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- PDB-7pwg: Cryo-EM structure of large subunit of Giardia lamblia ribosome at... -

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Basic information

Entry
Database: PDB / ID: 7pwg
TitleCryo-EM structure of large subunit of Giardia lamblia ribosome at 2.7 A resolution
Components
  • (60S ribosomal protein ...) x 5
  • (Ribosomal protein ...) x 32
  • E-site tRNA
  • P-site tRNA
  • Ribosomal L38e
  • Ubiquitin/Ribosomal protein L40e
  • rRNA 28S
  • rRNA 5.8S
  • rRNA 5S
KeywordsRIBOSOME / giardia / parasite
Function / homology
Function and homology information


maturation of LSU-rRNA / cytosolic ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding ...maturation of LSU-rRNA / cytosolic ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Ribosomal protein L40e, archaeal / : / Ribosomal protein L2, archaeal-type / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family ...Ribosomal protein L40e, archaeal / : / Ribosomal protein L2, archaeal-type / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal L40e family / Ribosomal protein L18e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / 60S ribosomal protein L35 / : / 60S ribosomal protein L19 / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein L7A/L8 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L30/YlxQ / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein L18e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L14e domain / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L14 / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L35A superfamily / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L14 / Ribosomal protein L15e, conserved site / Ribosomal protein L15e signature. / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L37e, conserved site / Ribosomal protein L37e signature. / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L37e / Ribosomal protein L37e
Similarity search - Domain/homology
: / TRIETHYLENE GLYCOL / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L39 / Ribosomal protein L29 / Ribosomal protein L27 / Ribosomal protein L21 ...: / TRIETHYLENE GLYCOL / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L39 / Ribosomal protein L29 / Ribosomal protein L27 / Ribosomal protein L21 / Ribosomal L38e / Ribosomal protein L14 / Ribosomal protein L18 / Ribosomal protein L30 / 60S ribosomal protein L13 / Large ribosomal subunit protein uL4 / Ribosomal protein L15 / Ribosomal protein L17 / Ribosomal protein L26 / Ribosomal protein L19 / Ribosomal protein L11 / Ribosomal protein L35a / 60S ribosomal protein L7a / Ribosomal protein L37 / Ribosomal protein L10 / Ribosomal protein L32 / Ribosomal protein L34 / Ribosomal protein L31e / Ribosomal protein L23A / Ribosomal protein L37a / Ribosomal protein L6 / Ribosomal protein L44 / Ribosomal protein L24A / Ribosomal protein L7 / Ribosomal protein L3 / Ribosomal protein L23 / 60S ribosomal protein L18a / Ribosomal protein L13a / Large ribosomal subunit protein eL22 / 50S ribosomal protein L40e / Ribosomal protein L36e / 60S ribosomal protein L29 / Ribosomal protein L27a / Ribosomal protein L8 / Ribosomal protein L5
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 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: rRNA 28S
3: rRNA 5S
4: rRNA 5.8S
A: Ribosomal protein L2
B: Ribosomal protein L3
C: Ribosomal protein L4
D: Ribosomal protein L5
F: Ribosomal protein L7
G: 60S ribosomal protein L7a
H: Ribosomal protein L6
I: Ribosomal protein L10
J: Ribosomal protein L11
L: 60S ribosomal protein L13
M: Ribosomal protein L14
N: Ribosomal protein L15
O: Ribosomal protein L13a
P: Ribosomal protein L17
Q: Ribosomal protein L18
R: Ribosomal protein L19
S: 60S ribosomal protein L18a
T: Ribosomal protein L21
U: Ribosomal protein eL22
V: Ribosomal protein L23
X: Ribosomal protein L23A
Y: Ribosomal protein L26
Z: 60S ribosomal protein L27
a: Ribosomal protein L27a
b: 60S ribosomal protein L29
c: Ribosomal protein L30
d: Ribosomal protein L31B
e: Ribosomal protein L32
f: Ribosomal protein L35a
g: Ribosomal protein L34
h: Ribosomal protein L29
i: Ribosomal protein L36-1
j: Ribosomal protein L37
k: Ribosomal L38e
l: Ribosomal protein L39
m: Ubiquitin/Ribosomal protein L40e
o: Ribosomal protein L44
p: Ribosomal protein L37a
w: E-site tRNA
W: Ribosomal protein L24A
E: P-site tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,716,901338
Polymers1,706,95244
Non-polymers9,949294
Water79,2124397
1


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

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Components

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RNA chain , 5 types, 5 molecules 134wE

#1: RNA chain rRNA 28S


Mass: 878254.500 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
#2: 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) / Strain: ATCC 50803 / WB clone C6
#3: 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) / Strain: ATCC 50803 / WB clone C6
#42: RNA chain E-site tRNA


Mass: 24500.553 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
#44: 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) / Strain: ATCC 50803 / WB clone C6

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Ribosomal protein ... , 32 types, 32 molecules ABCDFHIJMNOPQRTUVXYacdefghijlopW

#4: 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
#5: 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
#6: 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
#7: 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
#8: 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
#10: 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
#11: 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
#12: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#27: 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
#29: 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
#30: 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
#31: 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
#32: 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
#33: 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
#34: Protein Ribosomal protein L29


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: A0A644FBK5
#35: 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
#36: 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
#38: 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
#40: 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
#41: 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
#43: 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

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

#9: 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
#13: 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
#20: 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
#26: 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
#28: 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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Protein , 2 types, 2 molecules km

#37: 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
#39: 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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Non-polymers , 4 types, 4691 molecules

#45: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 112 / Source method: obtained synthetically / Formula: Mg
#46: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 181 / Source method: obtained synthetically / Formula: K
#47: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#48: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4397 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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-#44 / Source: NATURAL
Source (natural)Organism: Giardia intestinalis (strain ATCC 50803 / WB clone C6) (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)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM software
IDNameCategory
2EPUimage acquisition
7Cootmodel fitting
13PHENIXmodel refinement
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_d0.0095112188
ELECTRON MICROSCOPYf_angle_d0.9903164775
ELECTRON MICROSCOPYf_chiral_restr0.056320413
ELECTRON MICROSCOPYf_plane_restr0.006210797
ELECTRON MICROSCOPYf_dihedral_angle_d18.535450574

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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