3J7A

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

> Summary

Summary for 3J7A

Related3J79
EMDB informationEMD-2660 EMD-2661
DescriptorPROTEIN/RNA Complex
Functional Keywordsemetine, ribosome-inhibitor complex, ribosome/inhibitor
Biological sourcePlasmodium falciparum
Cellular locationCytoplasm  O97313 Q8IJD4
Total number of polymer chains33
Total molecular weight1263065.72
Authors
Wong, W.,Bai, X.C.,Brown, A.,Fernandez, I.S.,Hanssen, E.,Condron, M.,Tan, Y.H.,Baum, J.,Scheres, S.H.W. (deposition date: 2014-06-03, release date: 2014-07-16, Last modification date: 2015-06-03)
Primary citation
Wong, W.,Bai, X.C.,Brown, A.,Fernandez, I.S.,Hanssen, E.,Condron, M.,Tan, Y.H.,Baum, J.,Scheres, S.H.
Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine.
Elife, 3:e03080-e03080, 2014
PubMed: 24913268
DOI: 10.7554/eLife.03080
MImport into Mendeley
Experimental method
ELECTRON MICROSCOPY
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Structure validation

ClashscoreRamachandran outliersSidechain outliersRNA backbone44.2%14.2%0.39MetricValuePercentile RanksWorseBetterPercentile relative to all structuresPercentile relative to all EM structures

More Asymmetric unit images

Molmil generated image of 3j7a
no rotation
Molmil generated image of 3j7a
rotated about x axis by 90°
Molmil generated image of 3j7a
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A18S ribosomal RNApolymer2092671338.81
Plasmodium falciparum
B40S ribosomal protein eS1polymer26230111.91
UniProt (O97313)
Pfam (PF01015)
Plasmodium falciparum
C40S ribosomal protein uS2polymer26329891.41
UniProt (Q8IJD4)
Pfam (PF00318)
Plasmodium falciparum
D40S ribosomal protein uS3polymer22124710.11
UniProt (Q8IKH8)
Pfam (PF00189)
Pfam (PF07650)
Plasmodium falciparum
E40S ribosomal protein uS4polymer18922172.31
UniProt (Q8I3R0)
Pfam (PF00163)
Pfam (PF01479)
Plasmodium falciparum
F40S ribosomal protein eS4polymer26129830.51
UniProt (Q8IIU8)
Pfam (PF00900)
Pfam (PF08071)
Pfam (PF16121)
Plasmodium falciparum
G40S ribosomal protein uS5polymer27230009.01
UniProt (Q8IL02)
Pfam (PF00333)
Pfam (PF03719)
Plasmodium falciparum
H40S ribosomal protein eS6polymer30635474.01
UniProt (Q8IDR9)
Pfam (PF01092)
Plasmodium falciparum
I40S ribosomal protein uS7polymer19521898.61
UniProt (Q8IBN5)
Pfam (PF00177)
Plasmodium falciparum
J40S ribosomal protein eS7polymer19422524.91
UniProt (Q8IET7)
Pfam (PF01251)
Plasmodium falciparum
K40S ribosomal protein uS8polymer13014900.81
UniProt (O77395)
Pfam (PF00410)
Plasmodium falciparum
L40S ribosomal protein eS8polymer21825106.21
UniProt (Q8IM10)
Pfam (PF01201)
Plasmodium falciparum
M40S ribosomal protein uS9polymer14416318.41
UniProt (Q8IAX5)
Pfam (PF00380)
Plasmodium falciparum
N40S ribosomal protein uS10polymer11813535.01
UniProt (Q8IK02)
Pfam (PF00338)
Plasmodium falciparum
O40S ribosomal protein eS10polymer13716510.41
UniProt (Q8IBQ5)
Pfam (PF03501)
Plasmodium falciparum
P40S ribosomal protein uS11polymer15116105.71
UniProt (Q8I3U6)
Pfam (PF00411)
Plasmodium falciparum
Q40S ribosomal protein uS12polymer14516167.11
UniProt (O97248)
Pfam (PF00164)
Plasmodium falciparum
R40S ribosomal protein eS12polymer14115414.61
UniProt (O97249)
Pfam (PF01248)
Plasmodium falciparum
S40S ribosomal protein uS13polymer15617929.11
UniProt (Q8IIA2)
Pfam (PF00416)
Plasmodium falciparum
T40S ribosomal protein uS14polymer546430.71
UniProt (C0H4K8)
Pfam (PF00253)
Plasmodium falciparum
U40S ribosomal protein uS15polymer15117286.61
UniProt (Q8IDB0)
Pfam (PF00312)
Pfam (PF08069)
Plasmodium falciparum
V40S ribosomal protein uS17polymer16118801.31
UniProt (O77381)
Pfam (PF00366)
Pfam (PF16205)
Plasmodium falciparum
W40S ribosomal protein eS17polymer13716097.11
UniProt (Q8I502)
Pfam (PF00833)
Plasmodium falciparum
X40S ribosomal protein uS19polymer14516800.91
UniProt (C0H5C2)
Pfam (PF00203)
Plasmodium falciparum
Y40S ribosomal protein eS19polymer17019758.11
UniProt (Q8IFP2)
Pfam (PF01090)
Plasmodium falciparum
Z40S ribosomal protein eS21polymer829157.51
UniProt (Q8IHS5)
Pfam (PF01249)
Plasmodium falciparum
140S ribosomal protein eS24polymer13315431.61
UniProt (Q8I3R6)
Pfam (PF01282)
Plasmodium falciparum
240S ribosomal protein eS25polymer10511692.01
UniProt (Q8ILN8)
Pfam (PF03297)
Plasmodium falciparum
340S ribosomal protein eS26polymer10712539.81
UniProt (O96258)
Pfam (PF01283)
Plasmodium falciparum
440S ribosomal protein eS27polymer829154.91
UniProt (Q8IEN2)
Pfam (PF01667)
Plasmodium falciparum
540S ribosomal protein eS28polymer677508.91
UniProt (Q8IKL9)
Pfam (PF01200)
Plasmodium falciparum
640S ribosomal protein eS30polymer586508.81
UniProt (O96269)
Pfam (PF04758)
Plasmodium falciparum
7tRNApolymer7423774.21
Plasmodium falciparum
MAGNESIUM IONnon-polymer24.367
EMETINEnon-polymer480.61
ZINC IONnon-polymer65.41

