7PWO | pdb_00007pwo

Cryo-EM structure of Giardia lamblia ribosome at 2.75 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 1.2 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 S19eA [auth T1]139Giardia lamblia ATCC 50803Mutation(s): 0 
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Find proteins for A0A644F964 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S13B [auth N1]154Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
Find proteins for A8BE02 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S9C [auth J1]189Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
Find proteins for A8BKS8 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S3D [auth D1]217Giardia lamblia ATCC 50803Mutation(s): 0 
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Find proteins for A8B8Z2 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S23E [auth X1]143Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S18F [auth S1]154Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S16G [auth Q1]158Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S2H [auth C1]242Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aI [auth B1]248Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S27J [auth b1]124Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26K [auth a1]109Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21L [auth V1]89Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S17M [auth R1]137Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S10BN [auth K1]134Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8O [auth I1]174Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30P [auth e1]69Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
Find proteins for A0A644F843 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7Q [auth H1]190Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL41R [auth n1]41Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
Find proteins for V6TX21 (Giardia intestinalis)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S28S [auth c1]64Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S14T [auth O1]145Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15AU [auth W1]130Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4V [auth E1]268Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
SSU ribosomal protein S17PW [auth L1]199Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
Find proteins for V6TVJ7 (Giardia intestinalis)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S20X [auth U1]126Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L2BA [auth A2]251Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L3CA [auth B2]379Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L4DA [auth C2]316Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L5EA [auth D2]297Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L7FA [auth F2]235Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aGA [auth G2]225Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L6HA [auth H2]185Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L10IA [auth I2]210Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L11JA [auth J2]173Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13KA [auth L2]234Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L14LA [auth M2]131Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15MA [auth N2]204Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L13aNA [auth O2]197Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L17OA [auth P2]164Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L18PA [auth Q2]179Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L19QA [auth R2]196Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aRA [auth S2]173Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L21SA [auth T2]159Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL22TA [auth U2]171Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23UA [auth V2]142Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
Find proteins for A8BS37 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23AVA [auth X2]141Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26WA [auth Y2]135Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27XA [auth Z2]135Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L27aYA [auth a2]149Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29ZA [auth b2]62Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L30AB [auth c2]109Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
Find proteins for A8B5N7 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L31BBB [auth d2]106Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L32CB [auth e2]136Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L35aDB [auth f2]123Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
Find proteins for A8BKK5 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L34EB [auth g2]120Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L35FB [auth h2]124Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L36-1GB [auth i2]90Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37HB [auth j2]89Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal L38eIB [auth k2]77Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L39JB [auth l2]51Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
Find proteins for A0A644EZB9 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin/Ribosomal protein L40eKB [auth m2]127Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L44LB [auth o2]106Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37aMB [auth p2]94Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24AOB [auth W2]102Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S29AQB [auth d1]137Giardia lamblia ATCC 50803Mutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S5RB [auth F1]190Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S24SB [auth Y1]132Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6TB [auth G1]248Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAVB [auth A1]245Giardia lamblia ATCC 50803Mutation(s): 0 
UniProt
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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 
AC [auth X1]
AD [auth 1]
AG [auth 1]
AH [auth 1]
AI [auth 1]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AE [auth 1]
AF [auth 1]
AX [auth 2]
BE [auth 1]
BF [auth 1]
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
RECONSTRUCTIONRELION3.1

Structure Validation

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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
  • Version 1.1: 2024-04-24
    Changes: Data collection
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary