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- PDB-7pwo: Cryo-EM structure of Giardia lamblia ribosome at 2.75 A resolution -

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Basic information

Entry
Database: PDB / ID: 7pwo
TitleCryo-EM structure of Giardia lamblia ribosome at 2.75 A resolution
Components
  • (40S ribosomal protein ...) x 9
  • (60S ribosomal protein ...) x 5
  • (Ribosomal protein ...) x 51
  • E-site tRNA
  • P-site tRNA
  • Ribosomal L38e
  • SSU ribosomal protein S17P
  • Ubiquitin/Ribosomal protein L40e
  • rRNA 18S
  • rRNA 28S
  • rRNA 5.8S
  • rRNA 5S
KeywordsRIBOSOME / giardia / parasite
Function / homology
Function and homology information


endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic 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) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic 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) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Ribosomal protein L40e, archaeal / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily ...Ribosomal protein L40e, archaeal / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal L29e protein family / 40S Ribosomal protein S10 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein S24e / Ribosomal protein S23, eukaryotic/archaeal / 60S ribosomal protein L19 / Ribosomal protein S24e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein S27 / Ribosomal protein L30/YlxQ / 60S ribosomal protein L35 / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L7A/L8 / Ribosomal protein S3Ae / Ribosomal protein S28e conserved site / Ribosomal S3Ae family
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L39 / 40S ribosomal protein S30 / Ribosomal protein S19e / Ribosomal protein L27 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L39 / 40S ribosomal protein S30 / Ribosomal protein S19e / Ribosomal protein L27 / 40S ribosomal protein S8 / Ribosomal protein L21 / Ribosomal L38e / 40S ribosomal protein S21 / Ribosomal protein S28 / Ribosomal protein L14 / Ribosomal protein S20 / Ribosomal protein L18 / Ribosomal protein S24 / Ribosomal protein L30 / 40S ribosomal protein S6 / 60S ribosomal protein L13 / Ribosomal protein S29A / Ribosomal protein L4 / 40S ribosomal protein S3 / Ribosomal protein L15 / Ribosomal protein S13 / Ribosomal protein L17 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S4 / Ribosomal protein L26 / Ribosomal protein L19 / Ribosomal protein L11 / Ribosomal protein S27 / Ribosomal protein S16 / Ribosomal protein L35a / Ribosomal protein S9 / 60S ribosomal protein L7a / Ribosomal protein L37 / Ribosomal protein L10 / Ribosomal protein L32 / Large ribosomal subunit protein eL34 / Ribosomal protein L31B / Ribosomal protein L23A / Ribosomal protein S2 / Ribosomal protein L37a / Ribosomal protein L6 / Ribosomal protein L44 / 40S ribosomal protein S26 / Ribosomal protein S17 / Ribosomal protein L35 / Ribosomal protein L24A / Ribosomal protein S10B / Ribosomal protein L7 / Ribosomal protein L3 / Ribosomal protein L23 / Small ribosomal subunit protein eS1 / Ribosomal protein S23 / 60S ribosomal protein L18a / 40S ribosomal protein S7 / Ribosomal protein L13a / Large ribosomal subunit protein eL22 / 50S ribosomal protein L40e / Ribosomal protein L36-1 / 60S ribosomal protein L29 / Ribosomal protein S18 / Ribosomal protein L27a / Ribosomal protein S5 / Ribosomal protein L2 / Ribosomal protein L5 / Ribosomal protein S15A / Ribosomal protein S14 / SSU ribosomal protein S17P / 60S ribosomal protein L41
Similarity search - Component
Biological speciesGiardia lamblia ATCC 50803 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsHiregange, D.G. / Rivalta, A. / Bose, T. / Breiner-Goldstein, E. / Samiya, S. / Cimicata, G. / Kulakova, L. / Zimmerman, E. / Bashan, A. / Herzberg, O. / Yonath, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI119788 United States
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Cryo-EM structure of the ancient eukaryotic ribosome from the human parasite Giardia lamblia.
Authors: Disha-Gajanan Hiregange / Andre Rivalta / Tanaya Bose / Elinor Breiner-Goldstein / Sarit Samiya / Giuseppe Cimicata / Liudmila Kulakova / Ella Zimmerman / Anat Bashan / Osnat Herzberg / Ada Yonath /
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 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.
History
DepositionOct 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
T1: Ribosomal protein S19e
N1: Ribosomal protein S13
J1: Ribosomal protein S9
D1: Ribosomal protein S3
X1: Ribosomal protein S23
S1: Ribosomal protein S18
Q1: Ribosomal protein S16
C1: Ribosomal protein S2
B1: 40S ribosomal protein S3a
b1: Ribosomal protein S27
a1: 40S ribosomal protein S26
V1: 40S ribosomal protein S21
R1: Ribosomal protein S17
K1: Ribosomal protein S10B
I1: 40S ribosomal protein S8
e1: 40S ribosomal protein S30
H1: 40S ribosomal protein S7
n1: Ribosomal protein eL41
c1: Ribosomal protein S28
O1: Ribosomal protein S14
W1: Ribosomal protein S15A
E1: 40S ribosomal protein S4
L1: SSU ribosomal protein S17P
U1: Ribosomal protein S20
1: rRNA 28S
3: rRNA 5S
42: rRNA 5.8S
A2: Ribosomal protein L2
B2: Ribosomal protein L3
C2: Ribosomal protein L4
D2: Ribosomal protein L5
F2: Ribosomal protein L7
G2: 60S ribosomal protein L7a
H2: Ribosomal protein L6
I2: Ribosomal protein L10
J2: Ribosomal protein L11
L2: 60S ribosomal protein L13
M2: Ribosomal protein L14
N2: Ribosomal protein L15
O2: Ribosomal protein L13a
P2: Ribosomal protein L17
Q2: Ribosomal protein L18
R2: Ribosomal protein L19
S2: 60S ribosomal protein L18a
T2: Ribosomal protein L21
U2: Ribosomal protein eL22
V2: Ribosomal protein L23
X2: Ribosomal protein L23A
Y2: Ribosomal protein L26
Z2: 60S ribosomal protein L27
a2: Ribosomal protein L27a
b2: 60S ribosomal protein L29
c2: Ribosomal protein L30
d2: Ribosomal protein L31B
e2: Ribosomal protein L32
f2: Ribosomal protein L35a
g2: Ribosomal protein L34
h2: Ribosomal protein L35
i2: Ribosomal protein L36-1
j2: Ribosomal protein L37
k2: Ribosomal L38e
l2: Ribosomal protein L39
m2: Ubiquitin/Ribosomal protein L40e
o2: Ribosomal protein L44
p2: Ribosomal protein L37a
w2: E-site tRNA
W2: Ribosomal protein L24A
E: P-site tRNA
d1: Ribosomal protein S29A
F1: Ribosomal protein S5
Y1: Ribosomal protein S24
G1: 40S ribosomal protein S6
2: rRNA 18S
A1: 40S ribosomal protein SA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,699,464630
Polymers2,679,21974
Non-polymers20,244556
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Ribosomal protein ... , 51 types, 51 molecules T1N1J1D1X1S1Q1C1b1R1K1n1c1O1W1U1A2B2C2D2F2H2I2J2M2N2O2P2Q2R2...

