3JBN

Cryo-electron microscopy reconstruction of the Plasmodium falciparum 80S ribosome bound to P-tRNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dynamical features of the Plasmodium falciparum ribosome during translation.

Sun, M.Li, W.Blomqvist, K.Das, S.Hashem, Y.Dvorin, J.D.Frank, J.

(2015) Nucleic Acids Res. 43: 10515-10524

  • DOI: 10.1093/nar/gkv991
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Plasmodium falciparum, the mosquito-transmitted Apicomplexan parasite, causes the most severe form of human malaria. In the asexual blood-stage, the parasite resides within erythrocytes where it proliferates, multiplies and finally spreads to new ery ...

    Plasmodium falciparum, the mosquito-transmitted Apicomplexan parasite, causes the most severe form of human malaria. In the asexual blood-stage, the parasite resides within erythrocytes where it proliferates, multiplies and finally spreads to new erythrocytes. Development of drugs targeting the ribosome, the site of protein synthesis, requires specific knowledge of its structure and work cycle, and, critically, the ways they differ from those in the human host. Here, we present five cryo-electron microscopy (cryo-EM) reconstructions of ribosomes purified from P. falciparum blood-stage schizonts at sub-nanometer resolution. Atomic models were built from these density maps by flexible fitting. Significantly, our study has taken advantage of new capabilities of cryo-EM, in visualizing several structures co-existing in the sample at once, at a resolution sufficient for building atomic models. We have discovered structural and dynamic features that differentiate the ribosomes of P. falciparum from those of mammalian system. Prompted by the absence of RACK1 on the ribosome in our and an earlier study we confirmed that RACK1 does not specifically co-purify with the 80S fraction in schizonts. More extensive studies, using cryo-EM methodology, of translation in the parasite will provide structural knowledge that may lead to development of novel anti-malarials.


    Related Citations: 
    • 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: --


