7CPV

Cryo-EM structure of 80S ribosome from mouse testis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A male germ-cell-specific ribosome controls male fertility.

Li, H.Huo, Y.He, X.Yao, L.Zhang, H.Cui, Y.Xiao, H.Xie, W.Zhang, D.Wang, Y.Zhang, S.Tu, H.Cheng, Y.Guo, Y.Cao, X.Zhu, Y.Jiang, T.Guo, X.Qin, Y.Sha, J.

(2022) Nature 612: 725-731

  • DOI: https://doi.org/10.1038/s41586-022-05508-0
  • Primary Citation of Related Structures:  
    7CPU, 7CPV

  • PubMed Abstract: 

    Ribosomes are highly sophisticated translation machines that have been demonstrated to be heterogeneous in the regulation of protein synthesis 1,2 . Male germ cell development involves complex translational regulation during sperm formation 3 . However, it remains unclear whether translation during sperm formation is performed by a specific ribosome. Here we report a ribosome with a specialized nascent polypeptide exit tunnel, Ribosome ST , that is assembled with the male germ-cell-specific protein RPL39L, the paralogue of core ribosome (Ribosome Core ) protein RPL39. Deletion of Ribosome ST in mice causes defective sperm formation, resulting in substantially reduced fertility. Our comparison of single-particle cryo-electron microscopy structures of ribosomes from mouse kidneys and testes indicates that Ribosome ST features a ribosomal polypeptide exit tunnel of distinct size and charge states compared with Ribosome Core . Ribosome ST predominantly cotranslationally regulates the folding of a subset of male germ-cell-specific proteins that are essential for the formation of sperm. Moreover, we found that specialized functions of Ribosome ST were not replaceable by Ribosome Core . Taken together, identification of this sperm-specific ribosome should greatly expand our understanding of ribosome function and tissue-specific regulation of protein expression pattern in mammals.