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains33
Total molecular weight1260891.3
Non-Polymers*Number of molecules69
Total molecular weight2174.5
All*Total molecular weight1263065.7
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:ELECTRON MICROSCOPY

Cell axes1.0001.0001.000
Cell angles90.0090.0090.00
SpacegroupP 1
Resolution limits -
the highest resolution shell value -

Data Collection Statistics

Resolution limits -
the highest resolution shell value -

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
R0022627cellular_componentcytosolic small ribosomal subunit
R0003735molecular_functionstructural constituent of ribosome
R0006412biological_processtranslation
60022627cellular_componentcytosolic small ribosomal subunit
60003735molecular_functionstructural constituent of ribosome
60006412biological_processtranslation
B0005829cellular_componentcytosol
B0022627cellular_componentcytosolic small ribosomal subunit
B0003735molecular_functionstructural constituent of ribosome
B0006412biological_processtranslation
C0030686cellular_component90S preribosome
C0022627cellular_componentcytosolic small ribosomal subunit
C0003735molecular_functionstructural constituent of ribosome
C0000447biological_processendonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
C0000461biological_processendonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
C0000028biological_processribosomal small subunit assembly
C0006407biological_processrRNA export from nucleus
C0006412biological_processtranslation
L0022627cellular_componentcytosolic small ribosomal subunit
L0003735molecular_functionstructural constituent of ribosome
L0000462biological_processmaturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
L0006412biological_processtranslation
30022627cellular_componentcytosolic small ribosomal subunit
30003729molecular_functionmRNA binding
30003735molecular_functionstructural constituent of ribosome
30006412biological_processtranslation
F0022627cellular_componentcytosolic small ribosomal subunit
F0015935cellular_componentsmall ribosomal subunit
F0003723molecular_functionRNA binding
F0019843molecular_functionrRNA binding
F0003735molecular_functionstructural constituent of ribosome
F0006412biological_processtranslation
50022627cellular_componentcytosolic small ribosomal subunit
50003723molecular_functionRNA binding
50003735molecular_functionstructural constituent of ribosome
50030490biological_processmaturation of SSU-rRNA
50000028biological_processribosomal small subunit assembly
50006412biological_processtranslation
20022627cellular_componentcytosolic small ribosomal subunit
20003735molecular_functionstructural constituent of ribosome
20006412biological_processtranslation
Z0022627cellular_componentcytosolic small ribosomal subunit
Z0003735molecular_functionstructural constituent of ribosome
Z0000447biological_processendonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
Z0000461biological_processendonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
Z0006412biological_processtranslation
D0022627cellular_componentcytosolic small ribosomal subunit
D0005634cellular_componentnucleus
D0003684molecular_functiondamaged DNA binding
D0008534molecular_functionoxidized purine nucleobase lesion DNA N-glycosylase activity
D0003723molecular_functionRNA binding
D0003735molecular_functionstructural constituent of ribosome
D0006281biological_processDNA repair
D0006412biological_processtranslation
W0022627cellular_componentcytosolic small ribosomal subunit
W0005739cellular_componentmitochondrion
W0003735molecular_functionstructural constituent of ribosome
W0000028biological_processribosomal small subunit assembly
W0006412biological_processtranslation
S0005829cellular_componentcytosol
S0015935cellular_componentsmall ribosomal subunit
S0003723molecular_functionRNA binding
S0003735molecular_functionstructural constituent of ribosome
S0042254biological_processribosome biogenesis
S0006412biological_processtranslation
G0022627cellular_componentcytosolic small ribosomal subunit
G0003723molecular_functionRNA binding
