Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 20-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 752.36 kDa 
• Atom Count: 50569 
• Residue Count: 3826 
• Unique protein chains: 20
• Unique nucleic acid chains: 1

6SPC

Pseudomonas aeruginosa 30s ribosome from an aminoglycoside resistant clinical isolate

• DOI: 10.2210/pdb6SPC/pdb
• EMDataResource: EMD-10281

• Classification: RIBOSOME
• Organism(s): Pseudomonas aeruginosa
• Mutation(s): No 


• Deposited: 2019-09-01 Released: 2019-10-16 
• Deposition Author(s): Halfon, Y., Jimenez-Fernande, A., La Ros, R., Espinos, R., Krogh Johansen, H., Matzov, D., Eyal, Z., Bashan, A., Zimmerman, E., Belousoff, M., Molin, S., Yonath, A.
• Funding Organization(s): Danish Council for Independent Research, Novo Nordisk Foundation, European Research Council, European Union

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.95 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure ofPseudomonas aeruginosaribosomes from an aminoglycoside-resistant clinical isolate.

Halfon, Y., Jimenez-Fernandez, A., La Rosa, R., Espinosa Portero, R., Krogh Johansen, H., Matzov, D., Eyal, Z., Bashan, A., Zimmerman, E., Belousoff, M., Molin, S., Yonath, A.

(2019) Proc Natl Acad Sci U S A 116: 22275-22281

• PubMed: 31611393 
• DOI: 10.1073/pnas.1909831116
• Primary Citation of Related Structures:  
  6SPD, 6SPC, 6SPF, 6SPE, 6SPG, 6SPB


• PubMed Abstract: 
  

Resistance to antibiotics has become a major threat to modern medicine. The ribosome plays a fundamental role in cell vitality by the translation of the genetic code into proteins; hence, it is a major target for clinically useful antibiotics. We report here the cryo-electron microscopy structures of the ribosome of a pathogenic aminoglycoside (AG)-resistant Pseudomonas aeruginosa strain, as well as of a nonresistance strain isolated from a cystic fibrosis patient. The structural studies disclosed defective ribosome complex formation due to a conformational change of rRNA helix H69, an essential intersubunit bridge, and a secondary binding site of the AGs. In addition, a stable conformation of nucleotides A1486 and A1487, pointing into helix h44, is created compared to a non-AG-bound ribosome. We suggest that altering the conformations of ribosomal protein uL6 and rRNA helix H69, which interact with initiation-factor IF2, interferes with proper protein synthesis initiation.

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Organizational Affiliation: 

Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel; [e-mail] [e-mail].

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	b	221	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsB, C0044_27165, CAZ10_16950, CGU42_10015, DZ962_06265, E4V10_14175, ECC04_007955, EQH76_06925, F3H14_17655, F7O90_05300, F7O98_07180, FC629_06800, FDK04_07450, GNQ48_06145, IPC116_02385, IPC1323_02415, IPC1481_21420, IPC1509_01455, IPC36_27390, IPC582_14765, IPC620_10205, IPC669_07310, NCTC10662_04841, NCTC12951_02118, NCTC13621_00721, PAMH19_1431, PERCYII40_1477, RW109_RW109_02159
Find proteins for A0A072ZPV8 (Pseudomonas aeruginosa) Explore A0A072ZPV8  Go to UniProtKB:  A0A072ZPV8

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	c	203	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsC, CAZ10_34040, CGU42_31625, CSB93_1990, DT376_00190, DY930_32620, DY940_31640, DZ962_26010, E4V10_35080, ECC04_011105, EQH76_33195, F3H14_34325, F7O90_22660, F7O94_06870, F7O98_30210, FC629_03710, FDK04_03975, GNQ48_26655, IPC116_30655, IPC1323_25355, IPC1481_00045, IPC1509_31145, IPC36_29185, IPC582_29415, IPC620_12045, IPC669_33975, NCTC10662_00339, NCTC12924_03227, NCTC12951_02826, NCTC13437_03817, NCTC13621_06482, NCTC13628_01549, PERCYII40_0750, RW109_RW109_01350
Find proteins for A0A140S919 (Pseudomonas aeruginosa) Explore A0A140S919  Go to UniProtKB:  A0A140S919

