Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 29-mer - A1BCDEFGHIJKLMNOPQRSTUVWXYZabc 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1458.45 kDa 
• Atom Count: 94306 
• Residue Count: 6449 
• Unique protein chains: 29
• Unique nucleic acid chains: 2

5V7Q

Cryo-EM structure of the large ribosomal subunit from Mycobacterium tuberculosis bound with a potent linezolid analog

• DOI: 10.2210/pdb5V7Q/pdb
• EMDataResource: EMD-8641

• Classification: RIBOSOME
• Organism(s): Mycobacterium tuberculosis
• Mutation(s): No 


• Deposited: 2017-03-20 Released: 2017-09-20 
• Deposition Author(s): Yang, K., Chang, J.-Y., Cui, Z., Zhang, J.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis.

Yang, K., Chang, J.Y., Cui, Z., Li, X., Meng, R., Duan, L., Thongchol, J., Jakana, J., Huwe, C.M., Sacchettini, J.C., Zhang, J.

(2017) Nucleic Acids Res 45: 10884-10894

• PubMed: 28977617 
• DOI: 10.1093/nar/gkx785
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Ribosomes from Mycobacterium tuberculosis (Mtb) possess species-specific ribosomal RNA (rRNA) expansion segments and ribosomal proteins (rProtein). Here, we present the near-atomic structures of the Mtb 50S ribosomal subunit and the complete Mtb 70S ribosome, solved by cryo-electron microscopy. Upon joining of the large and small ribosomal subunits, a 100-nt long expansion segment of the Mtb 23S rRNA, named H54a or the 'handle', switches interactions from with rRNA helix H68 and rProtein uL2 to with rProtein bS6, forming a new intersubunit bridge 'B9'. In Mtb 70S, bridge B9 is mostly maintained, leading to correlated motions among the handle, the L1 stalk and the small subunit in the rotated and non-rotated states. Two new protein densities were discovered near the decoding center and the peptidyl transferase center, respectively. These results provide a structural basis for studying translation in Mtb as well as developing new tuberculosis drugs.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L32	0	57	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rpmF, rpmF_1, rpmF_2, DSI38_18430, E5M05_21345, ERS007663_04026, ERS007665_03842, ERS007670_03634, ERS007679_01959, ERS007679_04546, ERS007681_04590, ERS007688_04223, ERS007720_04765, ERS007722_04489, ERS007741_04583, ERS013471_04149, ERS023446_04200, ERS027646_04445, ERS027659_04299, ERS027661_04209, ERS075361_04102, ERS094182_04418, F6W99_03678, FRD82_10340, GJE03_05200, SAMEA2683035_04216
Find proteins for A0A045IMI5 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045IMI5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L33	1	55	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rpmG2, rpmG, CAB90_00725, DSI38_24525, E5M05_06820, ERS007657_00226, ERS007661_00236, ERS007663_02220, ERS007665_02168, ERS007670_00505, ERS007703_00858, ERS007720_00737, ERS007741_01187, ERS013471_03613, ERS023446_03037, ERS027646_03149, ERS027659_00131, ERS027661_00210, ERS075361_00848, ERS094182_01375, F6W99_03307, FRD82_08750, GJE03_03350, SAMEA2683035_02069
Find proteins for A0A045HU86 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045HU86

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L34	2	47	Mycobacterium tuberculosis	Mutation(s): 0
Find proteins for P9WH93 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Go to UniProtKB:  P9WH93

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L35	3	64	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rpmI, DSI38_22585, E5M05_05770, ERS007661_03227, ERS007665_02257, ERS007670_01092, ERS007679_04341, ERS007681_04552, ERS007688_04034, ERS007703_01078, ERS007722_00425, ERS007741_03331, ERS013471_01258, ERS023446_00487, ERS024276_03476, ERS027646_00659, ERS027659_00624, ERS027661_00568, ERS075361_00026, ERS094182_02202, F6W99_00189, FRD82_08480, GJE03_08615, SAMEA2683035_01443
Find proteins for A0A045KKY9 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045KKY9

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L36	4	37	Mycobacterium tuberculosis	Mutation(s): 0
Find proteins for P9WH89 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Go to UniProtKB:  P9WH89

