8P60

Spraguea lophii ribosome dimer

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

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


Literature

CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state.

McLaren, M., Conners, R., Isupov, M.N., Gil-Diez, P., Gambelli, L., Gold, V.A.M., Walter, A., Connell, S.R., Williams, B., Daum, B.

(2023) Nat Microbiol 8: 1834-1845

  • DOI: https://doi.org/10.1038/s41564-023-01469-w
  • Primary Citation of Related Structures:  
    8P5D, 8P60

  • PubMed Abstract: 

    Translational control is an essential process for the cell to adapt to varying physiological or environmental conditions. To survive adverse conditions such as low nutrient levels, translation can be shut down almost entirely by inhibiting ribosomal function. Here we investigated eukaryotic hibernating ribosomes from the microsporidian parasite Spraguea lophii in situ by a combination of electron cryo-tomography and single-particle electron cryo-microscopy. We show that microsporidian spores contain hibernating ribosomes that are locked in a dimeric (100S) state, which is formed by a unique dimerization mechanism involving the beak region. The ribosomes within the dimer are fully assembled, suggesting that they are ready to be activated once the host cell is invaded. This study provides structural evidence for dimerization acting as a mechanism for ribosomal hibernation in microsporidia, and therefore demonstrates that eukaryotes utilize this mechanism in translational control.

    • Organizational Affiliation: 