#1: Protein Ribosomal protein S19e


Mass: 15463.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A0A644F964
#2: Protein Ribosomal protein S13


Mass: 17627.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BE02
#3: Protein Ribosomal protein S9


Mass: 21699.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BKS8
#4: Protein Ribosomal protein S3


Mass: 24779.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B8Z2
#5: Protein Ribosomal protein S23


Mass: 15897.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BS96
#6: Protein Ribosomal protein S18


Mass: 17510.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BZ58
#7: Protein Ribosomal protein S16


Mass: 17634.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BKC6
#8: Protein Ribosomal protein S2


Mass: 26765.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BMZ1
#10: Protein Ribosomal protein S27


Mass: 14117.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BJL1
#13: Protein Ribosomal protein S17


Mass: 15757.351 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BRG5
#14: Protein Ribosomal protein S10B


Mass: 15406.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BRX3
#18: Protein/peptide Ribosomal protein eL41


Mass: 5194.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: V6TX21
#19: Protein Ribosomal protein S28


Mass: 7358.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B4F3
#20: Protein Ribosomal protein S14


Mass: 15755.995 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: E2RU83
#21: Protein Ribosomal protein S15A


Mass: 14770.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: E2RU77
#24: Protein Ribosomal protein S20


Mass: 14073.192 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B4G0
#28: Protein Ribosomal protein L2 / Ribosomal protein L8


Mass: 27090.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: E2RTN4
#29: Protein Ribosomal protein L3


Mass: 42715.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BRZ3
#30: Protein Ribosomal protein L4


Mass: 35048.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B7H8
#31: Protein Ribosomal protein L5


Mass: 33961.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: E2RU47
#32: Protein Ribosomal protein L7


Mass: 27103.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BRY6
#34: Protein Ribosomal protein L6 / Ribosomal protein L9


Mass: 20889.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BNT5
#35: Protein Ribosomal protein L10


Mass: 24283.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BM86
#36: Protein Ribosomal protein L11


Mass: 19767.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BI95
#38: Protein Ribosomal protein L14


Mass: 14785.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B4F8
#39: Protein Ribosomal protein L15


Mass: 24353.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B8Z6
#40: Protein Ribosomal protein L13a


Mass: 22921.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BU75
#41: Protein Ribosomal protein L17


Mass: 18722.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BE76
#42: Protein Ribosomal protein L18