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L31	6	80	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rpmE, rpmE_1, CAB90_01471, DSI38_18515, E5M05_19670, ERS007657_01524, ERS007663_00111, ERS007665_02410, ERS007670_01886, ERS007679_00565, ERS007681_00043, ERS007688_00317, ERS007703_00166, ERS007720_01198, ERS007722_00196, ERS007741_01521, ERS013471_00790, ERS023446_01602, ERS024276_01318, ERS027646_00440, ERS027659_04256, ERS027661_00027, ERS075361_01596, ERS094182_01710, F6W99_04019, FRD82_19480, GJE03_06880, SAMEA2683035_01562
Find proteins for A0A045HLX7 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045HLX7

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L2	C	280	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rplB, DSI38_05180, E5M05_12090, ERS007663_03147, ERS007665_03130, ERS007670_02768, ERS007679_03325, ERS007681_04144, ERS007688_02437, ERS007703_03955, ERS007720_01130, ERS007722_04351, ERS007741_01510, ERS013471_00612, ERS023446_00447, ERS024276_02370, ERS027646_00066, ERS027659_01091, ERS027661_02293, ERS075361_00775, ERS094182_01303, F6W99_03379, FRD82_02370, GJE03_03730, SAMEA2683035_02486
Find proteins for A0A045H5T7 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045H5T7

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L3	D	217	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rplC, DSI38_24900, E5M05_06445, ERS007661_02454, ERS007663_03778, ERS007665_01163, ERS007670_00571, ERS007679_01243, ERS007703_00888, ERS007720_01133, ERS007741_01514, ERS013471_00609, ERS023446_00444, ERS024276_00865, ERS027646_00069, ERS027659_01094, ERS075361_00778, ERS094182_01306, F6W99_03376, FRD82_02355, GJE03_03715, SAMEA2683035_02489
Find proteins for A0A045HU18 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045HU18

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L4	E	223	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rplD, DSI38_24905, E5M05_06440, ERS007657_02866, ERS007688_02439, ERS007720_01132, ERS007722_04434, ERS013471_00610, ERS023446_00445, ERS027646_00068, ERS027659_01093, ERS027661_02295, ERS075361_00777, ERS094182_01305, F6W99_03377, FRD82_02360, GJE03_03720, SAMEA2683035_02488
Find proteins for A0A045J9H1 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045J9H1

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L5	F	187	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rplE, DSI38_05240, E5M05_12030, ERS007657_01335, ERS007663_00382, ERS007665_03572, ERS007670_00651, ERS007679_00528, ERS007681_00691, ERS007688_00815, ERS007703_01055, ERS007720_04267, ERS007722_04137, ERS007741_01217, ERS013471_02706, ERS023446_00459, ERS024276_00085, ERS027646_00054, ERS027659_00069, ERS027661_00856, ERS075361_00763, ERS094182_01291, F6W99_03391, GJE03_03790, SAMEA2683035_02474
Find proteins for A0A045HUU0 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045HUU0

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L6	G	179	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rplF, DSI38_05255, E5M05_12015, ERS007657_03368, ERS007661_03155, ERS007663_00385, ERS007665_03982, ERS007670_00648, ERS007679_00525, ERS007681_00688, ERS007688_04166, ERS007703_01052, ERS007720_03567, ERS007722_04517, ERS007741_01214, ERS013471_02709, ERS023446_00462, ERS024276_00088, ERS027659_00066, ERS027661_00853, ERS075361_00760, ERS094182_01288, FRD82_05680, GJE03_03805, SAMEA2683035_02471
Find proteins for A0A045JJU1 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045JJU1

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L9	H	152	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rplI, rplI_1, DSI38_19150, E5M05_14340, ERS007657_02922, ERS007661_02345, ERS007663_00754, ERS007665_01876, ERS007670_02092, ERS007688_00902, ERS007703_00885, ERS007720_02802, ERS007722_00899, ERS013471_02691, ERS027646_03501, ERS027659_02995, ERS027661_04424, ERS075361_00493, ERS094182_00620, F6W99_02688, FRD82_07235, GJE03_00305, SAMEA2683035_00198
Find proteins for A0A045JW48 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045JW48

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L14	K	122	Mycobacterium tuberculosis	Mutation(s): 0
Find proteins for P9WHD9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Go to UniProtKB:  P9WHD9

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L15	L	146	Mycobacterium tuberculosis	Mutation(s): 0
Find proteins for P9WHD7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Go to UniProtKB:  P9WHD7

