Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

7QIZ

Specific features and methylation sites of a plant 80S ribosome

This is a non-PDB format compatible entry.

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (D)	60S ribosomal protein L8	polymer	260	28331.9	1	UniProt (P29766) Pfam (PF00181) Pfam (PF03947)	Solanum lycopersicum (tomato)	L2,Ribosomal protein TL2
2	B (F)	Ribos_L4_asso_C domain-containing protein	polymer	406	44852.0	1	UniProt (A0A3Q7HW81) Pfam (PF00573) Pfam (PF14374)	Solanum lycopersicum (tomato)
3	C (E)	Ribosomal protein L3	polymer	389	44518.2	1	UniProt (Q6SKP4) Pfam (PF00297)	Solanum lycopersicum (tomato)
4	D (G)	Ribosomal_L18_c domain-containing protein	polymer	301	34667.3	1	UniProt (A0A3Q7H274) Pfam (PF17144) Pfam (PF14204)	Solanum lycopersicum (tomato)
5	E (H)	Ribosomal_L6e_N domain-containing protein	polymer	229	25621.5	1	UniProt (A0A3Q7GMA5) Pfam (PF03868) Pfam (PF01159)	Solanum lycopersicum (tomato)
6	F (I)	Thaliana 60S ribosomal protein L7	polymer	242	28058.0	1	UniProt (M1BRF8) Pfam (PF08079) Pfam (PF00327)	Solanum lycopersicum (tomato)
7	G (J)	Ribosomal_L7Ae domain-containing protein	polymer	258	29362.1	1	UniProt (A0A3Q7GV73) Pfam (PF01248)	Solanum lycopersicum (tomato)
8	H (K)	60S ribosomal protein uL6	polymer	194	22004.6	1	UniProt (A0A3Q7JDZ0) Pfam (PF00347)	Solanum lycopersicum (tomato)
9	I (L)	60S ribosomal protein L10	polymer	220	24913.3	1	UniProt (Q3SC85) Pfam (PF00252)	Solanum lycopersicum (tomato)
10	J (M)	60S ribosomal protein uL5	polymer	181	20826.2	1	UniProt (K4CG62) Pfam (PF00281) Pfam (PF00673)	Solanum lycopersicum (tomato)
11	K (N)	60S ribosomal protein L13	polymer	206	23620.6	1	UniProt (A0A3Q7JCM5) Pfam (PF01294)	Solanum lycopersicum (tomato)
12	L (O)	Ribosomal_L14e domain-containing protein	polymer	133	15400.4	1	UniProt (A0A3Q7J0J5) Pfam (PF01929)	Solanum lycopersicum (tomato)
13	M (P)	Ribosomal protein L15	polymer	204	24233.3	1	UniProt (A0A3Q7HQH0) Pfam (PF00827)	Solanum lycopersicum (tomato)
14	N (Q)	Pectinesterase	polymer	206	23613.2	1	UniProt (A0A3Q7HGG4) Pfam (PF00572)	Solanum lycopersicum (tomato)
15	O (R)	50S ribosomal protein L22, chloroplastic	polymer	173	19785.7	1	UniProt (A0A3Q7FNQ5) Pfam (PF00237)	Solanum lycopersicum (tomato)
16	P (S)	Ribosomal_L18e/L15P domain-containing protein	polymer	187	20764.5	1	UniProt (A0A3Q7I5W4) Pfam (PF17135)	Solanum lycopersicum (tomato)
17	Q (T)	Ribosomal protein L19	polymer	213	24786.6	1	UniProt (A0A3Q7GQ29) Pfam (PF01280) Pfam (PF25476)	Solanum lycopersicum (tomato)
18	R (U)	60S ribosomal protein L18a	polymer	178	21476.3	1	UniProt (A0A3Q7IGB1) Pfam (PF01775)	Solanum lycopersicum (tomato)
19	S (V)	60S ribosomal protein eL21	polymer	164	18715.8	1	UniProt (A0A3Q7IJQ0) Pfam (PF01157)	Solanum lycopersicum (tomato)
