7PWG

Cryo-EM structure of large subunit of Giardia lamblia ribosome at 2.7 A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L2D [auth A]251Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L3E [auth B]379Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L4F [auth C]316Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L5G [auth D]297Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L7H [auth F]235Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aI [auth G]225Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L6J [auth H]185Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L10K [auth I]210Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L11L [auth J]173Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13M [auth L]234Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L14N [auth M]131Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15O [auth N]204Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L13aP [auth O]197Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L17Q [auth P]164Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L18R [auth Q]179Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L19S [auth R]196Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aT [auth S]173Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L21U [auth T]159Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL22V [auth U]171Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23W [auth V]142Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23A141Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26135Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27135Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L27aAA [auth a]149Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29BA [auth b]62Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L30CA [auth c]109Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L31BDA [auth d]106Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L32EA [auth e]136Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L35aFA [auth f]123Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L34GA [auth g]120Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L29HA [auth h]124Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L36-1IA [auth i]90Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37JA [auth j]89Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal L38eKA [auth k]77Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L39LA [auth l]51Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin/Ribosomal protein L40eMA [auth m]127Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L44NA [auth o]106Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37aOA [auth p]94Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24AQA [auth W]102Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
rRNA 28SA [auth 1]2,707Giardia lamblia ATCC 50803
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Entity ID: 2
MoleculeChains LengthOrganismImage
rRNA 5SB [auth 3]120Giardia lamblia ATCC 50803
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Entity ID: 3
MoleculeChains LengthOrganismImage
rRNA 5.8SC [auth 4]139Giardia lamblia ATCC 50803
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Entity ID: 42
MoleculeChains LengthOrganismImage
E-site tRNAPA [auth w]76Giardia lamblia ATCC 50803
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Entity ID: 44
MoleculeChains LengthOrganismImage
P-site tRNARA [auth E]3Giardia lamblia ATCC 50803
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

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UK [auth 1]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
K
Query on K