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L17	N	180	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rplQ, DSI38_18605, E5M05_17290, ERS007657_02051, ERS007661_01802, ERS007663_01918, ERS007665_01053, ERS007670_00939, ERS007679_01859, ERS007681_04003, ERS007688_02122, ERS007703_04393, ERS007720_00530, ERS007722_04216, ERS007741_04240, ERS013471_02378, ERS023446_02771, ERS024276_02876, ERS027646_02176, ERS075361_03463, ERS094182_03732, F6W99_02117, FRD82_04060, GJE03_18195, SAMEA2683035_02864
Find proteins for A0A045IVA2 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045IVA2

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L18	O	122	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rplR, DSI38_05260, E5M05_12010, ERS007663_00386, ERS007679_00524, ERS013471_02710, ERS023446_00463, ERS024276_00089, ERS027646_02859, ERS075361_00759, ERS094182_01287, FRD82_05685, GJE03_03810, SAMEA2683035_02470
Find proteins for A0A045JK28 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045JK28

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L19	P	113	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rplS, CAB90_03238, DSI38_22250, E5M05_16570, ERS007657_02841, ERS007661_01764, ERS007663_00418, ERS007665_00244, ERS007670_00278, ERS007679_00186, ERS007681_01828, ERS007688_00353, ERS007703_01238, ERS007720_04647, ERS007722_00517, ERS007741_02533, ERS013471_00426, ERS023446_00748, ERS024276_01347, ERS027646_00405, ERS027659_03521, ERS075361_01973, ERS094182_02054, F6W99_01517, FRD82_03580, GJE03_15215, SAMEA2683035_02093
Find proteins for A0A045IDD2 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045IDD2

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L20	Q	129	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rplT, DSI38_22580, E5M05_05775, ERS007661_03228, ERS007663_02622, ERS007665_02256, ERS007670_01093, ERS007679_04340, ERS007681_04551, ERS007688_04033, ERS007703_01077, ERS007720_00251, ERS007722_00424, ERS007741_03330, ERS013471_01259, ERS023446_00486, ERS024276_03477, ERS027659_00623, ERS075361_00025, ERS094182_02203, F6W99_00190, FRD82_08485, GJE03_08620, SAMEA2683035_01442
Find proteins for A0A045KJ85 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045KJ85

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details
LSU ribosomal protein L21p	R	104	Mycobacterium tuberculosis	Mutation(s): 0
Find proteins for P9WHC3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Go to UniProtKB:  P9WHC3

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L22	S	197	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rplV, DSI38_05190, E5M05_12080, ERS013471_00614, ERS023446_00449, ERS027646_00064, ERS075361_00773, ERS094182_01301, F6W99_03381, FRD82_02380, SAMEA2683035_02484
Find proteins for A0A045H760 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045H760

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L24	U	105	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rplX, DSI38_05235, E5M05_12035, ERS007657_01334, ERS007661_00777, ERS007663_00381, ERS007665_03573, ERS007670_00652, ERS007679_00529, ERS007681_00692, ERS007688_00816, ERS007703_01056, ERS007720_04268, ERS007722_04138, ERS007741_01218, ERS013471_02705, ERS023446_00458, ERS024276_00084, ERS027646_00055, ERS027659_00070, ERS027661_00857, ERS075361_00764, ERS094182_01292, F6W99_03390, FRD82_05660, GJE03_03785, SAMEA2683035_02475
Find proteins for A0A045IXU4 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045IXU4

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L25	V	215	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rplY, ctc, DSI38_18055, E5M05_14015, ERS007663_03728, ERS007665_00848, ERS007679_02013, ERS007722_02123, ERS013471_01423, ERS023446_01711, ERS027646_00593, ERS027659_03496, ERS075361_03206, ERS094182_03338, F6W99_03715, FRD82_15100, GJE03_05395, SAMEA2683035_03111
Find proteins for A0A045JAK4 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045JAK4

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L27	W	86	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rpmA, DSI38_26120, E5M05_05365, ERS007657_02111, ERS007661_02794, ERS007663_04002, ERS007665_02935, ERS007670_02518, ERS007679_03235, ERS007681_04426, ERS007688_02560, ERS007703_03827, ERS007720_03483, ERS007722_04004, ERS007741_01817, ERS013471_00617, ERS023446_00589, ERS024276_01323, ERS027646_01111, ERS075361_02829, ERS094182_02991, F6W99_01055, FRD82_05160, GJE03_12850, SAMEA2683035_00540
Find proteins for A0A045K0G1 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045K0G1

