3J79

Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine, large subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine.

Wong, W.Bai, X.C.Brown, A.Fernandez, I.S.Hanssen, E.Condron, M.Tan, Y.H.Baum, J.Scheres, S.H.

(2014) Elife 3: e03080-e03080

  • DOI: 10.7554/eLife.03080
  • Primary Citation of Related Structures:  
    3J79, 3J7A, 6OKK

  • PubMed Abstract: 
  • Malaria inflicts an enormous burden on global human health. The emergence of parasite resistance to front-line drugs has prompted a renewed focus on the repositioning of clinically approved drugs as potential anti-malarial therapies. Antibiotics that inhibit protein translation are promising candidates for repositioning ...

    Malaria inflicts an enormous burden on global human health. The emergence of parasite resistance to front-line drugs has prompted a renewed focus on the repositioning of clinically approved drugs as potential anti-malarial therapies. Antibiotics that inhibit protein translation are promising candidates for repositioning. We have solved the cryo-EM structure of the cytoplasmic ribosome from the human malaria parasite, Plasmodium falciparum, in complex with emetine at 3.2 Å resolution. Emetine is an anti-protozoan drug used in the treatment of ameobiasis that also displays potent anti-malarial activity. Emetine interacts with the E-site of the ribosomal small subunit and shares a similar binding site with the antibiotic pactamycin, thereby delivering its therapeutic effect by blocking mRNA/tRNA translocation. As the first cryo-EM structure that visualizes an antibiotic bound to any ribosome at atomic resolution, this establishes cryo-EM as a powerful tool for screening and guiding the design of drugs that target parasite translation machinery.


    Organizational Affiliation

    Structural Studies, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein uL2D260Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0516900
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Find proteins for Q8I3T9 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein uL3E386Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1027800
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Find proteins for Q8IJC6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein uL4F411Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0507100
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Find proteins for Q8I431 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein uL5G173Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0719600
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein uL6H190Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1323100
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Find proteins for Q8IE85 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 9
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60S ribosomal protein eL6I221Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 10
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60S ribosomal protein eL8J283Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1424400
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Entity ID: 11
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60S ribosomal protein uL13K202Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1004000
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Entity ID: 12
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60S ribosomal protein eL13L215Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0814000
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Entity ID: 13
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60S ribosomal protein uL14M139Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1331800
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Find proteins for Q8IE09 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 14
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60S ribosomal protein eL14N165Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1431700
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Find proteins for Q8ILE8 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 15
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60S ribosomal protein uL15O148Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0618300
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Find proteins for C6KT23 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 16
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60S ribosomal protein eL15P205Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0415900
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Entity ID: 17
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60S ribosomal protein uL16Q219Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1414300
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Entity ID: 18
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60S ribosomal protein uL18R294Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1424100
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Entity ID: 19
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60S ribosomal protein eL18S187Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1341300
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Find proteins for C0H5G3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 20
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60S ribosomal protein eL19T182Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0614500
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Find proteins for C6KSY6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 21
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60S ribosomal protein eL20U184Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1341200
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Find proteins for Q8IDS6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 22
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60S ribosomal protein eL21V161Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1426000
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Find proteins for Q8ILK3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 23
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60S ribosomal protein uL22W203Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1351400
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Find proteins for Q8IDI5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 24
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60S ribosomal protein eL22X139Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0821700
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Find proteins for Q8IB51 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 25
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60S ribosomal protein uL23Y190Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1323400
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Find proteins for Q8IE82 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 26
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60S ribosomal protein uL24Z126Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0312800
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Find proteins for O77364 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 27
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60S ribosomal protein eL24AA [auth 0]162Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1309100
UniProt
Find proteins for Q8IEM3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 28
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60S ribosomal protein eL27BA [auth 1]146Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1460700
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Find proteins for Q8IKM5 (Plasmodium falciparum (isolate 3D7))
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60S ribosomal protein eL28CA [auth 2]127Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1142500
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Entity ID: 30
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60S ribosomal protein uL29DA [auth 3]124Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1124900
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Find proteins for Q8IIB4 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 31
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60S ribosomal protein eL29EA [auth 4]67Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1460300
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Find proteins for C6S3J6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 32
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60S ribosomal protein uL30FA [auth 5]257Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0307200
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Find proteins for O97250 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 33
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60S ribosomal protein eL30GA [auth 6]108Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1019400
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Find proteins for Q8IJK8 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 34
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60S ribosomal protein eL31HA [auth 7]120Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0503800
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Find proteins for Q8I463 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 35
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60S ribosomal protein eL32IA [auth 8]131Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0903900
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Entity ID: 36
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60S ribosomal protein eL33JA [auth 9]140Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1142600
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Entity ID: 37
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60S ribosomal protein eL34KA [auth a]150Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0710600
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Entity ID: 38
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60S ribosomal protein eL36LA [auth b]112Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1109900
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Find proteins for Q8I713 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 39
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60S ribosomal protein eL37MA [auth c]92Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0706400
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Find proteins for C0H4L5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 40
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60S ribosomal protein eL38NA [auth d]87Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1130100
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Find proteins for Q8II62 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 41
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60S ribosomal protein eL39OA [auth e]51Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0611700
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Entity ID: 42
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60S ribosomal protein eL40PA [auth f]128Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1365900
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Find proteins for Q8ID50 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 43
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60S ribosomal protein eL41QA [auth g]39Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1144300
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Find proteins for C6S3G4 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 44
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60S ribosomal protein eL43RA [auth h]96Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPL37APFB0455w
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Find proteins for O96184 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 45
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60S ribosomal protein eL44SA [auth i]104Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPL44MAL3P2.9PFC0200W
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Find proteins for O97231 (Plasmodium falciparum (isolate 3D7))
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UniProt GroupO97231
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Entity ID: 1
MoleculeChainsLengthOrganismImage
28S ribosomal RNAA3,788Plasmodium falciparum 3D7
Protein Feature View
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB119Plasmodium falciparum 3D7
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNAC159Plasmodium falciparum 3D7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AH [auth a],
BH [auth c],
CH [auth f],
DH [auth h],
EH [auth i]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
LG [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MG [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
OG [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
PG [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
QG [auth B],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth B],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
SG [auth B],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TG [auth C],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
UG [auth C],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
VG [auth C],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
WG [auth C],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
XG [auth C],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth M],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A],
ZG [auth Q]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2014-12-17
    Changes: Other
  • Version 1.3: 2015-06-03
    Changes: Database references
  • Version 1.4: 2018-07-18
    Changes: Data collection