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	d	205	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsD, C0044_31420, CAZ10_34130, CGU42_31535, DT376_00280, DY930_32530, DZ962_25920, E4V10_29810, ECC04_011015, EQH76_33105, F3H14_34415, F7O90_22570, F7O98_30300, FC629_03800, FDK04_04065, GNQ48_26565, IPC116_30745, IPC1323_25445, IPC1481_00135, IPC1509_31055, IPC36_29095, IPC582_29325, IPC620_12135, IPC669_33885, NCTC10662_00319, NCTC12951_02808, NCTC13437_03799, PAMH19_0755, PERCYII40_0767, RW109_RW109_01368
Find proteins for A0A072ZDF7 (Pseudomonas aeruginosa) Explore A0A072ZDF7  Go to UniProtKB:  A0A072ZDF7

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	e	149	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsE, C0044_31385, CAZ10_34095, CGU42_31570, CSB93_2001, DT376_00245, DY930_32565, DY940_31585, DZ962_25955, E4V10_35025, ECC04_011050, EQH76_33140, F3H14_34380, F7O90_22605, F7O94_06925, F7O98_30265, FC629_03765, FDK04_04030, GNQ48_26600, IPC116_30710, IPC1323_25410, IPC1481_00100, IPC1509_31090, IPC36_29130, IPC582_29360, IPC620_12100, IPC669_33920, NCTC10662_00327, NCTC12924_03239, NCTC12951_02815, NCTC13437_03806, NCTC13621_06493, NCTC13628_01538, PAMH19_0748, PERCYII40_0761, RW109_RW109_01361
Find proteins for A0A241XG65 (Pseudomonas aeruginosa) Explore A0A241XG65  Go to UniProtKB:  A0A241XG65

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6	f	100	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsF, ALP65_00135, C0044_36460, CAZ10_01825, CGU42_14415, CSB93_0497, DT376_23925, DY930_00855, DY940_13895, DZ962_07925, E4V10_33565, ECC04_029555, EQH76_01285, F3H14_02340, F7O90_19175, F7O94_03430, F7O98_00175, FC629_29155, FDK04_28025, GNQ48_04620, IPC116_07740, IPC1323_06510, IPC1481_04065, IPC1509_09165, IPC36_09895, IPC582_07745, IPC620_01295, IPC669_02460, NCTC10662_01918, NCTC12924_01788, NCTC12951_04315, NCTC13437_05458, NCTC13621_03610, NCTC13628_02906, PAMH19_2645, PERCYII40_5678, RW109_RW109_06527
Find proteins for A0A069Q263 (Pseudomonas aeruginosa) Explore A0A069Q263  Go to UniProtKB:  A0A069Q263

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	g	154	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsG, C0044_31505, CAZ10_33990, CGU42_06805, CSB93_1980, DT376_04900, DY930_35305, DY940_33545, DZ962_26060, E4V10_33925, ECC04_011155, EQH76_33245, F3H14_34855, F7O90_22710, F7O94_06820, F7O98_29760, FC629_03660, FDK04_03925, GNQ48_26705, IPC116_31495, IPC1323_32620, IPC1481_09765, IPC1509_31195, IPC36_29740, IPC582_29470, IPC620_11990, IPC669_34030, NCTC10662_00349, NCTC12924_03215, NCTC12951_02836, NCTC13621_06471, NCTC13628_01559, PAMH19_0725, PERCYII40_0740, RW109_RW109_01340
Find proteins for A0A2V3F2U6 (Pseudomonas aeruginosa) Explore A0A2V3F2U6  Go to UniProtKB:  A0A2V3F2U6

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	h	125	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsH, C0044_31370, CAZ10_34080, CGU42_31585, CSB93_1998, DT376_00230, DY930_32580, DY940_31600, DZ962_25970, E4V10_35040, ECC04_011065, EQH76_33155, F3H14_34365, F7O90_22620, F7O94_06910, F7O98_30250, FC629_03750, FDK04_04015, GNQ48_26615, IPC116_30695, IPC1323_25395, IPC1481_00085, IPC1509_31105, IPC36_29145, IPC582_29375, IPC620_12085, IPC669_33935, NCTC10662_00330, NCTC12924_03236, NCTC12951_02818, NCTC13437_03809, NCTC13621_06490, NCTC13628_01541, PAMH19_0745, PERCYII40_0758, RW109_RW109_01358
Find proteins for E2RXT9 (Pseudomonas aeruginosa) Explore E2RXT9  Go to UniProtKB:  E2RXT9