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AF [auth 1]
AG [auth 1]
AH [auth 1]
AI [auth 1]
AJ [auth 1]
AF [auth 1],
AG [auth 1],
AH [auth 1],
AI [auth 1],
AJ [auth 1],
AK [auth 1],
BF [auth 1],
BG [auth 1],
BH [auth 1],
BI [auth 1],
BJ [auth 1],
BK [auth 1],
BL [auth A],
CF [auth 1],
CG [auth 1],
CH [auth 1],
CI [auth 1],
CJ [auth 1],
CK [auth 1],
CL [auth A],
DF [auth 1],
DG [auth 1],
DH [auth 1],
DI [auth 1],
DJ [auth 1],
DK [auth 1],
DL [auth A],
EF [auth 1],
EG [auth 1],
EH [auth 1],
EI [auth 1],
EJ [auth 1],
EK [auth 1],
EL [auth B],
FF [auth 1],
FG [auth 1],
FH [auth 1],
FI [auth 1],
FJ [auth 1],
FK [auth 1],
FL [auth B],
GF [auth 1],
GG [auth 1],
GH [auth 1],
GI [auth 1],
GJ [auth 1],
GK [auth 1],
GL [auth B],
HF [auth 1],
HG [auth 1],
HH [auth 1],
HI [auth 1],
HJ [auth 1],
HK [auth 1],
IF [auth 1],
IG [auth 1],
IH [auth 1],
II [auth 1],
IJ [auth 1],
IK [auth 1],
IL [auth C],
JF [auth 1],
JG [auth 1],
JH [auth 1],
JI [auth 1],
JJ [auth 1],
JK [auth 1],
JL [auth C],
KF [auth 1],
KG [auth 1],
KH [auth 1],
KI [auth 1],
KJ [auth 1],
KK [auth 1],
LF [auth 1],
LG [auth 1],
LH [auth 1],
LI [auth 1],
LJ [auth 1],
LK [auth 1],
MF [auth 1],
MG [auth 1],
MH [auth 1],
MI [auth 1],
MJ [auth 1],
MK [auth 1],
ML [auth I],
NE [auth 1],
NF [auth 1],
NG [auth 1],
NH [auth 1],
NI [auth 1],
NJ [auth 1],
NK [auth 1],
NL [auth L],
OE [auth 1],
OF [auth 1],
OG [auth 1],
OH [auth 1],
OI [auth 1],
OJ [auth 1],
OK [auth 1],
OL [auth N],
PE [auth 1],
PF [auth 1],
PG [auth 1],
PH [auth 1],
PI [auth 1],
PJ [auth 1],
PK [auth 1],
PL [auth N],
QE [auth 1],
QF [auth 1],
QG [auth 1],
QH [auth 1],
QI [auth 1],
QJ [auth 1],
QK [auth 1],
RE [auth 1],
RF [auth 1],
RG [auth 1],
RH [auth 1],
RI [auth 1],
RJ [auth 1],
RK [auth 1],
SE [auth 1],
SF [auth 1],
SG [auth 1],
SH [auth 1],
SI [auth 1],
SJ [auth 1],
SK [auth 1],
SL [auth V],
TE [auth 1],
TF [auth 1],
TG [auth 1],
TH [auth 1],
TI [auth 1],
TJ [auth 1],
TK [auth 1],
UE [auth 1],
UF [auth 1],
UG [auth 1],
UH [auth 1],
UI [auth 1],
UJ [auth 1],
UL [auth a],
VE [auth 1],
VF [auth 1],
VG [auth 1],
VH [auth 1],
VI [auth 1],
VJ [auth 1],
VK [auth 3],
WE [auth 1],
WF [auth 1],
WG [auth 1],
WH [auth 1],
WI [auth 1],
WJ [auth 1],
WL [auth e],
XE [auth 1],
XF [auth 1],
XG [auth 1],
XH [auth 1],
XI [auth 1],
XJ [auth 1],
XL [auth j],
YE [auth 1],
YF [auth 1],
YG [auth 1],
YH [auth 1],
YI [auth 1],
YJ [auth 1],
ZE [auth 1],
ZF [auth 1],
ZG [auth 1],
ZH [auth 1],
ZI [auth 1],
ZJ [auth 1],
ZL [auth o]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 1]
AC [auth 1]
AD [auth 1]
AE [auth 1]
AL [auth 4]
AB [auth 1],
AC [auth 1],
AD [auth 1],
AE [auth 1],
AL [auth 4],
BB [auth 1],
BC [auth 1],
BD [auth 1],
BE [auth 1],
CB [auth 1],
CC [auth 1],
CD [auth 1],
CE [auth 1],
DB [auth 1],
DC [auth 1],
DD [auth 1],
DE [auth 1],
EB [auth 1],
EC [auth 1],
ED [auth 1],
EE [auth 1],
FB [auth 1],
FC [auth 1],
FD [auth 1],
FE [auth 1],
GB [auth 1],
GC [auth 1],
GD [auth 1],
GE [auth 1],
HB [auth 1],
HC [auth 1],
HD [auth 1],
HE [auth 1],
HL [auth C],
IB [auth 1],
IC [auth 1],
ID [auth 1],
IE [auth 1],
JB [auth 1],
JC [auth 1],
JD [auth 1],
JE [auth 1],
KB [auth 1],
KC [auth 1],
KD [auth 1],
KE [auth 1],
KL [auth F],
LB [auth 1],
LC [auth 1],
LD [auth 1],
LE [auth 1],
LL [auth I],
MB [auth 1],
MC [auth 1],
MD [auth 1],
ME [auth 1],
NB [auth 1],
NC [auth 1],
ND [auth 1],
OB [auth 1],
OC [auth 1],
OD [auth 1],
PB [auth 1],
PC [auth 1],
PD [auth 1],
QB [auth 1],
QC [auth 1],
QD [auth 1],
QL [auth P],
RB [auth 1],
RC [auth 1],
RD [auth 1],
RL [auth V],
SA [auth 1],
SB [auth 1],
SC [auth 1],
SD [auth 1],
TA [auth 1],
TB [auth 1],
TC [auth 1],
TD [auth 1],
TL [auth a],
UA [auth 1],
UB [auth 1],
UC [auth 1],
UD [auth 1],
VA [auth 1],
VB [auth 1],
VC [auth 1],
VD [auth 1],
VL [auth b],
WA [auth 1],
WB [auth 1],
WC [auth 1],
WD [auth 1],
WK [auth 4],
XA [auth 1],
XB [auth 1],
XC [auth 1],
XD [auth 1],
XK [auth 4],
YA [auth 1],
YB [auth 1],
YC [auth 1],
YD [auth 1],
YK [auth 4],
YL [auth o],
ZA [auth 1],
ZB [auth 1],
ZC [auth 1],
ZD [auth 1],
ZK [auth 4]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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: 2022-04-20
    Type: Initial release