7PWF

Cryo-EM structure of small subunit of Giardia lamblia ribosome at 2.9 A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of the ancient eukaryotic ribosome from the human parasite Giardia lamblia.

Hiregange, D.G.Rivalta, A.Bose, T.Breiner-Goldstein, E.Samiya, S.Cimicata, G.Kulakova, L.Zimmerman, E.Bashan, A.Herzberg, O.Yonath, A.

(2022) Nucleic Acids Res 50: 1770-1782

  • DOI: https://doi.org/10.1093/nar/gkac046
  • Primary Citation of Related Structures:  
    7PWF, 7PWG, 7PWO

  • PubMed Abstract: 

    Giardiasis is a disease caused by the protist Giardia lamblia. As no human vaccines have been approved so far against it, and resistance to current drugs is spreading, new strategies for combating giardiasis need to be developed. The G. lamblia ribosome may provide a promising therapeutic target due to its distinct sequence differences from ribosomes of most eukaryotes and prokaryotes. Here, we report the cryo-electron microscopy structure of the G. lamblia (WB strain) ribosome determined at 2.75 Å resolution. The ribosomal RNA is the shortest known among eukaryotes, and lacks nearly all the eukaryote-specific ribosomal RNA expansion segments. In contrast, the ribosomal proteins are typically eukaryotic with some species-specific insertions/extensions. Most typical inter-subunit bridges are maintained except for one missing contact site. Unique structural features are located mainly at the ribosome's periphery. These may be exploited as target sites for the design of new compounds that inhibit selectively the parasite's ribosomal activity.