20	T (W)	60S ribosomal protein eL22	polymer	124	13996.1	1	UniProt (A0A3Q7I7E8) Pfam (PF01776)	Solanum lycopersicum (tomato)
21	U (X)	60S ribosomal protein uL14	polymer	140	15040.9	1	UniProt (K4CUW3) Pfam (PF00238)	Solanum lycopersicum (tomato)
22	V (Y)	TRASH domain-containing protein	polymer	165	18712.1	1	UniProt (A0A3Q7IN69) Pfam (PF01246)	Solanum lycopersicum (tomato)
23	W (Z)	Ribosomal_L23eN domain-containing protein	polymer	154	17427.7	1	UniProt (A0A3Q7INK3) Pfam (PF03939) Pfam (PF00276)	Solanum lycopersicum (tomato)
24	X (a)	KOW domain-containing protein	polymer	146	16750.5	1	UniProt (A0A3Q7FBC6) Pfam (PF16906) Pfam (PF00467)	Solanum lycopersicum (tomato)
25	Y (b)	60S ribosomal protein L27	polymer	135	15698.6	1	UniProt (A0A3Q7GZ83) Pfam (PF01777)	Solanum lycopersicum (tomato)
26	Z (c)	Ribosomal_L18e/L15P domain-containing protein	polymer	148	16479.4	1	UniProt (A0A3Q7GZ10) Pfam (PF00828)	Solanum lycopersicum (tomato)
27	AA (d)	60S ribosomal protein L29	polymer	60	6989.9	1	UniProt (A0A3Q7GK12) Pfam (PF01779)	Solanum lycopersicum (tomato)
28	BA (e)	60S ribosomal protein eL30	polymer	112	12367.5	1		Solanum lycopersicum (tomato)
29	CA (f)	60S ribosomal protein eL31	polymer	120	13890.2	1	UniProt (A0A3Q7JRW8) Pfam (PF01198)	Solanum lycopersicum (tomato)
30	DA (g)	60S ribosomal protein eL32	polymer	133	15673.5	1	UniProt (A0A3Q7F2B5) Pfam (PF01655)	Solanum lycopersicum (tomato)
31	EA (h)	60S ribosomal protein eL33	polymer	112	12952.2	1	UniProt (A0A3Q7FPS6) Pfam (PF01247)	Solanum lycopersicum (tomato)
32	FA (i)	60S ribosomal protein eL34	polymer	120	13815.4	1	UniProt (A0A3Q7GDM4) Pfam (PF01199)	Solanum lycopersicum (tomato)
33	GA (j)	Similar to 60S ribosomal protein L35	polymer	123	14324.4	1	UniProt (Q53U38) Pfam (PF00831)	Solanum lycopersicum (tomato)
34	HA (k)	60S ribosomal protein L36	polymer	110	12406.9	1	UniProt (A0A3Q7GUG2) Pfam (PF01158)	Solanum lycopersicum (tomato)
35	IA (l)	Ribosomal protein L37	polymer	95	10809.6	1	UniProt (A0A3Q7FV98) Pfam (PF01907)	Solanum lycopersicum (tomato)
36	JA (m)	60S ribosomal protein L38	polymer	69	8101.7	1	UniProt (P46291) Pfam (PF01781)	Solanum lycopersicum (tomato)
37	KA (n)	60S ribosomal protein eL39	polymer	51	6489.8	1	UniProt (A0A3Q7J415) Pfam (PF00832)	Solanum lycopersicum (tomato)
38	LA (o)	Ubiquitin	polymer	128	14745.4	1	UniProt (K4B017) Pfam (PF00240) Pfam (PF01020)	Solanum lycopersicum (tomato)
39	MA (p)	60S ribosomal protein eL42	polymer	105	12037.3	1	UniProt (A0A3Q7FPL2) Pfam (PF00935)	Solanum lycopersicum (tomato)
40	NA (q)	60S ribosomal protein eL43	polymer	92	10280.1	1	UniProt (K4CND1) Pfam (PF01780)	Solanum lycopersicum (tomato)