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	i	126	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsI, ALP65_00500, C0044_32845, CAZ10_21155, CGU42_01015, DT376_14745, DY930_32390, DZ962_00640, E4V10_06560, ECC04_026685, EQH76_10260, F3H14_31335, F7O90_09115, F7O98_01535, FC629_25630, FDK04_24855, GNQ48_11360, IPC116_09660, IPC1323_21695, IPC1481_10990, IPC1509_19845, IPC36_15330, IPC582_20470, IPC620_22140, IPC669_10625, NCTC10662_02638, NCTC12951_06565, NCTC13437_06123, NCTC13621_04202, PAMH19_3730, PERCYII40_5091, RW109_RW109_05771
Find proteins for A0A069PXX1 (Pseudomonas aeruginosa) Explore A0A069PXX1  Go to UniProtKB:  A0A069PXX1

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	j	96	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsJ, C0044_31435, CAZ10_34005, CGU42_31660, CSB93_1983, DT376_00155, DY930_32655, DY940_31675, DZ962_26045, E4V10_35115, ECC04_011140, EQH76_33230, F3H14_34290, F7O90_22695, F7O94_06835, F7O98_30175, FC629_03675, FDK04_03940, GNQ48_26690, IPC116_30620, IPC1323_25320, IPC1481_00010, IPC1509_31180, IPC36_29220, IPC582_29450, IPC620_12010, IPC669_34010, NCTC10662_00346, NCTC12924_03219, NCTC12951_02833, NCTC13437_03824, NCTC13621_06475, NCTC13628_01556, PERCYII40_0743, RW109_RW109_01343
Find proteins for E2RXT0 (Pseudomonas aeruginosa) Explore E2RXT0  Go to UniProtKB:  E2RXT0

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	k	115	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsK, C0044_31415, CAZ10_34125, CGU42_31540, CSB93_2007, DT376_00275, DY930_32535, DY940_31555, DZ962_25925, E4V10_29815, ECC04_011020, EQH76_33110, F3H14_34410, F7O90_22575, F7O94_06955, F7O98_30295, FC629_03795, FDK04_04060, GNQ48_26570, IPC116_30740, IPC1323_25440, IPC1481_00130, IPC1509_31060, IPC36_29100, IPC582_29330, IPC620_12130, IPC669_33890, NCTC10662_00320, NCTC12924_03245, NCTC12951_02809, NCTC13437_03800, NCTC13628_01532, PAMH19_0754, PERCYII40_0766, RW109_RW109_01367
Find proteins for E2RXU4 (Pseudomonas aeruginosa) Explore E2RXU4  Go to UniProtKB:  E2RXU4

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	l	120	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsL, C0044_31510, CAZ10_33985, CGU42_06810, CSB93_1979, DT376_04905, DY930_35300, DY940_33550, DZ962_26065, E4V10_33930, EQH76_33250, F3H14_34850, F7O90_22715, F7O94_06815, F7O98_29755, FC629_03655, FDK04_03920, GNQ48_26710, IPC116_31500, IPC1323_32615, IPC1481_09760, IPC1509_31200, IPC36_29745, IPC582_29475, IPC620_11985, IPC669_34035, PAMH19_0724, PERCYII40_0739, RW109_RW109_01339
Find proteins for A0A071L394 (Pseudomonas aeruginosa) Explore A0A071L394  Go to UniProtKB:  A0A071L394

