6AZ1

Cryo-EM structure of the small subunit of Leishmania ribosome bound to paromomycin

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (A)	Ribosomal protein s1e	polymer	264	30092.1	1	UniProt (E9BRS2)	Leishmania donovani
2	B (B)	ribosomal protein S2	polymer	246	27564.7	1	Pfam (PF00318) UniProt (by SIFTS) (A4IDS4)	Leishmania donovani
3	C (C)	ribosomal protein S3	polymer	219	24511.8	1	UniProt (E9BQ25)	Leishmania donovani
4	D (D)	ribosomal protein S4	polymer	190	22184.9	1	UniProt (E9BTJ0) UniProt (by SIFTS) (A0A3S5H5Z2)	Leishmania donovani
5	E (E)	ribosomal protein S4e	polymer	273	30711.1	1	UniProt (E9BBI6) UniProt (by SIFTS) (A0A3Q8I8K3)	Leishmania donovani
6	F (F)	ribosomal protein S5	polymer	265	28803.2	1	UniProt (E9BNF0) UniProt (by SIFTS) (A0A3S7X558)	Leishmania donovani
7	G (G)	ribosomal protein S6e	polymer	249	28341.2	1	UniProt (by SIFTS) (O44012)	Leishmania donovani
8	H (H)	ribosomal protein S7	polymer	190	21311.6	1	Pfam (PF00177) UniProt (by SIFTS) (A0A381MCG8)	Leishmania donovani
9	I (I)	ribosomal protein S7e	polymer	200	23867.3	1	UniProt (E9B7A8) UniProt (by SIFTS) (A0A3S7WNJ7)	Leishmania donovani
10	J (J)	ribosomal protein S8	polymer	130	14719.3	1	UniProt (E9BAV6)	Leishmania donovani
11	K (K)	ribosomal protein S8e	polymer	220	25038.3	1	UniProt (E9BH78) UniProt (by SIFTS) (A0A3Q8ID68)	Leishmania donovani
12	L (L)	ribosomal protein S9	polymer	149	16718.6	1	UniProt (E9BI96)	Leishmania donovani
13	M (M)	ribosomal protein S10	polymer	116	13049.1	1	UniProt (by SIFTS) (E9BJI2)	Leishmania donovani
14	N (N)	ribosomal protein S10e	polymer	153	17432.9	1	UniProt (E9BTG4)	Leishmania donovani
15	O (O)	ribosomal protein S11	polymer	144	15609.1	1	UniProt (E9BMA8) UniProt (by SIFTS) (A0A3S7X3Z7)	Leishmania donovani
16	P (P)	ribosomal protein S12	polymer	143	15952.7	1	UniProt (E9BFB6)	Leishmania donovani
17	Q (Q)	ribosomal protein S12e	polymer	141	15611.8	1	UniProt (E9BBC0) UniProt (by SIFTS) (A0A3S5H6N5)	Leishmania donovani
18	R (R)	ribosomal protein S13	polymer	153	17443.4	1	UniProt (E9BTF9)	Leishmania donovani
19	S (S)	ribosomal protein S14	polymer	57	6696.9	1	UniProt (E9BJV7)	Leishmania donovani
20	T (T)	ribosomal protein S15	polymer	151	17455.7	1	UniProt (E9BPR7) UniProt (by SIFTS) (A0A3S7X790)	Leishmania donovani
21	U (U)	ribosomal protein S17	polymer	173	19985.4	1	UniProt (by SIFTS) (Q9TXA6)	Leishmania donovani
22	V (V)	ribosomal protein S17e	polymer	143	16521.5	1	UniProt (E9BJZ5)	Leishmania donovani
23	W (W)	ribosomal protein S19	polymer	152	17528.5	1	UniProt (by SIFTS) (E9BFQ0)	Leishmania donovani
24	X (X)	ribosomal protein S19e	polymer	179	20188.6	1	UniProt (E9BR60)	Leishmania donovani
25	Y (Y)	ribosomal protein S21e	polymer	159	16669.1	1	UniProt (by SIFTS) (E9BAR6)	Leishmania donovani
26	Z (Z)	ribosomal protein S24e	polymer	137	15808.9	1	UniProt (E9BU11) UniProt (by SIFTS) (A0A3Q8IKW0)	Leishmania donovani
27	AA (a)	ribosomal protein S25e	polymer	120	13071.4	1	UniProt (E9BHM6)	Leishmania donovani
28	BA (b)	ribosomal protein S26e	polymer	112	12794.3	1	UniProt (E9BK95)	Leishmania donovani
29	CA (c)	ribosomal protein S27e	polymer	86	9819.5	1	UniProt (E9BUA2) UniProt (by SIFTS) (A0A3Q8ID11)	Leishmania donovani
30	DA (d)	ribosomal protein S28e	polymer	87	9763.2	1	UniProt (E9BIH3)	Leishmania donovani
31	EA (e)	ribosomal protein S30e	polymer	66	7394.9	1	UniProt (E9BLG3)	Leishmania donovani
32	FA (f)	ribosomal protein S31e	polymer	152	17015.7	1	UniProt (E9BTC5) UniProt (by SIFTS) (A0A3S7XAC2)	Leishmania donovani
33	GA (g)	LACK1	polymer	312	34459.5	1	UniProt (Q9BIJ5)	Leishmania donovani
34	HA (1)	ribosomal RNA 18S	polymer	2203	710287.4	1	GenBank (322500086)	Leishmania donovani
35	IA (2)	tRNA-Phe	polymer	76	24599.7	1	GenBank (1229082179)	Escherichia coli
36	JA (3)	P-site tRNA	polymer	77	24786.8	1	GenBank (817573384)	Escherichia coli
37	KA (4)	E-site tRNA	polymer	76	24485.5	1	GenBank (1229082179)	Escherichia coli
38	LA (5)	mRNA	polymer	13	4085.5	1		Leishmania donovani
39	AB, BB, CB, DB, EB... (1, C, D, S, 5)	MAGNESIUM ION	non-polymer		24.3	24	Chemie (MG)
40	QA, RA, SA, TA, UA... (1)	PAROMOMYCIN	non-polymer		615.6	6	Chemie (PAR)
41	AC, BC, CC, DC, EC... (R, S, T, X, Y...)	water	water		18.0	262	Chemie (HOH)