  • Organizational Affiliation

    State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8A [auth LA]257Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3B [auth LB]403Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4C [auth LC]419Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5D [auth LD]297Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6E [auth LE]296Mus musculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7F [auth LF]270Mus musculusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aG [auth LG]266Mus musculusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9H [auth LH]192Mus musculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10-likeI [auth LI]214Mus musculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11J [auth LJ]178Mus musculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13K [auth LL]211Mus musculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14L [auth LM]217Mus musculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15M [auth LN]204Mus musculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aN [auth LO]203Mus musculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17O [auth LP]184Mus musculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18P [auth LQ]188Mus musculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19Q [auth LR]196Mus musculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aR [auth LS]176Mus musculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21S [auth LT]160Mus musculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22T [auth LU]128Mus musculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23U [auth LV]140Mus musculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24V [auth LW]157Mus musculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aW [auth LX]156Mus musculusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26X [auth LY]145Mus musculusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27Y [auth LZ]136Mus musculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aZ [auth La]148Mus musculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29AA [auth Lb]160Mus musculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30BA [auth Lc]115Mus musculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31CA [auth Ld]125Mus musculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32DA [auth Le]135Mus musculusMutation(s): 0 
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IMPC:  MGI:98038
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aEA [auth Lf]110Mus musculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34FA [auth Lg]117Mus musculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35GA [auth Lh]123Mus musculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36HA [auth Li]105Mus musculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37IA [auth Lj]97Mus musculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38JA [auth Lk]70Mus musculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L39-likeKA [auth Ll]51Mus musculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40LA [auth Lm]128Mus musculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41MA [auth Ln]25Mus musculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aNA [auth Lo]106Mus musculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aOA [auth Lp]92Mus musculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28PA [auth Lr]137Mus musculusMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAUA [auth SA]295Mus musculusMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aVA [auth SB]264Mus musculusMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3WA [auth SD]243Mus musculusMutation(s): 0 
EC: 4.2.99.18
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformXA [auth SE]263Mus musculusMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5YA [auth SF]204Mus musculusMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7ZA [auth SH]194Mus musculusMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8AB [auth SI]208Mus musculusMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10BB [auth SK]165Mus musculusMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11CB [auth SL]158Mus musculusMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15DB [auth SP]145Mus musculusMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16EB [auth SQ]146Mus musculusMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17FB [auth SR]135Mus musculusMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18GB [auth SS]152Mus musculusMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19HB [auth ST]145Mus musculusMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20IB [auth SU]119Mus musculusMutation(s): 0 
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IMPC:  MGI:1914677
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21JB [auth SV]83Mus musculusMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23KB [auth SX]143Mus musculusMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26LB [auth Sa]115Mus musculusMutation(s): 0 
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IMPC:  MGI:1351628
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28MB [auth Sc]69Mus musculusMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29NB [auth Sd]56Mus musculusMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1OB [auth Sg]317Mus musculusMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2PB [auth SC]293Mus musculusMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6QB [auth SG]249Mus musculusMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9RB [auth SJ]194Mus musculusMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13SB [auth SN]151Mus musculusMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14TB [auth SO]151Mus musculusMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aUB [auth SW]130Mus musculusMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24VB [auth SY]133Mus musculusMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25WB [auth SZ]125Mus musculusMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27XB [auth Sb]84Mus musculusMutation(s): 0 