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L28	X	64	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rpmB, DSI38_02185, E5M05_08730, ERS007661_04635, ERS007663_03554, ERS007665_03011, ERS007670_03542, ERS007681_04087, ERS007688_02903, ERS007703_04315, ERS007720_04214, ERS007722_04168, ERS007741_02790, ERS013471_01068, ERS023446_00060, ERS024276_02871, ERS027646_03183, ERS027659_02720, ERS027661_04716, ERS075361_02425, ERS094182_02233, F6W99_01593, FRD82_13340, GJE03_15605, SAMEA2683035_02287
Find proteins for A0A045IDB8 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045IDB8

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L29	Y	77	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rpmC, CAB90_00808, DSI38_05205, E5M05_12065, ERS007657_03995, ERS007661_03836, ERS007663_03740, ERS007665_03747, ERS007670_03629, ERS007679_04276, ERS007681_00698, ERS007688_04127, ERS007703_04864, ERS007720_04527, ERS007722_04454, ERS007741_04797, ERS013471_02699, ERS023446_00452, ERS024276_01879, ERS027646_00061, ERS027659_03088, ERS027661_03491, ERS075361_00770, ERS094182_01298, F6W99_03384, FRD82_02395, GJE03_03755, SAMEA2683035_02481
Find proteins for A0A045IQ64 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045IQ64

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L30	Z	65	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rpmD, CAB90_00821, DSI38_05270, E5M05_12000, ERS007657_03125, ERS007661_02721, ERS007663_00388, ERS007665_03587, ERS007670_04003, ERS007679_00522, ERS007681_04223, ERS007688_04068, ERS007703_04691, ERS007720_03565, ERS007722_04392, ERS007741_04384, ERS013471_02712, ERS023446_00465, ERS024276_03086, ERS027646_02857, ERS027659_04272, ERS027661_02662, ERS075361_00757, ERS094182_01285, F6W99_03397, FRD82_05695, GJE03_03820, SAMEA2683035_02468
Find proteins for A0A045H4J2 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045H4J2

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L13	J	147	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rplM, ERS007657_03631, ERS007661_03121, ERS007663_03035, ERS007665_03001, ERS007679_01993, ERS007681_03424, ERS007703_03116, ERS007722_03078, ERS027646_01625, ERS027659_01778, ERS027661_01576
Find proteins for A0A0T9D5H2 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A0T9D5H2

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L16	M	138	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rplP, CAB90_00807, DSI38_05200, E5M05_12070, ERS007670_03628, ERS007679_04277, ERS007688_04128, ERS007703_04865, ERS007720_04528, ERS007722_04455, ERS013471_02698, ERS023446_00451, ERS024276_01878, ERS027646_00062, ERS027659_03089, ERS027661_03490, ERS075361_00771, ERS094182_01299, F6W99_03383, FRD82_02390, GJE03_03750, SAMEA2683035_02482
Find proteins for A0A045IWV9 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045IWV9

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L23	T	100	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rplW, DSI38_24910, E5M05_06435, ERS007657_02865, ERS007663_03148, ERS007670_02769, ERS007679_03326, ERS007681_04108, ERS007688_02438, ERS007703_03956, ERS007720_01131, ERS007722_04433, ERS007741_01511, ERS013471_00611, ERS023446_00446, ERS024276_02371, ERS027646_00067, ERS027659_01092, ERS027661_02294, ERS075361_00776, ERS094182_01304, F6W99_03378, FRD82_02365, GJE03_03725, SAMEA2683035_02487
Find proteins for A0A045J9M3 (Mycobacterium tuberculosis) Go to UniProtKB:  A0A045J9M3

Entity ID: 7
Molecule	Chains	Length	Organism
23S rRNA	A	3138	Mycobacterium tuberculosis

Entity ID: 8
Molecule	Chains	Length	Organism
5S ribosomal RNA	B	115	Mycobacterium tuberculosis

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
917	A	N-({(5S)-2-oxo-3-[4-(1,3-thiazol-5-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)acetamide C15 H15 N3 O3 S WTZZWIUUAPRUHM-ZDUSSCGKSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-03-20 
• Released Date: 2017-09-20 
Deposition Author(s): Yang, K., Chang, J.-Y., Cui, Z., Zhang, J.

Revision History 

• Version 1.0: 2017-09-20
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Database references
• Version 1.2: 2017-11-01
  Changes: Database references