Sequence modifications

A: 0 - 263 (UniProt: E9BRS2)

PDB	External Database	Details
Ser 15	Gly 16	conflict

F: 1 - 265 (UniProt: E9BNF0)

PDB	External Database	Details
Thr 4	Ala 4	conflict
Gln 8	-	insertion
Ala 10	Asn 9	conflict
Ala 12	Gly 11	conflict
Ala 13	Val 12	conflict
Asp 14	Glu 13	conflict
Val 15	Ala 14	conflict

P: 1 - 143 (UniProt: E9BFB6)

PDB	External Database	Details
Arg 18	Cys 18	conflict
Ala 34	Ser 34	conflict
Lys 36	Arg 36	conflict
Ser 127	Asn 127	conflict

f: 1 - 152 (UniProt: E9BTC5)

PDB	External Database	Details
Ile 5	Val 5	conflict

1: 1 - 2203 (GenBank: 322500086)

PDB	External Database	Details
M1y 1539	U 1020612	conflict
C4j 1543	U 1020608	conflict

2: 4 - 76 (GenBank: 1229082179)

PDB	External Database	Details
G 1	-	expression tag
C 2	-	expression tag
G 3	-	expression tag
C 70	G 899645	conflict

4: 4 - 76 (GenBank: 1229082179)

PDB	External Database	Details
G 1	-	expression tag
C 2	-	expression tag
G 3	-	expression tag
C 70	G 899645	conflict

Contents of the asymmetric unit

Polymers	Number of chains	38
	Total formula weight	1412381.0
Non-Polymers*	Number of molecules	30
	Total formula weight	4277.1
All*	Total formula weight	1416658.1

*Water molecules are not included.