G0003735molecular_functionstructural constituent of ribosome
G0006412biological_processtranslation
N0022627cellular_componentcytosolic small ribosomal subunit
N0003735molecular_functionstructural constituent of ribosome
N0006412biological_processtranslation
P0022627cellular_componentcytosolic small ribosomal subunit
P0048027molecular_functionmRNA 5'-UTR binding
P0003723molecular_functionRNA binding
P0070181molecular_functionsmall ribosomal subunit rRNA binding
P0003735molecular_functionstructural constituent of ribosome
P0000462biological_processmaturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
P0000028biological_processribosomal small subunit assembly
P0006412biological_processtranslation
O0022627cellular_componentcytosolic small ribosomal subunit
O0003735molecular_functionstructural constituent of ribosome
O0000028biological_processribosomal small subunit assembly
O0006412biological_processtranslation
Y0022627cellular_componentcytosolic small ribosomal subunit
Y0003735molecular_functionstructural constituent of ribosome
Y0000028biological_processribosomal small subunit assembly
Y0006412biological_processtranslation
T0022627cellular_componentcytosolic small ribosomal subunit
T0003735molecular_functionstructural constituent of ribosome
T0008270molecular_functionzinc ion binding
T0006412biological_processtranslation
40022627cellular_componentcytosolic small ribosomal subunit
40003735molecular_functionstructural constituent of ribosome
40000028biological_processribosomal small subunit assembly
40006412biological_processtranslation
M0022627cellular_componentcytosolic small ribosomal subunit
M0003735molecular_functionstructural constituent of ribosome
M0000462biological_processmaturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
M0006412biological_processtranslation
10022627cellular_componentcytosolic small ribosomal subunit
10003735molecular_functionstructural constituent of ribosome
10000462biological_processmaturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
10006412biological_processtranslation
J0022627cellular_componentcytosolic small ribosomal subunit
J0003735molecular_functionstructural constituent of ribosome
J0006412biological_processtranslation
I0022627cellular_componentcytosolic small ribosomal subunit
I0003723molecular_functionRNA binding
I0003735molecular_functionstructural constituent of ribosome
I0006412biological_processtranslation
U0022627cellular_componentcytosolic small ribosomal subunit
U0005730cellular_componentnucleolus
U0070181molecular_functionsmall ribosomal subunit rRNA binding
U0003735molecular_functionstructural constituent of ribosome
U0006412biological_processtranslation
H0022627cellular_componentcytosolic small ribosomal subunit
H0003735molecular_functionstructural constituent of ribosome
H0042274biological_processribosomal small subunit biogenesis
H0006364biological_processrRNA processing
H0006412biological_processtranslation
Q0022627cellular_componentcytosolic small ribosomal subunit
Q0003735molecular_functionstructural constituent of ribosome
Q0006412biological_processtranslation
E0022627cellular_componentcytosolic small ribosomal subunit
E0019843molecular_functionrRNA binding
E0003735molecular_functionstructural constituent of ribosome
E0045903biological_processpositive regulation of translational fidelity
E0006412biological_processtranslation
V0022627cellular_componentcytosolic small ribosomal subunit
V0003735molecular_functionstructural constituent of ribosome
V0006412biological_processtranslation
K0022627cellular_componentcytosolic small ribosomal subunit
K0003735molecular_functionstructural constituent of ribosome
K0006412biological_processtranslation
X0022627cellular_componentcytosolic small ribosomal subunit
X0003723molecular_functionRNA binding
X0003735molecular_functionstructural constituent of ribosome
X0000028biological_processribosomal small subunit assembly
X0006412biological_processtranslation
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC12BINDING SITE FOR RESIDUE MG A 2101
ChainResidue
AG10
AA1930