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IMPC:  MGI:1888676
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30YB [auth Se]133Mus musculusMutation(s): 0 
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Entity ID: 43
MoleculeChains LengthOrganismImage
Mus musculus 28S ribosomal RNAQA [auth L5]4,731Mus musculus
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Entity ID: 44
MoleculeChains LengthOrganismImage
Mus musculus 5S ribosomal RNARA [auth L7]120Mus musculus
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Entity ID: 45
MoleculeChains LengthOrganismImage
Mus musculus 5.8S ribosomal RNASA [auth L8]158Mus musculus
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Entity ID: 46
MoleculeChains LengthOrganismImage
Mus musculus 18S ribosomal RNATA [auth S2]1,870Mus musculus
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Entity ID: 78
MoleculeChains LengthOrganismImage
Met-tRNAZB [auth S6]75Mus musculus
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
GC [auth Lg]
HC [auth Lj]
IC [auth Lm]
JC [auth Lo]
KC [auth Lp]
GC [auth Lg],
HC [auth Lj],
IC [auth Lm],
JC [auth Lo],
KC [auth Lp],
SL [auth Sa],
TL [auth Sd]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth LN]
AD [auth L5]
AE [auth L5]
AF [auth L5]
AG [auth L5]
AC [auth LN],
AD [auth L5],
AE [auth L5],
AF [auth L5],
AG [auth L5],
AH [auth L5],
AI [auth L5],
AJ [auth L5],
AK [auth S2],
AL [auth S2],
BC [auth LP],
BD [auth L5],
BE [auth L5],
BF [auth L5],
BG [auth L5],
BH [auth L5],
BI [auth L5],
BJ [auth L5],
BK [auth S2],
BL [auth S2],
CC [auth LT],
CD [auth L5],
CE [auth L5],
CF [auth L5],
CG [auth L5],
CH [auth L5],
CI [auth L5],
CJ [auth L7],
CK [auth S2],
CL [auth S2],
DC [auth LV],
DD [auth L5],
DE [auth L5],
DF [auth L5],
DG [auth L5],
DH [auth L5],
DI [auth L5],
DJ [auth L7],
DK [auth S2],
DL [auth S2],
EC [auth Le],
ED [auth L5],
EE [auth L5],
EF [auth L5],
EG [auth L5],
EH [auth L5],
EI [auth L5],
EJ [auth L7],
EK [auth S2],
EL [auth S2],
FC [auth Lf],
FD [auth L5],
FE [auth L5],
FF [auth L5],
FG [auth L5],
FH [auth L5],
FI [auth L5],
FJ [auth L8],
FK [auth S2],
FL [auth S2],
GD [auth L5],
GE [auth L5],
GF [auth L5],
GG [auth L5],
GH [auth L5],
GI [auth L5],
GJ [auth L8],
GK [auth S2],
GL [auth S2],
HD [auth L5],
HE [auth L5],
HF [auth L5],
HG [auth L5],
HH [auth L5],
HI [auth L5],
HJ [auth L8],
HK [auth S2],
HL [auth S2],
ID [auth L5],
IE [auth L5],
IF [auth L5],
IG [auth L5],
IH [auth L5],
II [auth L5],
IJ [auth L8],
IK [auth S2],
IL [auth S2],
JD [auth L5],
JE [auth L5],
JF [auth L5],
JG [auth L5],
JH [auth L5],
JI [auth L5],
JJ [auth L8],
JK [auth S2],
JL [auth S2],
KD [auth L5],
KE [auth L5],
KF [auth L5],
KG [auth L5],
KH [auth L5],
KI [auth L5],
KJ [auth S2],
KK [auth S2],
KL [auth S2],
LC [auth L5],
LD [auth L5],
LE [auth L5],
LF [auth L5],
LG [auth L5],
LH [auth L5],
LI [auth L5],
LJ [auth S2],
LK [auth S2],
LL [auth S2],
MC [auth L5],
MD [auth L5],
ME [auth L5],
MF [auth L5],
MG [auth L5],
MH [auth L5],
MI [auth L5],
MJ [auth S2],
MK [auth S2],
ML [auth S2],
NC [auth L5],
ND [auth L5],
NE [auth L5],
NF [auth L5],
NG [auth L5],
NH [auth L5],
NI [auth L5],
NJ [auth S2],
NK [auth S2],
NL [auth S2],
OC [auth L5],
OD [auth L5],
OE [auth L5],
OF [auth L5],
OG [auth L5],
OH [auth L5],
OI [auth L5],
OJ [auth S2],
OK [auth S2],
OL [auth S2],
PC [auth L5],
PD [auth L5],
PE [auth L5],
PF [auth L5],
PG [auth L5],
PH [auth L5],
PI [auth L5],
PJ [auth S2],
PK [auth S2],
PL [auth S2],
QC [auth L5],
QD [auth L5],
QE [auth L5],
QF [auth L5],
QG [auth L5],
QH [auth L5],
QI [auth L5],
QJ [auth S2],
QK [auth S2],
QL [auth S2],
RC [auth L5],
RD [auth L5],
RE [auth L5],
RF [auth L5],
RG [auth L5],
RH [auth L5],
RI [auth L5],
RJ [auth S2],
RK [auth S2],
RL [auth SF],
SC [auth L5],
SD [auth L5],
SE [auth L5],
SF [auth L5],
SG [auth L5],
SH [auth L5],
SI [auth L5],
SJ [auth S2],
SK [auth S2],
TC [auth L5],
TD [auth L5],
TE [auth L5],
TF [auth L5],
TG [auth L5],
TH [auth L5],
TI [auth L5],
TJ [auth S2],
TK [auth S2],
UC [auth L5],
UD [auth L5],
UE [auth L5],
UF [auth L5],
UG [auth L5],
UH [auth L5],
UI [auth L5],
UJ [auth S2],
UK [auth S2],
VC [auth L5],
VD [auth L5],
VE [auth L5],
VF [auth L5],
VG [auth L5],
VH [auth L5],
VI [auth L5],
VJ [auth S2],
VK [auth S2],
WC [auth L5],
WD [auth L5],
WE [auth L5],
WF [auth L5],
WG [auth L5],
WH [auth L5],
WI [auth L5],
WJ [auth S2],
WK [auth S2],
XC [auth L5],
XD [auth L5],
XE [auth L5],
XF [auth L5],
XG [auth L5],
XH [auth L5],
XI [auth L5],
XJ [auth S2],
XK [auth S2],
YC [auth L5],
YD [auth L5],
YE [auth L5],
YF [auth L5],
YG [auth L5],
YH [auth L5],
YI [auth L5],
YJ [auth S2],
YK [auth S2],
ZC [auth L5],
ZD [auth L5],
ZE [auth L5],
ZF [auth L5],
ZG [auth L5],
ZH [auth L5],
ZI [auth L5],
ZJ [auth S2],
ZK [auth S2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31890784
National Natural Science Foundation of China (NSFC)China81701511
National Natural Science Foundation of China (NSFC)China31830043

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-12-21
    Changes: Database references
  • Version 1.2: 2023-01-11
    Changes: Database references
  • Version 1.3: 2024-05-29
    Changes: Data collection