6ZU5 | pdb_00006zu5

Structure of the Paranosema locustae ribosome in complex with Lso2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome.

Ehrenbolger, K.Jespersen, N.Sharma, H.Sokolova, Y.Y.Tokarev, Y.S.Vossbrinck, C.R.Barandun, J.

(2020) PLoS Biol 18: e3000958-e3000958

  • DOI: https://doi.org/10.1371/journal.pbio.3000958
  • Primary Citation of Related Structures:  
    6ZU5

  • PubMed Abstract: 

    Assembling and powering ribosomes are energy-intensive processes requiring fine-tuned cellular control mechanisms. In organisms operating under strict nutrient limitations, such as pathogenic microsporidia, conservation of energy via ribosomal hibernation and recycling is critical. The mechanisms by which hibernation is achieved in microsporidia, however, remain poorly understood. Here, we present the cryo-electron microscopy structure of the ribosome from Paranosema locustae spores, bound by the conserved eukaryotic hibernation and recycling factor Lso2. The microsporidian Lso2 homolog adopts a V-shaped conformation to bridge the mRNA decoding site and the large subunit tRNA binding sites, providing a reversible ribosome inactivation mechanism. Although microsporidian ribosomes are highly compacted, the P. locustae ribosome retains several rRNA segments absent in other microsporidia, and represents an intermediate state of rRNA reduction. In one case, the near complete reduction of an expansion segment has resulted in a single bound nucleotide, which may act as an architectural co-factor to stabilize a protein-protein interface. The presented structure highlights the reductive evolution in these emerging pathogens and sheds light on a conserved mechanism for eukaryotic ribosome hibernation.


  • Organizational Affiliation
    • Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Science for Life Laboratory, Umeå University, Umeå, Sweden.

Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
uL2C [auth LA0]247Antonospora locustaeMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
uL15D [auth LAA]155Antonospora locustaeMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
uL3E [auth LB0]385Antonospora locustaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
eL29F [auth LBB]64Antonospora locustaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
uL4G [auth LC0]330Antonospora locustaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
eL30H [auth LCC]108Antonospora locustaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
uL18I [auth LD0]266Antonospora locustaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
eL31J [auth LDD]109Antonospora locustaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
eL6K [auth LE0]180Antonospora locustaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
eL32L [auth LEE]132Antonospora locustaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
uL30M [auth LF0]254Antonospora locustaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
eL33N [auth LFF]108Antonospora locustaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
eL8O [auth LG0]216Antonospora locustaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
eL34P [auth LGG]113Antonospora locustaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
uL6Q [auth LH0]186Antonospora locustaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
uL29R [auth LHH]126Antonospora locustaeMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
uL16S [auth LI0]218Antonospora locustaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
eL36T [auth LII]98Antonospora locustaeMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
uL5U [auth LJ0]174Antonospora locustaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
eL37V [auth LJJ]95Antonospora locustaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
eL13W [auth LL0]166Antonospora locustaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
eL39X [auth LLL]51Antonospora locustaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
eL14Y [auth LM0]108Antonospora locustaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
eL40Z [auth LMM]132Antonospora locustaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
eL15AA [auth LN0]204Antonospora locustaeMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Lso2BA [auth LNN]77Antonospora locustaeMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
uL13CA [auth LO0]198Antonospora locustaeMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
eL42DA [auth LOO]112Antonospora locustaeMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
uL22EA [auth LP0]171Antonospora locustaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eL43FA [auth LPP]86Antonospora locustaeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
eL18GA [auth LQ0]178Antonospora locustaeMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
eL19HA [auth LR0]166Antonospora locustaeMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
eL20IA [auth LS0]175Antonospora locustaeMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
eL21JA [auth LT0]160Antonospora locustaeMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
eL22KA [auth LU0]114Antonospora locustaeMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
uL14LA [auth LV0]140Antonospora locustaeMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
eL24MA [auth LW0]133Antonospora locustaeMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
uL23NA [auth LX0]106Antonospora locustaeMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
uL24OA [auth LY0]140Antonospora locustaeMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
eL27PA [auth LZ0]127Antonospora locustaeMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
uS2RA [auth SA0]242Antonospora locustaeMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
eS26SA [auth SAA]104Antonospora locustaeMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
eS1TA [auth SB0]230Antonospora locustaeMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
eS27UA [auth SBB]86Antonospora locustaeMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
uS5VA [auth SC0]255Antonospora locustaeMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
eS28WA [auth SCC]65Antonospora locustaeMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
uS3XA [auth SD0]217Antonospora locustaeMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
uS14YA [auth SDD]63Antonospora locustaeMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
eS4ZA [auth SE0]267Antonospora locustaeMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
eS30AB [auth SEE]60Antonospora locustaeMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
uS7BB [auth SF0]195Antonospora locustaeMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
eS6CB [auth SG0]222Antonospora locustaeMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
RACK1DB [auth SGG]330Antonospora locustaeMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
eS7EB [auth SH0]176Antonospora locustaeMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
eS8FB [auth SI0]175Antonospora locustaeMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
uS4GB [auth SJ0]187Antonospora locustaeMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
eS10HB [auth SK0]102Antonospora locustaeMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
uS17IB [auth SL0]160Antonospora locustaeMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
uS15JB [auth SN0]146Antonospora locustaeMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
uS11KB [auth SO0]135Antonospora locustaeMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
uS19LB [auth SP0]146Antonospora locustaeMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
uS9MB [auth SQ0]145Antonospora locustaeMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
eS17NB [auth SR0]123Antonospora locustaeMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
uS13OB [auth SS0]161Antonospora locustaeMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
eS19PB [auth ST0]141Antonospora locustaeMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
uS10QB [auth SU0]111Antonospora locustaeMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
eS21RB [auth SV0]66Antonospora locustaeMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
uS8SB [auth SW0]127Antonospora locustaeMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
uS12TB [auth SX0]140Antonospora locustaeMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
eS24UB [auth SY0]133Antonospora locustaeMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
eS25VB [auth SZ0]126Antonospora locustaeMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
25S rRNAA [auth L50]2,639Antonospora locustae
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S rRNAB [auth L70]119Antonospora locustae
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 43
MoleculeChains LengthOrganismImage
18S rRNAQA [auth S60]1,400Antonospora locustae
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