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY 10027, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS3
D
209Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IKH8 (Plasmodium falciparum)
Go to UniProtKB:  Q8IKH8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS4
E
185Plasmodium falciparumMutation(s): 0 
Find proteins for Q8I3R0 (Plasmodium falciparum)
Go to UniProtKB:  Q8I3R0
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS5
G
224Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IL02 (Plasmodium falciparum)
Go to UniProtKB:  Q8IL02
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS7
I
189Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IBN5 (Plasmodium falciparum)
Go to UniProtKB:  Q8IBN5
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS8
K
129Plasmodium falciparumMutation(s): 0 
Find proteins for O77395 (Plasmodium falciparum)
Go to UniProtKB:  O77395
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS9
M
138Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IAX5 (Plasmodium falciparum)
Go to UniProtKB:  Q8IAX5
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS17
W
108Plasmodium falciparumMutation(s): 0 
Find proteins for Q8I502 (Plasmodium falciparum)
Go to UniProtKB:  Q8I502
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS12
R
114Plasmodium falciparumMutation(s): 0 
Gene Names: RPS12
Find proteins for O97249 (Plasmodium falciparum)
Go to Gene View: RPS12
Go to UniProtKB:  O97249
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS10
O
79Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IBQ5 (Plasmodium falciparum)
Go to UniProtKB:  Q8IBQ5
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS19
Y
154Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IFP2 (Plasmodium falciparum)
Go to UniProtKB:  Q8IFP2
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS21
Z
72Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IHS5 (Plasmodium falciparum)
Go to UniProtKB:  Q8IHS5
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS24
1
120Plasmodium falciparumMutation(s): 0 
Find proteins for Q8I3R6 (Plasmodium falciparum)
Go to UniProtKB:  Q8I3R6
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS25
2
68Plasmodium falciparumMutation(s): 0 
Find proteins for Q8ILN8 (Plasmodium falciparum)
Go to UniProtKB:  Q8ILN8
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS26
3
95Plasmodium falciparumMutation(s): 0 
Find proteins for O96258 (Plasmodium falciparum)
Go to UniProtKB:  O96258
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS27
4
76Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IEN2 (Plasmodium falciparum)
Go to UniProtKB:  Q8IEN2
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS28
5
65Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IKL9 (Plasmodium falciparum)
Go to UniProtKB:  Q8IKL9
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS30
6
43Plasmodium falciparumMutation(s): 0 
Gene Names: RPS30
Find proteins for O96269 (Plasmodium falciparum)
Go to UniProtKB:  O96269
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS1
B
210Plasmodium falciparumMutation(s): 0 
Find proteins for O97313 (Plasmodium falciparum)
Go to UniProtKB:  O97313
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS4
F
257Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IIU8 (Plasmodium falciparum)
Go to UniProtKB:  Q8IIU8
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS6
H
214Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IDR9 (Plasmodium falciparum)
Go to UniProtKB:  Q8IDR9
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS7
J
188Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IET7 (Plasmodium falciparum)
Go to UniProtKB:  Q8IET7
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS8
L
214Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IM10 (Plasmodium falciparum)
Go to UniProtKB:  Q8IM10
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS10
N
98Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IK02 (Plasmodium falciparum)
Go to UniProtKB:  Q8IK02
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS11
P
127Plasmodium falciparumMutation(s): 0 
Find proteins for Q8I3U6 (Plasmodium falciparum)
Go to UniProtKB:  Q8I3U6
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS12
Q
144Plasmodium falciparumMutation(s): 0 
Find proteins for O97248 (Plasmodium falciparum)
Go to UniProtKB:  O97248
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS13
S
128Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IIA2 (Plasmodium falciparum)
Go to UniProtKB:  Q8IIA2
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS14
T
48Plasmodium falciparumMutation(s): 0 
Find proteins for C0H4K8 (Plasmodium falciparum)
Go to UniProtKB:  C0H4K8
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS15
U
149Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IDB0 (Plasmodium falciparum)
Go to UniProtKB:  Q8IDB0
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS17
V
156Plasmodium falciparumMutation(s): 0 
Find proteins for O77381 (Plasmodium falciparum)
Go to UniProtKB:  O77381
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS19
X
103Plasmodium falciparumMutation(s): 0 
Find proteins for C0H5C2 (Plasmodium falciparum)
Go to UniProtKB:  C0H5C2
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS2
C
195Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IJD4 (Plasmodium falciparum)
Go to UniProtKB:  Q8IJD4
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL13
AL
211Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IAX6 (Plasmodium falciparum)
Go to UniProtKB:  Q8IAX6
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL27
A1
145Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IKM5 (Plasmodium falciparum)
Go to UniProtKB:  Q8IKM5
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL28
A2
118Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IHU0 (Plasmodium falciparum)
Go to UniProtKB:  Q8IHU0
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL29
A4
66Plasmodium falciparumMutation(s): 0 
Find proteins for C6S3J6 (Plasmodium falciparum)
Go to UniProtKB:  C6S3J6
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL30
A6
98Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IJK8 (Plasmodium falciparum)
Go to UniProtKB:  Q8IJK8
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL31
A7
102Plasmodium falciparumMutation(s): 0 
Find proteins for Q8I463 (Plasmodium falciparum)
Go to UniProtKB:  Q8I463
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL14
AN
146Plasmodium falciparumMutation(s): 0 
Find proteins for Q8ILE8 (Plasmodium falciparum)
Go to UniProtKB:  Q8ILE8
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL32
A8