AC21BINDING SITE FOR RESIDUE MG A 2102
ChainResidue
AG16

AC32BINDING SITE FOR RESIDUE MG A 2103
ChainResidue
AA102
AC367

AC45BINDING SITE FOR RESIDUE MG A 2104
ChainResidue
AA102
AU103
AU104
AA366
AC367

AC52BINDING SITE FOR RESIDUE MG A 2105
ChainResidue
AC49
AA431

AC62BINDING SITE FOR RESIDUE MG A 2106
ChainResidue
AA452
AU454

AC72BINDING SITE FOR RESIDUE MG A 2107
ChainResidue
AA60
AA459

AC81BINDING SITE FOR RESIDUE MG A 2108
ChainResidue
AA87

AC91BINDING SITE FOR RESIDUE MG A 2109
ChainResidue
AG97

BC11BINDING SITE FOR RESIDUE MG A 2111
ChainResidue
AU408

BC23BINDING SITE FOR RESIDUE MG A 2112
ChainResidue
AG328
AG343
AA347

BC33BINDING SITE FOR RESIDUE MG A 2113
ChainResidue
AG42
AA43
AU100

BC42BINDING SITE FOR RESIDUE MG A 2114
ChainResidue
AU44
AA47

BC51BINDING SITE FOR RESIDUE MG A 2115
ChainResidue
AG435

BC63BINDING SITE FOR RESIDUE MG A 2116
ChainResidue
AG383
AA384
AU385

BC72BINDING SITE FOR RESIDUE MG A 2117
ChainResidue
AA407
AU408

BC82BINDING SITE FOR RESIDUE MG A 2118
ChainResidue
AC430
AG432

BC92BINDING SITE FOR RESIDUE MG A 2119
ChainResidue
AA466
AG467

CC11BINDING SITE FOR RESIDUE MG A 2120
ChainResidue
AA28

CC23BINDING SITE FOR RESIDUE MG A 2121
ChainResidue
AU35
AG522
AC537

CC31BINDING SITE FOR RESIDUE MG A 2123
ChainResidue
AG568

CC42BINDING SITE FOR RESIDUE MG A 2124
ChainResidue
AA577
AG578

CC51BINDING SITE FOR RESIDUE MG A 2125
ChainResidue
AA611

CC63BINDING SITE FOR RESIDUE MG A 2126
ChainResidue
AG377
AA612
AA614

CC71BINDING SITE FOR RESIDUE MG A 2127
ChainResidue
AC621

CC84BINDING SITE FOR RESIDUE MG A 2128
ChainResidue
AU625
AA626
AA627
AA628

CC91BINDING SITE FOR RESIDUE MG A 2129
ChainResidue
AC630

DC14BINDING SITE FOR RESIDUE MG A 2130
ChainResidue
AA629
AC630
AC632
AU1100

DC22BINDING SITE FOR RESIDUE MG A 2131
ChainResidue
AA637
AG638

DC32BINDING SITE FOR RESIDUE MG A 2132
ChainResidue
AA642
AA643

DC42BINDING SITE FOR RESIDUE MG A 2133
ChainResidue
AA930
AA931

DC51BINDING SITE FOR RESIDUE MG A 2135
ChainResidue
AG1007

DC63BINDING SITE FOR RESIDUE MG A 2136
ChainResidue
AU1059
AG1060
AG1080

DC71BINDING SITE FOR RESIDUE MG A 2137
ChainResidue
AU1081

DC81BINDING SITE FOR RESIDUE MG A 2138
ChainResidue
AG1054

DC95BINDING SITE FOR RESIDUE MG A 2139
ChainResidue
AG964
AU965
AG983
AA984
AU986