41	OA (r)	Ribosomal_L28e domain-containing protein	polymer	143	16018.6	1	UniProt (A0A3Q7FVJ9) Pfam (PF01778)	Solanum lycopersicum (tomato)
42	PA (s)	tRNA	polymer	2	589.4	1		Solanum lycopersicum (tomato)
43	QA (2)	25S rRNA	polymer	3391	1098453.0	1	GenBank (2090998066)	Solanum lycopersicum (tomato)
44	RA (5)	5S rRNA	polymer	120	38634.9	1	GenBank (19159)	Solanum lycopersicum (tomato)
45	SA (8)	5.8S rRNA	polymer	165	53173.6	1	GenBank (1418500722)	Solanum lycopersicum (tomato)
46	TA (S2)	18S	polymer	1808	583609.1	1		Solanum lycopersicum (tomato)
47	UA (NA)	KH type-2 domain-containing protein	polymer	239	26828.4	1	UniProt (A0A3Q7HBR5) Pfam (PF07650) Pfam (PF00189)	Solanum lycopersicum (tomato)
48	VA (OA)	Ribosomal_S7 domain-containing protein	polymer	211	23686.2	1	UniProt (A0A3Q7IVL4) Pfam (PF00177)	Solanum lycopersicum (tomato)
49	WA (PA)	S10_plectin domain-containing protein	polymer	180	19882.5	1	UniProt (A0A3Q7JYM3) Pfam (PF03501)	Solanum lycopersicum (tomato)
50	XA (QA)	40S ribosomal protein uS19	polymer	151	17352.5	1	UniProt (A0A3Q7F5X2) Pfam (PF00203)	Solanum lycopersicum (tomato)
51	YA (RA)	40S ribosomal protein uS9	polymer	147	16805.8	1	UniProt (A0A3Q7GDB0) Pfam (PF00380)	Solanum lycopersicum (tomato)
52	ZA (TA)	40S ribosomal protein uS13	polymer	152	17574.5	1	UniProt (A0A3Q7FJL7) Pfam (PF00416)	Solanum lycopersicum (tomato)
53	AB (UA)	40S ribosomal protein eS19	polymer	143	16056.4	1	UniProt (A0A3Q7FTS1) Pfam (PF01090)	Solanum lycopersicum (tomato)
54	BB (VA)	Ribosomal_S10 domain-containing protein	polymer	123	13735.1	1	UniProt (A0A3Q7EMX2) Pfam (PF00338)	Solanum lycopersicum (tomato)
55	CB (WA)	40S ribosomal protein eS28	polymer	65	7551.8	1	UniProt (K4B4Z0) Pfam (PF01200)	Solanum lycopersicum (tomato)
56	DB (XA)	40S ribosomal protein uS14	polymer	56	6455.6	1	UniProt (A0A3Q7ITW7) Pfam (PF00253)	Solanum lycopersicum (tomato)
57	EB (YA)	Mitogen-activated protein kinase	polymer	326	35993.6	1	UniProt (A0A3Q7GX91) Pfam (PF00400)	Solanum lycopersicum (tomato)
58	FB (ZA)	40S ribosomal protein S25	polymer	108	11995.2	1	UniProt (A0A3Q7F3F2) Pfam (PF03297)	Solanum lycopersicum (tomato)
59	GB (aA)	tRNA_1	polymer	14	4470.7	1		Solanum lycopersicum (tomato)
60	HB (bA)	mRNA	polymer	3	895.6	1		Solanum lycopersicum (tomato)
61	IB (t)	60S ribosomal protein L41	polymer	25	3445.4	1	UniProt (K4C3A4) Pfam (PF05162)	Solanum lycopersicum (tomato)
62	JB (u)	40S ribosomal protein SA	polymer	296	32216.3	1	UniProt (A0A3Q7H1U4) Pfam (PF00318)	Solanum lycopersicum (tomato)
63	KB (v)	40S ribosomal protein S3a	polymer	260	29741.5	1	UniProt (A0A3Q7I881) Pfam (PF01015)	Solanum lycopersicum (tomato)
64	LB (w)	40S ribosomal protein S4	polymer	264	29959.2	1	UniProt (A0A3Q7GQU3) Pfam (PF08071) Pfam (PF00900) Pfam (PF00467) Pfam (PF16121)	Solanum lycopersicum (tomato)