125Plasmodium falciparumMutation(s): 0 
Find proteins for Q8I3B0 (Plasmodium falciparum)
Go to UniProtKB:  Q8I3B0
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL33
A9
103Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IHT9 (Plasmodium falciparum)
Go to UniProtKB:  Q8IHT9
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL34
Aa
106Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IBY4 (Plasmodium falciparum)
Go to UniProtKB:  Q8IBY4
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL36
Ab
105Plasmodium falciparumMutation(s): 0 
Find proteins for Q8I713 (Plasmodium falciparum)
Go to UniProtKB:  Q8I713
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL38
Ad
76Plasmodium falciparumMutation(s): 0 
Find proteins for Q8II62 (Plasmodium falciparum)
Go to UniProtKB:  Q8II62
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL39
Ae
50Plasmodium falciparumMutation(s): 0 
Find proteins for C0H4H3 (Plasmodium falciparum)
Go to UniProtKB:  C0H4H3
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL40
Af
51Plasmodium falciparumMutation(s): 0 
Find proteins for Q8ID50 (Plasmodium falciparum)
Go to UniProtKB:  Q8ID50
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL15
AP
204Plasmodium falciparumMutation(s): 0 
Find proteins for C0H4A6 (Plasmodium falciparum)
Go to UniProtKB:  C0H4A6
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL43
Ah
85Plasmodium falciparumMutation(s): 0 
Gene Names: RPL37A
Find proteins for O96184 (Plasmodium falciparum)
Go to Gene View: RPL37A
Go to UniProtKB:  O96184
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL44
Ai
95Plasmodium falciparumMutation(s): 0 
Gene Names: RPL44
Find proteins for O97231 (Plasmodium falciparum)
Go to UniProtKB:  O97231
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL6
AI
213Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IDV1 (Plasmodium falciparum)
Go to UniProtKB:  Q8IDV1
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL8
AJ
244Plasmodium falciparumMutation(s): 0 
Find proteins for Q8ILL2 (Plasmodium falciparum)
Go to UniProtKB:  Q8ILL2
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL37
Ac
89Plasmodium falciparumMutation(s): 0 
Find proteins for C0H4L5 (Plasmodium falciparum)
Go to UniProtKB:  C0H4L5
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL13
AK
201Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IJZ7 (Plasmodium falciparum)
Go to UniProtKB:  Q8IJZ7
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL14
AM
132Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IE09 (Plasmodium falciparum)
Go to UniProtKB:  Q8IE09
Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL18
AS
186Plasmodium falciparumMutation(s): 0 
Find proteins for C0H5G3 (Plasmodium falciparum)
Go to UniProtKB:  C0H5G3
Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL15
AO
147Plasmodium falciparumMutation(s): 0 
Find proteins for C6KT23 (Plasmodium falciparum)
Go to UniProtKB:  C6KT23
Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL16
AQ
205Plasmodium falciparumMutation(s): 0 
Find proteins for Q8ILV2 (Plasmodium falciparum)
Go to UniProtKB:  Q8ILV2
Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL18
AR
289Plasmodium falciparumMutation(s): 0 
Find proteins for Q8ILL3 (Plasmodium falciparum)
Go to UniProtKB:  Q8ILL3
Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL22
AW
170Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IDI5 (Plasmodium falciparum)
Go to UniProtKB:  Q8IDI5
Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL23
AY
101Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IE82 (Plasmodium falciparum)
Go to UniProtKB:  Q8IE82
Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL19
AT
181Plasmodium falciparumMutation(s): 0 
Find proteins for C6KSY6 (Plasmodium falciparum)
Go to UniProtKB:  C6KSY6
Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL24
AZ
121Plasmodium falciparumMutation(s): 0 
Find proteins for O77364 (Plasmodium falciparum)
Go to UniProtKB:  O77364
Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL29
A3
119Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IIB4 (Plasmodium falciparum)
Go to UniProtKB:  Q8IIB4
Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL30
A5
223Plasmodium falciparumMutation(s): 0 
Find proteins for O97250 (Plasmodium falciparum)
Go to UniProtKB:  O97250
Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL2
AD
247Plasmodium falciparumMutation(s): 0 
Find proteins for Q8I3T9 (Plasmodium falciparum)
Go to UniProtKB:  Q8I3T9
Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL3
AE
380Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IJC6 (Plasmodium falciparum)
Go to UniProtKB:  Q8IJC6
Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL4
AF
390Plasmodium falciparumMutation(s): 0 
Find proteins for Q8I431 (Plasmodium falciparum)
Go to UniProtKB:  Q8I431
Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL5
AG
159Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IBQ6 (Plasmodium falciparum)
Go to UniProtKB:  Q8IBQ6
Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL20
AU
180Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IDS6 (Plasmodium falciparum)
Go to UniProtKB:  Q8IDS6
Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL6
AH
185Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IE85 (Plasmodium falciparum)
Go to UniProtKB:  Q8IE85
Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL21
AV
155Plasmodium falciparumMutation(s): 0 
Find proteins for Q8ILK3 (Plasmodium falciparum)
Go to UniProtKB:  Q8ILK3
Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL41
Ag
37Plasmodium falciparumMutation(s): 0 
Find proteins for C6S3G4 (Plasmodium falciparum)
Go to UniProtKB:  C6S3G4
Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL22
AX
97Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IB51 (Plasmodium falciparum)
Go to UniProtKB:  Q8IB51
Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL24
A0
62Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IEM3 (Plasmodium falciparum)
Go to UniProtKB:  Q8IEM3
Entity ID: 1
MoleculeChainsLengthOrganism
18S ribosomal RNAA1608Plasmodium falciparum 3D7
Entity ID: 2
MoleculeChainsLengthOrganism
P-tRNA776Escherichia coli
Entity ID: 34
MoleculeChainsLengthOrganism
28S ribosomal RNAAA3193Plasmodium falciparum 3D7
Entity ID: 35
MoleculeChainsLengthOrganism
5.8S ribosomal RNAAC151Plasmodium falciparum 3D7
Entity ID: 36
MoleculeChainsLengthOrganism
5S ribosomal RNAAB118Plasmodium falciparum 3D7
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
AW
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-12-16
    Type: Database references
  • Version 1.2: 2018-07-18
    Type: Data collection