    Living Systems Institute, University of Exeter, Exeter, UK.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8C [auth LA0],
YB [auth KA0]		246Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L18e/L15PD [auth LAA],
ZB [auth KAA]		147Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3AC [auth KB0],
E [auth LB0]		392Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7XFB1 (Spraguea lophii (strain 42_110))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4BC [auth KC0],
F [auth LC0]		328Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7WCM8 (Spraguea lophii (strain 42_110))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3CC [auth KCC],
G [auth LCC]		110Spraguea lophii 42_110Mutation(s): 0 
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Find proteins for S7WAY0 (Spraguea lophii (strain 42_110))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5DC [auth KD0],
H [auth LD0]		291Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7XIG7 (Spraguea lophii (strain 42_110))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31EC [auth KDD],
I [auth LDD]		110Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7XW48 (Spraguea lophii (strain 42_110))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6FC [auth KE0],
J [auth LE0]		171Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7W5S3 (Spraguea lophii (strain 42_110))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32GC [auth KEE],
K [auth LEE]		139Spraguea lophii 42_110Mutation(s): 0 
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Find proteins for S7XKE0 (Spraguea lophii (strain 42_110))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7HC [auth KF0],
L [auth LF0]		235Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7W946 (Spraguea lophii (strain 42_110))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aIC [auth KFF],
M [auth LFF]		111Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7W662 (Spraguea lophii (strain 42_110))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8JC [auth KG0],
N [auth LG0]		206Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7XU63 (Spraguea lophii (strain 42_110))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L34KC [auth KGG],
O [auth LGG]		106Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7W7C6 (Spraguea lophii (strain 42_110))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9LC [auth KH0],
P [auth LH0]		187Spraguea lophii 42_110Mutation(s): 0 
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Find proteins for S7XRZ9 (Spraguea lophii (strain 42_110))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal L29 proteinMC [auth KHH],
Q [auth LHH]		119Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
S60 ribosomal protein L10NC [auth KI0],
R [auth LI0]		218Spraguea lophii 42_110Mutation(s): 0 
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Find proteins for S7WBF8 (Spraguea lophii (strain 42_110))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36OC [auth KII],
S [auth LII]		98Spraguea lophii 42_110Mutation(s): 0 
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Find proteins for S7WED1 (Spraguea lophii (strain 42_110))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11PC [auth KJ0],
T [auth LJ0]		171Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7WB69 (Spraguea lophii (strain 42_110))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37QC [auth KJJ],
U [auth LJJ]		92Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13RC [auth KL0],
V [auth LL0]		165Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7XVM9 (Spraguea lophii (strain 42_110))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39SC [auth KLL],
W [auth LLL]		52Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7XTP1 (Spraguea lophii (strain 42_110))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
TransposaseTC [auth KM0],
X [auth LM0]		115Spraguea lophii 42_110Mutation(s): 0 
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Find proteins for S7XVN9 (Spraguea lophii (strain 42_110))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinUC [auth KMM],
Y [auth LMM]		127Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7XSQ3 (Spraguea lophii (strain 42_110))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15VC [auth KN0],
Z [auth LN0]		204Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7W7A2 (Spraguea lophii (strain 42_110))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L13AAA [auth LO0],
WC [auth KO0]		198Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7XUD8 (Spraguea lophii (strain 42_110))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L44BA [auth LOO],
XC [auth KOO]		104Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7XL20 (Spraguea lophii (strain 42_110))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17CA [auth LP0],
YC [auth KP0]		167Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7WDR4 (Spraguea lophii (strain 42_110))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aDA [auth LPP],
ZC [auth KPP]		89Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18AD [auth KQ0],
EA [auth LQ0]		183Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7WAI2 (Spraguea lophii (strain 42_110))
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19BD [auth KR0],
FA [auth LR0]		168Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7WBY9 (Spraguea lophii (strain 42_110))
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20CD [auth KS0],
GA [auth LS0]		171Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60s ribosomal protein L21DD [auth KT0],
HA [auth LT0]		158Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7W8F6 (Spraguea lophii (strain 42_110))
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22ED [auth KU0],
IA [auth LU0]		113Spraguea lophii 42_110Mutation(s): 0 
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Find proteins for S7W958 (Spraguea lophii (strain 42_110))
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23FD [auth KV0],
JA [auth LV0]		142Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24EGD [auth KW0],
KA [auth LW0]		131Spraguea lophii 42_110Mutation(s): 0 
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Find proteins for S7XSY2 (Spraguea lophii (strain 42_110))
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aHD [auth KX0],
LA [auth LX0]		113Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26ID [auth KY0],
MA [auth LY0]		131Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7W884 (Spraguea lophii (strain 42_110))
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27JD [auth KZ0],
NA [auth LZ0]		153Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7XU08 (Spraguea lophii (strain 42_110))
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
DNL-type domain-containing proteinKD [auth MD2],
OA [auth MD1]		151Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7W5K5 (Spraguea lophii (strain 42_110))
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0MD [auth RA0],
QA [auth SA0]		233Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7W8R1 (Spraguea lophii (strain 42_110))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26ND [auth RAA],
RA [auth SAA]		102Spraguea lophii 42_110Mutation(s): 0 
UniProt
Find proteins for S7W9M7 (Spraguea lophii (strain 42_110))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1OD [auth RB0],
SA [auth SB0]		230Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27PD [auth RBB],
TA [auth SBB]		82Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2QD [auth RC0],
UA [auth SC0]		248Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28RD [auth RCC],
VA [auth SCC]		65Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3SD [auth RD0],
WA [auth SD0]		242Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29TD [auth RDD],
XA [auth SDD]		65Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4UD [auth RE0],
YA [auth SE0]		280Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30VD [auth REE],
ZA [auth SEE]		60Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5AB [auth SF0],
WD [auth RF0]		195Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin/40s ribosomal protein S27a fusionBB [auth SFF],
XD [auth RFF]		150Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6CB [auth SG0],
YD [auth RG0]		230Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide binding protein beta subunitDB [auth SGG],
ZD [auth RGG]		326Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7AE [auth RH0],
EB [auth SH0]		164Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8BE [auth RI0],
FB [auth SI0]		173Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9CE [auth RJ0],
GB [auth SJ0]		184Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10DE [auth RK0],
HB [auth SK0]		107Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11EE [auth RL0],
IB [auth SL0]		155Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12FE [auth RM0],
JB [auth SM0]		130Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13GE [auth RN0],
KB [auth SN0]		143Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14HE [auth RO0],
LB [auth SO0]		135Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16IE [auth RQ0],
MB [auth SQ0]		143Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17JE [auth RR0],
NB [auth SR0]		120Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18KE [auth RS0],
OB [auth SS0]		160Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein S19LE [auth RT0],
PB [auth ST0]		143Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20ME [auth RU0],
QB [auth SU0]		119Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S21ENE [auth RV0],
RB [auth SV0]		67Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15AOE [auth RW0],
SB [auth SW0]		128Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S12/S23PE [auth RX0],
TB [auth SX0]		141Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40s ribosomal protein s24QE [auth RY0],
UB [auth SY0]		146Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25RE [auth RZ0],
VB [auth SZ0]		128Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S19SE [auth SP0],
TE [auth RP0]		163Spraguea lophii 42_110Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA 28SA [auth L50],
WB [auth K50]		2,618Spraguea lophii 42_110
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA 5SB [auth L70],
XB [auth K70]		119Spraguea lophii 42_110
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Entity ID: 42
MoleculeChains LengthOrganismImage
RNA 16SLD [auth R60],
PA [auth S60]		1,368Spraguea lophii 42_110
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN
Download Ideal Coordinates CCD File 
AF [auth SBB]
BF [auth SDD]
CF [auth SFF]
DF [auth KGG]
EF [auth KJJ]
AF [auth SBB],
BF [auth SDD],
CF [auth SFF],
DF [auth KGG],
EF [auth KJJ],
FF [auth KMM],
GF [auth KOO],
HF [auth KPP],
IF [auth RAA],
JF [auth RBB],
KF [auth RDD],
LF [auth RFF],
UE [auth LGG],
VE [auth LJJ],
WE [auth LMM],
XE [auth LOO],
YE [auth LPP],
ZE [auth SAA]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC
RECONSTRUCTIONRELION3.1
RECONSTRUCTIONWarp1.1.0

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom212439/Z/18/Z

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Data processing, Database references, Refinement description
  • Version 1.2: 2023-09-06
    Changes: Data collection
  • Version 1.3: 2023-12-20
    Changes: Database references