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	m	109	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsM, C0044_31410, CAZ10_34120, CGU42_31545, DT376_00270, DY930_32540, DZ962_25930, E4V10_29820, ECC04_011025, EQH76_33115, F3H14_34405, F7O90_22580, F7O98_30290, FC629_03790, FDK04_04055, GNQ48_26575, IPC116_30735, IPC1323_25435, IPC1481_00125, IPC1509_31065, IPC36_29105, IPC582_29335, IPC620_12125, IPC669_33895, NCTC10662_00321, NCTC12951_02810, NCTC13437_03801, PAMH19_0753, PERCYII40_0765, RW109_RW109_01366
Find proteins for E2RXU3 (Pseudomonas aeruginosa) Explore E2RXU3  Go to UniProtKB:  E2RXU3

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14	n	98	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsN, C0044_31365, CAZ10_34075, CGU42_31590, DT376_00225, DY930_32585, DY940_31605, DZ962_25975, E4V10_35045, ECC04_011070, EQH76_33160, F3H14_34360, F7O90_22625, F7O94_06905, F7O98_30245, FC629_03745, FDK04_04010, GNQ48_26620, IPC116_30690, IPC1323_25390, IPC1481_00080, IPC1509_31110, IPC36_29150, IPC582_29380, IPC620_12080, IPC669_33940, NCTC10662_00331, NCTC12924_03235, NCTC12951_02819, NCTC13437_03810, NCTC13621_06489, NCTC13628_01542, PERCYII40_0757, RW109_RW109_01357
Find proteins for E2RXT8 (Pseudomonas aeruginosa) Explore E2RXT8  Go to UniProtKB:  E2RXT8

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	o	87	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsO, ALP65_03471, C0044_35085, CAZ10_02835, CGU42_13345, CSB93_0290, DT376_25075, DY930_25520, DY940_14885, DZ962_24985, E4V10_19450, ECC04_028550, EQH76_00265, F3H14_03350, F7O90_10295, F7O94_16100, F7O98_10330, FC629_27855, FDK04_27025, GNQ48_21280, IPC116_08750, IPC1323_05505, IPC1481_03065, IPC1509_27945, IPC36_08890, IPC582_08750, IPC620_00290, IPC669_03465, PAMH19_2450, PERCYII40_5476, RW109_RW109_06328
Find proteins for A0A071L3R7 (Pseudomonas aeruginosa) Explore A0A071L3R7  Go to UniProtKB:  A0A071L3R7

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	p	78	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsP, ALP65_02195, C0044_27775, CAZ10_17400, CSB93_2527, DT376_21845, DY930_07805, DY940_09935, E4V10_03605, ECC04_008405, F3H14_04560, F7O90_04560, F7O94_12905, FDK04_07000, IPC116_02835, IPC1323_02865, IPC1481_21870, IPC1509_02215, IPC36_20970, IPC582_15215, IPC620_11000, IPC669_07760, NCTC12924_03556, NCTC12951_02215, NCTC13621_00617, NCTC13628_00999, PAMH19_1344, RW109_RW109_02069
Find proteins for A0A2V4FRZ2 (Pseudomonas aeruginosa) Explore A0A2V4FRZ2  Go to UniProtKB:  A0A2V4FRZ2

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	q	76	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsQ, C0044_31345, CAZ10_34055, CGU42_31610, CSB93_1993, DT376_00205, DY930_32605, DY940_31625, DZ962_25995, E4V10_35065, ECC04_011090, EQH76_33180, F3H14_34340, F7O90_22645, F7O94_06885, F7O98_30225, FC629_03725, FDK04_03990, GNQ48_26640, IPC116_30670, IPC1323_25370, IPC1481_00060, IPC1509_31130, IPC36_29170, IPC582_29400, IPC620_12060, IPC669_33960, NCTC10662_00335, NCTC12924_03231, NCTC12951_02823, NCTC13437_03814, NCTC13628_01546, PAMH19_0740, PERCYII40_0753, RW109_RW109_01353
Find proteins for E2RXT5 (Pseudomonas aeruginosa) Explore E2RXT5  Go to UniProtKB:  E2RXT5

