40EFA [auth L40E]55Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JAP0 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L44eGA [auth L44E]92Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4J9B2 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7AeHA [auth L7A1],
IA [auth L7A2],
NB [auth SL7A]
123Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4J8P1 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15JA [auth L15P]144Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21eKA [auth L21E]97Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
DUF2280 domain-containing proteinLA [auth L45A]101Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4J9G6 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Conserved proteinMA [auth L46A]70Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4J953 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L47ANA [auth L47A]80Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for F2Z6C4 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1OA [auth AL1P]216Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for P35024 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2PA [auth AS2P]196Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for P39478 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4eQA [auth AS4E]240Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for O05634 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4RA [auth AS4P]166Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for P39467 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5SA [auth AS5P]204Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for O05641 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6eTA [auth AS6E]105Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JAI1 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8eUA [auth AS8E]126Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JAP5 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8VA [auth AS8P]130Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for O05636 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11WA [auth S11P]128Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for P39469 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12XA [auth S12P]143Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for P11524 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15YA [auth S15P]149Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17ZA [auth S17P]111Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JB49 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S24eAB [auth S24E]96Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JAF9 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S27eBB [auth S27E]59Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4J9B1 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3AeCB [auth S3AE]189Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JB17 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3DB [auth AS3P]201Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JB46 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7EB [auth AS7P]193Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for P17198 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10FB [auth S10P]100Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for P17199 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13GB [auth S13P]147Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for P39470 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZHB [auth S14P]52Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for O05635 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17eIB [auth S17E]62Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JAX5 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19JB [auth S19P]115Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JB44 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9KB [auth AS9P]136Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for P39468 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S28eLB [auth S28E]63Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JAV1 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S27aeMB [auth S27A]54Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4JAG0 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
PHE-PHE-PHE-PHE-PHE-PHEQB [auth APTP]6Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19eRB [auth S19E]150Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for Q4J8U1 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor 2SB [auth AEFG]729Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
UniProt
Find proteins for P23112 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 1
MoleculeChains LengthOrganismImage
23s rRNA (3000-MER)A [auth A23S]3,022Sulfolobus acidocaldarius DSM 639
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Entity ID: 2
MoleculeChains LengthOrganismImage
16s rRNA (1493-MER)B [auth A16S]1,503Sulfolobus acidocaldarius DSM 639
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Entity ID: 3
MoleculeChains LengthOrganismImage
5s rRNA (122-MER)C [auth A5S]122Sulfolobus acidocaldarius DSM 639
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Entity ID: 64
MoleculeChains LengthOrganismImage
mRNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')OB [auth AMRN]9Sulfolobus acidocaldarius DSM 639
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Entity ID: 65
MoleculeChains LengthOrganismImage
tRNA (76-MER)PB [auth APTN]76Sulfolobus acidocaldarius DSM 639
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP (Subject of Investigation/LOI)
Query on GNP

Download Ideal Coordinates CCD File 
YD [auth AEFG]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
UNK (Subject of Investigation/LOI)
Query on UNK

Download Ideal Coordinates CCD File 
AC [auth AS2P]
AD [auth AS2P]
BC [auth AS2P]
BD [auth AS2P]
CC [auth AS2P]
AC [auth AS2P],
AD [auth AS2P],
BC [auth AS2P],
BD [auth AS2P],
CC [auth AS2P],
CD [auth AS2P],
DC [auth AS2P],
DD [auth AS2P],
EC [auth AS2P],
ED [auth AS5P],
FC [auth AS2P],
FD [auth AS5P],
GC [auth AS2P],
GD [auth AS5P],
HC [auth AS2P],
HD [auth AS5P],
IC [auth AS2P],
ID [auth AS5P],
JC [auth AS2P],
JD [auth AS5P],
KC [auth AS2P],
KD [auth AS5P],
LC [auth AS2P],
LD [auth AS5P],
MC [auth AS2P],
MD [auth AS5P],
NC [auth AS2P],
ND [auth AS5P],
OC [auth AS2P],
OD [auth AS5P],
PC [auth AS2P],
PD [auth AS5P],
QC [auth AS2P],
QD [auth AS5P],
RC [auth AS2P],
RD [auth AS8P],
SC [auth AS2P],
SD [auth AS8P],
TB [auth AS2P],
TC [auth AS2P],
TD [auth AS8P],
UB [auth AS2P],
UC [auth AS2P],
UD [auth AS8P],
VB [auth AS2P],
VC [auth AS2P],
VD [auth AS8P],
WB [auth AS2P],
WC [auth AS2P],
WD [auth AS8P],
XB [auth AS2P],
XC [auth AS2P],
XD [auth AS8P],
YB [auth AS2P],
YC [auth AS2P],
ZB [auth AS2P],
ZC [auth AS2P]
UNKNOWN
C4 H9 N O2
QWCKQJZIFLGMSD-VKHMYHEASA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.62 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31971226

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Database references