65	MB (x)	40S ribosomal protein S7	polymer	191	22088.5	1	UniProt (A0A3Q7H0E8) Pfam (PF01251)	Solanum lycopersicum (tomato)
66	NB (y)	40S ribosomal protein S8	polymer	220	24918.7	1	UniProt (A0A3Q7HJ03) Pfam (PF01201)	Solanum lycopersicum (tomato)
67	OB (z)	Ribosomal_S17_N domain-containing protein	polymer	159	17740.8	1	UniProt (K4C998) Pfam (PF16205) Pfam (PF00366)	Solanum lycopersicum (tomato)
68	PB (AA)	40S ribosomal protein S17	polymer	144	16266.0	1	UniProt (P49215) Pfam (PF00833)	Solanum lycopersicum (tomato)
69	QB (BA)	40S ribosomal protein S21	polymer	82	9163.2	1	UniProt (A0A3Q7G7P4) Pfam (PF01249)	Solanum lycopersicum (tomato)
70	RB (CA)	40S body ribosomal protein uS12	polymer	142	15771.6	1	UniProt (K4D3L7) Pfam (PF00164)	Solanum lycopersicum (tomato)
71	SB (DA)	40S ribosomal protein S26	polymer	127	14608.2	1	UniProt (A0A3Q7GRY8) Pfam (PF01283)	Solanum lycopersicum (tomato)
72	TB (EA)	S5 DRBM domain-containing protein	polymer	280	30630.7	1	UniProt (A0A3Q7G7F0) Pfam (PF00333) Pfam (PF03719)	Solanum lycopersicum (tomato)
73	UB (FA)	40S ribosomal protein S6	polymer	249	28384.2	1	UniProt (A0A3Q7HSH1) Pfam (PF01092)	Solanum lycopersicum (tomato)
74	VB (GA)	40S body ribosomal protein uS4	polymer	197	23051.7	1	UniProt (K4ATQ2) Pfam (PF00163) Pfam (PF01479)	Solanum lycopersicum (tomato)
75	WB (HA)	30S ribosomal protein S15, chloroplastic	polymer	151	17099.3	1	UniProt (K4CYU9) Pfam (PF08069) Pfam (PF00312)	Solanum lycopersicum (tomato)
76	XB (IA)	Ribosomal protein S14	polymer	150	16389.9	1	UniProt (Q38JI8) Pfam (PF00411)	Solanum lycopersicum (tomato)	Ribosomal protein S14-like
77	YB (KA)	40S ribosomal protein S24	polymer	133	15445.3	1	UniProt (A0A3Q7I5D6) Pfam (PF01282)	Solanum lycopersicum (tomato)
78	ZB (LA)	40S ribosomal protein S27	polymer	86	9620.2	1	UniProt (A0A1U8DQX3)	Solanum lycopersicum (tomato)
79	AC (MA)	40S ribosomal protein S30	polymer	62	6953.3	1	UniProt (A0A0V0GRY5)	Solanum lycopersicum (tomato)
80	BC (JA)	40S ribosomal protein S15a-1	polymer	130	14552.0	1	UniProt (A0A1U7YEG5) Pfam (PF00410)	Solanum lycopersicum (tomato)	40S ribosomal protein S15a-1 isoform X1
81	AD, AE, AF, AR, BD... (2, S2, D, 8, E...)	POTASSIUM ION	non-polymer		39.1	119	Chemie (K)
82	AG, AH, AI, AJ, AK... (2, 5, S2, FA, E...)	MAGNESIUM ION	non-polymer		24.3	364	Chemie (MG)
83	AV, BV, QC, RC, TC... (XA, DA, l, o, p...)	ZINC ION	non-polymer		65.4	6	Chemie (ZN)
84	VF, WF, YF (2)	SPERMINE	non-polymer		202.3	3	Chemie (SPM)
85	XF (2)	SPERMIDINE	non-polymer		145.2	1	Chemie (SPD)
86	MR (S2)	1,4-DIAMINOBUTANE	non-polymer		88.2	1	Chemie (PUT)
87	VU (NA)	beta-D-glucopyranose	non-polymer		180.2	1	Chemie (BGC)
88	AW, AX, BW, BX, CW... (b, WA, c, XA, d...)	water	water		18.0	4728	Chemie (HOH)