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	r	56	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsR, ALP65_100000, C0044_36465, CAZ10_01830, CGU42_14410, CSB93_0496, DT376_23920, DY930_00850, DY940_13900, DZ962_07930, E4V10_33570, ECC04_029550, EQH76_01280, F3H14_02345, F7O90_19180, F7O94_03435, F7O98_00170, FC629_29150, FDK04_28020, GNQ48_04625, IPC116_07745, IPC1323_06505, IPC1481_04060, IPC1509_09160, IPC36_09890, IPC582_07750, IPC620_01290, IPC669_02465, NCTC10662_01919, NCTC12924_01787, NCTC12951_04316, NCTC13437_05459, NCTC13621_03611, NCTC13628_02907, PAMH19_2644, PERCYII40_5677, RW109_RW109_06526
Find proteins for A0A2V3DLV3 (Pseudomonas aeruginosa) Explore A0A2V3DLV3  Go to UniProtKB:  A0A2V3DLV3

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	s	80	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsS, C0044_31460, CAZ10_34030, CGU42_31635, CSB93_1988, DT376_00180, DY930_32630, DY940_31650, DZ962_26020, E4V10_35090, ECC04_011115, EQH76_33205, F3H14_34315, F7O90_22670, F7O94_06860, F7O98_30200, FC629_03700, FDK04_03965, GNQ48_26665, IPC116_30645, IPC1323_25345, IPC1481_00035, IPC1509_31155, IPC36_29195, IPC582_29425, IPC620_12035, IPC669_33985, NCTC10662_00341, NCTC12924_03225, NCTC12951_02828, NCTC13437_03819, NCTC13621_06480, NCTC13628_01551, PAMH19_0734, PERCYII40_0748, RW109_RW109_01348
Find proteins for E2RXT2 (Pseudomonas aeruginosa) Explore E2RXT2  Go to UniProtKB:  E2RXT2

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	t	86	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsT, ALP65_02387, C0044_33765, CGU42_09055, DT376_27735, DY930_16260, DZ962_01325, E4V10_23495, ECC04_027510, EQH76_19970, F3H14_29345, F7O90_04045, F7O98_13860, FC629_26825, FDK04_26040, GNQ48_15755, IPC116_10955, IPC1323_28175, IPC1481_25265, IPC1509_29025, IPC36_16020, IPC582_26590, IPC620_28985, IPC669_17730, NCTC10662_02375, NCTC13437_05865, PAMH19_3504, PERCYII40_5279, RW109_RW109_06138
Find proteins for A0A072ZDZ9 (Pseudomonas aeruginosa) Explore A0A072ZDZ9  Go to UniProtKB:  A0A072ZDZ9

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S21	u	34	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  rpsU, ALP65_01521, C0044_04175, CAZ10_18885, CGU42_09550, CSB93_1880, DT376_28965, DY930_23760, DY940_04010, DZ962_09105, E4V10_20540, ECC04_011700, EQH76_08100, F3H14_24115, F7O90_12275, F7O94_07255, F7O98_06760, FC629_03180, FDK04_03375, GNQ48_07015, IPC116_15985, IPC1323_10600, IPC1481_12505, IPC1509_08135, IPC36_17170, IPC582_28360, IPC620_04235, IPC669_27350, NCTC10662_00480, NCTC12924_03094, NCTC12951_02936, NCTC13437_03935, NCTC13621_06358, NCTC13628_01672, PAMH19_0634, PERCYII40_0643, RW109_RW109_01185
Find proteins for A0A069QC99 (Pseudomonas aeruginosa) Explore A0A069QC99  Go to UniProtKB:  A0A069QC99

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S rRNA	a	1519	Pseudomonas aeruginosa

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.95 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-09-01 
• Released Date: 2019-10-16 
Deposition Author(s): Halfon, Y., Jimenez-Fernande, A., La Ros, R., Espinos, R., Krogh Johansen, H., Matzov, D., Eyal, Z., Bashan, A., Zimmerman, E., Belousoff, M., Molin, S., Yonath, A.

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Funding Organization	Location	Grant Number
Danish Council for Independent Research	Denmark	DFF-4181-00115
Novo Nordisk Foundation	Denmark	--
European Research Council		322581
European Union		iNEXT, project number 653706, funded by the Horizon 2020 programme of the European Union

Revision History 

• Version 1.0: 2019-10-16
  Type: Initial release
  
• Version 1.1: 2019-10-23
  Changes: Data collection, Database references
• Version 1.2: 2019-11-06
  Changes: Data collection, Database references