Mass: 20207.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B4T7
#43: Protein Ribosomal protein L19


Mass: 23199.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BH61
#45: Protein Ribosomal protein L21


Mass: 18296.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B2Q4
#46: Protein Ribosomal protein eL22


Mass: 19942.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BW84
#47: Protein Ribosomal protein L23


Mass: 15450.040 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BS37
#48: Protein Ribosomal protein L23A


Mass: 16053.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BMP6
#49: Protein Ribosomal protein L26


Mass: 15621.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BFT3
#51: Protein Ribosomal protein L27a


Mass: 17166.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BZ78
#53: Protein Ribosomal protein L30


Mass: 11698.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B5N7
#54: Protein Ribosomal protein L31B / Ribosomal protein L31e


Mass: 12184.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BMP3
#55: Protein Ribosomal protein L32


Mass: 15985.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BMD9
#56: Protein Ribosomal protein L35a


Mass: 13913.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BKK5
#57: Protein Ribosomal protein L34


Mass: 13528.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BMF7
#58: Protein Ribosomal protein L35


Mass: 14292.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BRG7
#59: Protein Ribosomal protein L36-1 / Ribosomal protein L36e


Mass: 10586.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BYA6
#60: Protein Ribosomal protein L37


Mass: 10329.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BLV7
#62: Protein Ribosomal protein L39


Mass: 6353.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A0A644EZB9
#64: Protein Ribosomal protein L44


Mass: 12311.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BQU8
#65: Protein Ribosomal protein L37a


Mass: 10508.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BN26
#67: Protein Ribosomal protein L24A


Mass: 12005.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BRH7
#69: Protein Ribosomal protein S29A


Mass: 15499.780 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B7H6
#70: Protein Ribosomal protein S5


Mass: 21058.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BZD3
#71: Protein Ribosomal protein S24


Mass: 14872.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B593

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40S ribosomal protein ... , 9 types, 9 molecules B1a1V1I1e1H1E1G1A1

#9: Protein 40S ribosomal protein S3a


Mass: 28413.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BS79
#11: Protein 40S ribosomal protein S26


Mass: 12791.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BQZ7
#12: Protein 40S ribosomal protein S21


Mass: 9686.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B484
#15: Protein 40S ribosomal protein S8


Mass: 19451.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B252
#16: Protein 40S ribosomal protein S30


Mass: 7932.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A0A644F843
#17: Protein 40S ribosomal protein S7


Mass: 21786.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BT38
#22: Protein 40S ribosomal protein S4


Mass: 30464.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BFE3
#72: Protein 40S ribosomal protein S6


Mass: 28084.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B6L8
#74: Protein 40S ribosomal protein SA


Mass: 28101.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BE86

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Protein , 3 types, 3 molecules L1k2m2

#23: Protein SSU ribosomal protein S17P


Mass: 23244.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: V6TVJ7
#61: Protein Ribosomal L38e


Mass: 8605.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B481
#63: Protein Ubiquitin/Ribosomal protein L40e / Ubiquitin/ribosomal protein CEP52


Mass: 14343.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BXE1

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RNA chain , 6 types, 6 molecules 1342w2E2

#25: RNA chain rRNA 28S


Mass: 878238.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote)
#26: RNA chain rRNA 5S


Mass: 38671.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote)
#27: RNA chain rRNA 5.8S


Mass: 44971.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: GenBank: 9351
#66: RNA chain E-site tRNA


Mass: 4459.755 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote)
#68: RNA chain P-site tRNA


Mass: 894.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote)
#73: RNA chain rRNA 18S


Mass: 471124.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote)

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60S ribosomal protein ... , 5 types, 5 molecules G2L2S2Z2b2

#33: Protein 60S ribosomal protein L7a


Mass: 25427.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BLL7
#37: Protein 60S ribosomal protein L13


Mass: 26640.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B6M8
#44: Protein 60S ribosomal protein L18a


Mass: 20624.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BT04
#50: Protein 60S ribosomal protein L27


Mass: 15374.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B1T3
#52: Protein 60S ribosomal protein L29


Mass: 7363.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BYY2

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Non-polymers , 2 types, 556 molecules

#75: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 455 / Source method: obtained synthetically / Formula: K
#76: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 101 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Giardia lamblia ribosome / Type: RIBOSOME / Entity ID: #1-#74 / Source: NATURAL
Source (natural)Organism: Giardia lamblia ATCC 50803 (eukaryote)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5567

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
7Cootmodel fitting
9PHENIXmodel refinement
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91058 / Symmetry type: POINT
RefinementCross valid method: NONE
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0081174774
ELECTRON MICROSCOPYf_angle_d1.1149255886
ELECTRON MICROSCOPYf_chiral_restr0.070231736
ELECTRON MICROSCOPYf_plane_restr0.006217304
ELECTRON MICROSCOPYf_dihedral_angle_d18.532578126

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