Sequence modifications

F: 1 - 406 (UniProt: A0A3Q7HW81)

PDB	External Database	Details
Val 162	Ile 162	conflict
Asn 170	Val 170	conflict
Gln 277	Leu 277	conflict
Ala 366	Gln 366	conflict

G: 1 - 301 (UniProt: A0A3Q7H274)

PDB	External Database	Details
Phe 51	Leu 51	conflict
His 85	Arg 85	conflict

J: 1 - 258 (UniProt: A0A3Q7GV73)

PDB	External Database	Details
Ser 10	Ala 114	variant
Ala 18	Ser 122	variant
Leu 21	Val 125	variant

K: 1 - 194 (UniProt: A0A3Q7JDZ0)

PDB	External Database	Details
Gln 24	Leu 24	conflict
Val 27	Ile 27	conflict
Gly 65	Ser 65	conflict
Thr 69	Ala 69	conflict
Ser 109	Thr 109	conflict

N: 1 - 206 (UniProt: A0A3Q7JCM5)

PDB	External Database	Details
Arg 128	His 128	conflict

P: 1 - 204 (UniProt: A0A3Q7HQH0)

PDB	External Database	Details
Val 135	Ile 135	conflict
Gln 137	Ser 137	conflict

Q: 1 - 206 (UniProt: A0A3Q7HGG4)

PDB	External Database	Details
Tyr 206	Glu 206	variant

R: 1 - 173 (UniProt: A0A3Q7FNQ5)

PDB	External Database	Details
Ser 46	Arg 46	conflict

S: 1 - 187 (UniProt: A0A3Q7I5W4)

PDB	External Database	Details
Thr 17	Ile 17	conflict
Ala 37	Ser 37	conflict
Pro 60	Ala 60	conflict
Ile 68	Val 68	conflict
Ala 71	Met 71	conflict
Gly 75	Glu 75	conflict
Val 79	Ala 79	conflict
Leu 81	Val 81	conflict
Cys 100	Thr 100	conflict
Lys 103	Arg 103	conflict
Leu 136	Val 136	conflict
Pro 153	Lys 153	conflict

T: 1 - 213 (UniProt: A0A3Q7GQ29)

PDB	External Database	Details
Lys 178	Glu 178	conflict
Lys 179	Glu 179	conflict

U: 1 - 178 (UniProt: A0A3Q7IGB1)

PDB	External Database	Details
Thr 73	Lys 73	conflict
Ala 104	Gly 104	conflict

Y: 1 - 164 (UniProt: A0A3Q7IN69)

PDB	External Database	Details
Met 0	-	initiating methionine

Z: 1 - 154 (UniProt: A0A3Q7INK3)

PDB	External Database	Details
Ser 55	Asn 55	conflict
Val 61	Ile 61	conflict
Ala 73	Gln 73	conflict
Ile 74	Val 74	conflict
Tyr 77	Cys 77	conflict
Lys 101	His 101	conflict

a: 1 - 146 (UniProt: A0A3Q7FBC6)

PDB	External Database	Details
Val 25	Leu 25	conflict
Asn 43	Ser 43	conflict
Asn 99	His 99	conflict
Val 105	Ile 105	conflict

b: 1 - 135 (UniProt: A0A3Q7GZ83)

PDB	External Database	Details
Phe 117	Leu 117	conflict

c: 1 - 148 (UniProt: A0A3Q7GZ10)

PDB	External Database	Details
Val 82	Leu 82	conflict
Ile 129	Val 129	conflict

f: 1 - 120 (UniProt: A0A3Q7JRW8)

PDB	External Database	Details
Val 76	Ile 76	conflict

j: 1 - 123 (UniProt: Q53U38)

PDB	External Database	Details
Ala 67	Leu 67	conflict
Val 72	Ala 72	conflict
Ser 100	Ala 100	conflict
Met 112	Leu 112	conflict

k: 1 - 110 (UniProt: A0A3Q7GUG2)

PDB	External Database	Details
Lys 88	Arg 124	conflict

l: 1 - 95 (UniProt: A0A3Q7FV98)