  • Organizational Affiliation

    Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S29AA [auth d]137Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S19eB [auth T]139Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
Find proteins for A0A644F964 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S13C [auth N]154Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S9D [auth J]189Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S3E [auth D]217Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S23F [auth X]143Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S18G [auth S]154Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S16H [auth Q]158Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S2I [auth C]242Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAJ [auth A]245Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aK [auth B]248Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S24L [auth Y]132Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S27M [auth b]124Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26N [auth a]109Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25O [auth Z]88Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21P [auth V]89Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15Q [auth P]145Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S17137Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S10BS [auth K]134Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8T [auth I]174Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30U [auth e]69Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS7V [auth H]190Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL41W [auth n]41Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S28X [auth c]64Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S14Y [auth O]145Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15AZ [auth W]130Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4AA [auth E]268Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
SSU ribosomal protein S17PCA [auth L]199Giardia lamblia ATCC 50803Mutation(s): 1 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S20DA [auth U]126Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6EA [auth G]248Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S5FA [auth F]190Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 28
MoleculeChains LengthOrganismImage
rRNA 18SBA [auth 2]1,452Giardia lamblia ATCC 50803
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download Ideal Coordinates CCD File 
AB [auth O]
AC [auth 2]
AD [auth 2]
AE [auth 2]
AF [auth 2]
AB [auth O],
AC [auth 2],
AD [auth 2],
AE [auth 2],
AF [auth 2],
AG [auth 2],
AH [auth 2],
AI [auth 2],
AJ [auth 2],
AK [auth 2],
BB [auth W],
BC [auth 2],
BD [auth 2],
BE [auth 2],
BF [auth 2],
BG [auth 2],
BH [auth 2],
BI [auth 2],
BJ [auth 2],
BK [auth 2],
CB [auth E],
CC [auth 2],
CD [auth 2],
CE [auth 2],
CF [auth 2],
CG [auth 2],
CH [auth 2],
CI [auth 2],
CJ [auth 2],
CK [auth 2],
DB [auth E],
DC [auth 2],
DD [auth 2],
DE [auth 2],
DF [auth 2],
DG [auth 2],
DH [auth 2],
DI [auth 2],
DJ [auth 2],
DK [auth 2],
EB [auth E],
EC [auth 2],
ED [auth 2],
EE [auth 2],
EF [auth 2],
EG [auth 2],
EH [auth 2],
EI [auth 2],
EJ [auth 2],
EK [auth 2],
FB [auth 2],
FC [auth 2],
FD [auth 2],
FE [auth 2],
FF [auth 2],
FG [auth 2],
FH [auth 2],
FI [auth 2],
FJ [auth 2],
FK [auth 2],
GA [auth d],
GB [auth 2],
GC [auth 2],
GD [auth 2],
GE [auth 2],
GF [auth 2],
GG [auth 2],
GH [auth 2],
GI [auth 2],
GJ [auth 2],
GK [auth 2],
HA [auth N],
HB [auth 2],
HC [auth 2],
HD [auth 2],
HE [auth 2],
HF [auth 2],
HG [auth 2],
HH [auth 2],
HI [auth 2],
HJ [auth 2],
HK [auth 2],
IA [auth N],
IB [auth 2],
IC [auth 2],
ID [auth 2],
IE [auth 2],
IF [auth 2],
IG [auth 2],
IH [auth 2],
II [auth 2],
IJ [auth 2],
IK [auth 2],
JA [auth N],
JB [auth 2],
JC [auth 2],
JD [auth 2],
JE [auth 2],
JF [auth 2],
JG [auth 2],
JH [auth 2],
JI [auth 2],
JJ [auth 2],
JK [auth 2],
KA [auth N],
KB [auth 2],
KC [auth 2],
KD [auth 2],
KE [auth 2],
KF [auth 2],
KG [auth 2],
KH [auth 2],
KI [auth 2],
KJ [auth 2],
LA [auth N],
LB [auth 2],
LC [auth 2],
LD [auth 2],
LE [auth 2],
LF [auth 2],
LG [auth 2],
LH [auth 2],
LI [auth 2],
LJ [auth 2],
MA [auth N],
MB [auth 2],
MC [auth 2],
MD [auth 2],
ME [auth 2],
MF [auth 2],
MG [auth 2],
MH [auth 2],
MI [auth 2],
MJ [auth 2],
NA [auth N],
NB [auth 2],
NC [auth 2],
ND [auth 2],
NE [auth 2],
NF [auth 2],
NG [auth 2],
NH [auth 2],
NI [auth 2],
NJ [auth 2],
OB [auth 2],
OC [auth 2],
OD [auth 2],
OE [auth 2],
OF [auth 2],
OG [auth 2],
OH [auth 2],
OI [auth 2],
OJ [auth 2],
PA [auth S],
PB [auth 2],
PC [auth 2],
PD [auth 2],
PE [auth 2],
PF [auth 2],
PG [auth 2],
PH [auth 2],
PI [auth 2],
PJ [auth 2],
QA [auth S],
QB [auth 2],
QC [auth 2],
QD [auth 2],
QE [auth 2],
QF [auth 2],
QG [auth 2],
QH [auth 2],
QI [auth 2],
QJ [auth 2],
RA [auth A],
RB [auth 2],
RC [auth 2],
RD [auth 2],
RE [auth 2],
RF [auth 2],
RG [auth 2],
RH [auth 2],
RI [auth 2],
RJ [auth 2],
SA [auth b],
SB [auth 2],
SC [auth 2],
SD [auth 2],
SE [auth 2],
SF [auth 2],
SG [auth 2],
SH [auth 2],
SI [auth 2],
SJ [auth 2],
TA [auth R],
TB [auth 2],
TC [auth 2],
TD [auth 2],
TE [auth 2],
TF [auth 2],
TG [auth 2],
TH [auth 2],
TI [auth 2],
TJ [auth 2],
TL [auth L],
UB [auth 2],
UC [auth 2],
UD [auth 2],
UE [auth 2],
UF [auth 2],
UG [auth 2],
UH [auth 2],
UI [auth 2],
UJ [auth 2],
UL [auth L],
VA [auth O],
VB [auth 2],
VC [auth 2],
VD [auth 2],
VE [auth 2],
VF [auth 2],
VG [auth 2],
VH [auth 2],
VI [auth 2],
VJ [auth 2],
VL [auth L],
WA [auth O],
WB [auth 2],
WC [auth 2],
WD [auth 2],
WE [auth 2],
WF [auth 2],
WG [auth 2],
WH [auth 2],
WI [auth 2],
WJ [auth 2],
WL [auth G],
XA [auth O],
XB [auth 2],
XC [auth 2],
XD [auth 2],
XE [auth 2],
XF [auth 2],
XG [auth 2],
XH [auth 2],
XI [auth 2],
XJ [auth 2],
YA [auth O],
YB [auth 2],
YC [auth 2],
YD [auth 2],
YE [auth 2],
YF [auth 2],
YG [auth 2],
YH [auth 2],
YI [auth 2],
YJ [auth 2],
ZA [auth O],
ZB [auth 2],
ZC [auth 2],
ZD [auth 2],
ZE [auth 2],
ZF [auth 2],
ZG [auth 2],
ZH [auth 2],
ZI [auth 2],
ZJ [auth 2]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AL [auth 2]
BL [auth 2]
CL [auth 2]
DL [auth 2]
EL [auth 2]
AL [auth 2],
BL [auth 2],
CL [auth 2],
DL [auth 2],
EL [auth 2],
FL [auth 2],
GL [auth 2],
HL [auth 2],
IL [auth 2],
JL [auth 2],
KK [auth 2],
KL [auth 2],
LK [auth 2],
LL [auth 2],
MK [auth 2],
ML [auth 2],
NK [auth 2],
NL [auth 2],
OA [auth N],
OK [auth 2],
OL [auth 2],
PK [auth 2],
PL [auth 2],
QK [auth 2],
QL [auth 2],
RK [auth 2],
RL [auth 2],
SK [auth 2],
SL [auth 2],
TK [auth 2],
UA [auth I],
UK [auth 2],
VK [auth 2],
WK [auth 2],
XK [auth 2],
YK [auth 2],
ZK [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI119788

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2024-04-24
    Changes: Data collection