EC12BINDING SITE FOR RESIDUE MG A 2140
ChainResidue
AG997
AA998

EC21BINDING SITE FOR RESIDUE MG A 2141
ChainResidue
AG945

EC32BINDING SITE FOR RESIDUE MG A 2142
ChainResidue
3GLY16
AG1011

EC41BINDING SITE FOR RESIDUE MG A 2143
ChainResidue
AA1047

EC51BINDING SITE FOR RESIDUE MG A 2144
ChainResidue
AU1037

EC61BINDING SITE FOR RESIDUE MG A 2145
ChainResidue
AA1094

EC72BINDING SITE FOR RESIDUE MG A 2146
ChainResidue
AG1210
AG1211

EC83BINDING SITE FOR RESIDUE MG A 2147
ChainResidue
AA1261
AG1876
MTYR143

EC93BINDING SITE FOR RESIDUE MG A 2148
ChainResidue
AG1926
AU1927
AG2085

FC15BINDING SITE FOR RESIDUE MG A 2149
ChainResidue
AA2055
AG2059
AG2060
AU2062
AU2063

FC21BINDING SITE FOR RESIDUE MG A 2150
ChainResidue
AU2062

FC35BINDING SITE FOR RESIDUE MG A 2151
ChainResidue
AU2053
AA2054
AA2055
AG2059
AG2060

FC42BINDING SITE FOR RESIDUE MG A 2152
ChainResidue
AG20
AU21

FC51BINDING SITE FOR RESIDUE MG A 2153
ChainResidue
AG521

FC62BINDING SITE FOR RESIDUE MG A 2154
ChainResidue
AU1405
AG1406

FC72BINDING SITE FOR RESIDUE MG A 2155
ChainResidue
AA169
AC170

FC82BINDING SITE FOR RESIDUE MG A 2156
ChainResidue
AG394
AU408

FC95BINDING SITE FOR RESIDUE MG A 2157
ChainResidue
AG559
AG560
AC561
AA562
AA563

GC13BINDING SITE FOR RESIDUE MG A 2158
ChainResidue
AA1062
AA1074
AMG2159

GC23BINDING SITE FOR RESIDUE MG A 2159
ChainResidue
AG1063
AA1074
AMG2158

GC31BINDING SITE FOR RESIDUE MG A 2160
ChainResidue
AU1084

GC41BINDING SITE FOR RESIDUE MG A 2161
ChainResidue
AG1432

GC52BINDING SITE FOR RESIDUE MG A 2162
ChainResidue
AG1430
AG1432

GC64BINDING SITE FOR RESIDUE MG A 2163
ChainResidue
AG1374
AC1375
AG1674
AG1675

GC74BINDING SITE FOR RESIDUE MG A 2164
ChainResidue
AA1305
AC1306
AU1307
AG1701

GC83BINDING SITE FOR RESIDUE MG A 2165
ChainResidue
AA1303
AA1304
AC1896

GC91BINDING SITE FOR RESIDUE MG A 2166
ChainResidue
AU1703

HC11BINDING SITE FOR RESIDUE MG A 2167
ChainResidue
AG1302

HC26BINDING SITE FOR RESIDUE 34G A 2168
ChainResidue
AG973
AU1068
AC1075
AG2060
AU2061
PLEU151

HC35BINDING SITE FOR RESIDUE ZN T 100
ChainResidue
TCYS19
TCYS22
TASN24
TCYS37
TCYS40

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
34G_3j7a_A_21689EMETINE binding site
ChainResidueligand
AU972-G97334G: EMETINE
AA1067-C106934G: EMETINE
AC107534G: EMETINE
AG2060-U206134G: EMETINE
PLEU15134G: EMETINE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

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