PDB	External Database	Details
Leu 44	Lys 44	conflict

o: 1 - 128 (UniProt: K4B017)

PDB	External Database	Details
Arg 113	Lys 113	conflict

OA: 5 - 215 (UniProt: A0A3Q7IVL4)

PDB	External Database	Details
Gly 37	Asp 33	conflict
Met 43	Ile 39	conflict
Met 60	Thr 56	conflict
Gln 117	Leu 113	conflict

QA: 1 - 151 (UniProt: A0A3Q7F5X2)

PDB	External Database	Details
Gln 75	Pro 75	conflict

RA: 1 - 147 (UniProt: A0A3Q7GDB0)

PDB	External Database	Details
His 62	Gln 62	conflict
Gln 105	Thr 105	conflict

TA: 1 - 152 (UniProt: A0A3Q7FJL7)

PDB	External Database	Details
Leu 67	Val 67	conflict

UA: 1 - 143 (UniProt: A0A3Q7FTS1)

PDB	External Database	Details
Ser 6	Asn 6	conflict
Asp 14	Glu 14	conflict

XA: 1 - 56 (UniProt: A0A3Q7ITW7)

PDB	External Database	Details
Asn 13	Tyr 13	conflict

v: 1 - 260 (UniProt: A0A3Q7I881)

PDB	External Database	Details
Glu 39	Gly 39	conflict
Ala 141	Gly 141	conflict
Val 169	Arg 169	conflict
Arg 173	Val 173	conflict
Val 185	Ala 185	conflict
Phe 205	Tyr 205	conflict

w: 1 - 264 (UniProt: A0A3Q7GQU3)

PDB	External Database	Details
Leu 48	Met 48	conflict
Thr 91	Ser 91	conflict
Ser 98	Asn 98	conflict
Leu 114	Val 114	conflict
Ala 119	Ser 119	conflict
Asp 165	Glu 165	conflict
Ile 194	Val 194	conflict
Leu 195	Ile 195	conflict
Val 208	Leu 208	conflict
Ser 232	Thr 232	conflict
Ser 247	Thr 247	conflict
Met 256	Leu 256	conflict

x: 1 - 191 (UniProt: A0A3Q7H0E8)

PDB	External Database	Details
Ala 13	Asp 13	conflict
His 19	Phe 19	conflict
Ser 22	Thr 22	conflict
Gly 24	Ala 24	conflict

y: 1 - 222 (UniProt: A0A3Q7HJ03)

PDB	External Database	Details
Lys 18	Gln 18	conflict
Ser 20	Thr 20	conflict
Phe 66	Tyr 66	conflict
Asn 159	Lys 157	conflict
Ala 162	Lys 160	conflict
Lys 165	Thr 163	conflict
Ala 175	Ser 173	conflict
Leu 180	Tyr 178	conflict

AA: 1 - 144 (UniProt: P49215)

PDB	External Database	Details
Glu 87	Asp 87	conflict

BA: 1 - 82 (UniProt: A0A3Q7G7P4)

PDB	External Database	Details
Val 44	Arg 44	conflict
Met 68	Leu 68	conflict

IA: 1 - 150 (UniProt: Q38JI8)

PDB	External Database	Details
Ias 137	Asp 137	conflict

LA: 1 - 86 (UniProt: A0A1U8DQX3)

PDB	External Database	Details
Lys 19	Arg 19	conflict
Ile 76	Thr 76	conflict

JA: 1 - 130 (UniProt: A0A1U7YEG5)

PDB	External Database	Details
Ala 20	Arg 20	conflict
Ala 23	Arg 23	conflict
Glu 26	Met 26	conflict
Leu 27	Ile 27	conflict
Asp 49	Glu 49	conflict
Gln 51	Glu 51	conflict
Val 58	Ser 58	conflict
Ala 84	Lys 84	conflict
Thr 85	Glu 85	conflict

Sequence viewer

Contents of the asymmetric unit

Polymers	Number of chains	80
Polymers	Total formula weight	3162349.3
Non-Polymers*	Number of molecules	495
Non-Polymers*	Total formula weight	14912.7
All*	Total formula weight	3177262.0

*Water molecules are not included.

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		Validation report (PDF)