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YH [auth LH0]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
ZN
Query on ZN

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AJ [auth SBB]
BI [auth LMM]
BJ [auth SDD]
CI [auth LOO]
DI [auth LPP]
AJ [auth SBB],
BI [auth LMM],
BJ [auth SDD],
CI [auth LOO],
DI [auth LPP],
XH [auth LGG],
ZH [auth LJJ],
ZI [auth SAA]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth L50]
AD [auth L50]
AE [auth L50]
AF [auth L50]
AG [auth L50]
AC [auth L50],
AD [auth L50],
AE [auth L50],
AF [auth L50],
AG [auth L50],
AH [auth L50],
AI [auth LJJ],
BC [auth L50],
BD [auth L50],
BE [auth L50],
BF [auth L50],
BG [auth L50],
BH [auth L50],
CC [auth L50],
CD [auth L50],
CE [auth L50],
CF [auth L50],
CG [auth L50],
CH [auth L50],
DC [auth L50],
DD [auth L50],
DE [auth L50],
DF [auth L50],
DG [auth L50],
DH [auth L50],
EC [auth L50],
ED [auth L50],
EE [auth L50],
EF [auth L50],
EG [auth L50],
EH [auth L50],
EI [auth LV0],
FC [auth L50],
FD [auth L50],
FE [auth L50],
FF [auth L50],
FG [auth L50],
FH [auth L50],
FI [auth S60],
GC [auth L50],
GD [auth L50],
GE [auth L50],
GF [auth L50],
GG [auth L50],
GH [auth L50],
GI [auth S60],
HC [auth L50],
HD [auth L50],
HE [auth L50],
HF [auth L50],
HG [auth L50],
HH [auth L50],
HI [auth S60],
IC [auth L50],
ID [auth L50],
IE [auth L50],
IF [auth L50],
IG [auth L50],
IH [auth L50],
II [auth S60],
JC [auth L50],
JD [auth L50],
JE [auth L50],
JF [auth L50],
JG [auth L50],
JH [auth L50],
JI [auth S60],
KC [auth L50],
KD [auth L50],
KE [auth L50],
KF [auth L50],
KG [auth L50],
KH [auth L50],
KI [auth S60],
LC [auth L50],
LD [auth L50],
LE [auth L50],
LF [auth L50],
LG [auth L50],
LH [auth L50],
LI [auth S60],
MC [auth L50],
MD [auth L50],
ME [auth L50],
MF [auth L50],
MG [auth L50],
MH [auth L50],
MI [auth S60],
NC [auth L50],
ND [auth L50],
NE [auth L50],
NF [auth L50],
NG [auth L50],
NH [auth L50],
NI [auth S60],
OC [auth L50],
OD [auth L50],
OE [auth L50],
OF [auth L50],
OG [auth L50],
OH [auth L50],
OI [auth S60],
PC [auth L50],
PD [auth L50],
PE [auth L50],
PF [auth L50],
PG [auth L50],
PH [auth L50],
PI [auth S60],
QC [auth L50],
QD [auth L50],
QE [auth L50],
QF [auth L50],
QG [auth L50],
QH [auth L50],
QI [auth S60],
RC [auth L50],
RD [auth L50],
RE [auth L50],
RF [auth L50],
RG [auth L50],
RH [auth L50],
RI [auth S60],
SC [auth L50],
SD [auth L50],
SE [auth L50],
SF [auth L50],
SG [auth L50],
SH [auth L70],
SI [auth S60],
TC [auth L50],
TD [auth L50],
TE [auth L50],
TF [auth L50],
TG [auth L50],
TH [auth L70],
TI [auth S60],
UC [auth L50],
UD [auth L50],
UE [auth L50],
UF [auth L50],
UG [auth L50],
UH [auth L70],
UI [auth S60],
VC [auth L50],
VD [auth L50],
VE [auth L50],
VF [auth L50],
VG [auth L50],
VH [auth L70],
VI [auth S60],
WB [auth L50],
WC [auth L50],
WD [auth L50],
WE [auth L50],
WF [auth L50],
WG [auth L50],
WH [auth LA0],
WI [auth S60],
XB [auth L50],
XC [auth L50],
XD [auth L50],
XE [auth L50],
XF [auth L50],
XG [auth L50],
XI [auth S60],
YB [auth L50],
YC [auth L50],
YD [auth L50],
YE [auth L50],
YF [auth L50],
YG [auth L50],
YI [auth S60],
ZB [auth L50],
ZC [auth L50],
ZD [auth L50],
ZE [auth L50],
ZF [auth L50],
ZG [auth L50]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.14-3260

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2019-02011

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Refinement description