Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

7O5B

Cryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-nascent chain complex with (p)ppGpp-SRP bound

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 (U)	tRNA	polymer	77	24815.7	1	GenBank (1837880844)	Bacillus subtilis subsp. subtilis str. 168
2	B (V)	mRNA	polymer	8	2612.7	1		Bacillus subtilis subsp. subtilis str. 168
3	C (W)	SRP RNA (266-MER)	polymer	266	85909.7	1	GenBank (1837880844)	Bacillus subtilis subsp. subtilis str. 168
4	D (g)	Signal recognition particle protein	polymer	447	49739.0	1	UniProt (P37105) Pfam (PF02881) Pfam (PF00448) Pfam (PF02978)	Bacillus subtilis subsp. subtilis str. 168	Fifty-four homolog
5	E (h)	MifM-stalling construct	polymer	96	10874.6	1		Bacillus subtilis subsp. subtilis str. 168
6	F (p)	50S ribosomal protein L10	polymer	166	18131.8	1	UniProt (P42923) Pfam (PF00466)	Bacillus subtilis subsp. subtilis str. 168	BL5,Cold acclimatization protein,CAP,Vegetative protein 300,VEG300
7	G (q)	50S ribosomal protein L11	polymer	141	14951.4	1	UniProt (Q06796) Pfam (PF03946) Pfam (PF00298)	Bacillus subtilis subsp. subtilis str. 168	BL11
8	H (X)	23S rRNA (2887-MER)	polymer	2887	936486.9	1	GenBank (1491848961)	Bacillus subtilis subsp. subtilis str. 168
9	I (Y)	5S rRNA (112-MER)	polymer	112	36157.5	1	GenBank (1150402534)	Bacillus subtilis subsp. subtilis str. 168
10	J (Z)	50S ribosomal protein L2	polymer	277	30335.1	1	UniProt (P42919) Pfam (PF00181) Pfam (PF03947)	Bacillus subtilis subsp. subtilis str. 168	BL2
11	K (a)	50S ribosomal protein L3	polymer	208	22594.2	1	UniProt (P42920) Pfam (PF00297)	Bacillus subtilis subsp. subtilis str. 168	BL3
12	L (b)	50S ribosomal protein L4	polymer	207	22425.0	1	UniProt (P42921) Pfam (PF00573)	Bacillus subtilis subsp. subtilis str. 168
13	M (c)	50S ribosomal protein L5	polymer	179	20177.6	1	UniProt (P12877) Pfam (PF00281) Pfam (PF00673)	Bacillus subtilis subsp. subtilis str. 168	BL6
14	N (d)	50S ribosomal protein L6	polymer	179	19543.4	1	UniProt (P46898) Pfam (PF00347)	Bacillus subtilis subsp. subtilis str. 168	BL10
15	O (e)	50S ribosomal protein L13	polymer	145	16407.1	1	UniProt (P70974) Pfam (PF00572)	Bacillus subtilis subsp. subtilis str. 168
16	P (f)	50S ribosomal protein L14	polymer	122	13175.3	1	UniProt (P12875) Pfam (PF00238)	Bacillus subtilis subsp. subtilis str. 168
17	Q (i)	50S ribosomal protein L15	polymer	146	15410.7	1	UniProt (P19946) Pfam (PF00828)	Bacillus subtilis subsp. subtilis str. 168
18	R (j)	50S ribosomal protein L16	polymer	144	16223.0	1	UniProt (P14577) Pfam (PF00252)	Bacillus subtilis subsp. subtilis str. 168
19	S (k)	50S ribosomal protein L17	polymer	120	13774.8	1	UniProt (P20277) Pfam (PF01196)	Bacillus subtilis subsp. subtilis str. 168	BL15,BL21
20	T (l)	50S ribosomal protein L18	polymer	120	12993.8	1	UniProt (P46899) Pfam (PF00861)	Bacillus subtilis subsp. subtilis str. 168	BL16
21	U (m)	50S ribosomal protein L19	polymer	115	13416.9	1	UniProt (O31742) Pfam (PF01245)	Bacillus subtilis subsp. subtilis str. 168
22	V (n)	50S ribosomal protein L20	polymer	119	13669.2	1	UniProt (P55873) Pfam (PF00453)	Bacillus subtilis subsp. subtilis str. 168
23	W (o)	50S ribosomal protein L21	polymer	102	11296.1	1	UniProt (P26908) Pfam (PF00829)	Bacillus subtilis subsp. subtilis str. 168	BL20
24	X (r)	50S ribosomal protein L22	polymer	113	12481.6	1	UniProt (P42060) Pfam (PF00237)	Bacillus subtilis subsp. subtilis str. 168
25	Y (s)	50S ribosomal protein L23	polymer	95	10978.8	1	UniProt (P42924) Pfam (PF00276)	Bacillus subtilis subsp. subtilis str. 168
26	Z (t)	50S ribosomal protein L24	polymer	103	11166.1	1	UniProt (P0CI78) Pfam (PF00467) Pfam (PF17136)	Bacillus subtilis subsp. subtilis str. 168	12 kDa DNA-binding protein,BL23,HPB12
27	AA (u)	50S ribosomal protein L27	polymer	94	10391.9	1	UniProt (P05657) Pfam (PF01016)	Bacillus subtilis subsp. subtilis str. 168	BL24,BL30
28	BA (v)	50S ribosomal protein L28	polymer	62	6826.1	1	UniProt (P37807) Pfam (PF00830)	Bacillus subtilis subsp. subtilis str. 168
29	CA (w)	50S ribosomal protein L29	polymer	66	7728.0	1	UniProt (P12873) Pfam (PF00831)	Bacillus subtilis subsp. subtilis str. 168
30	DA (x)	50S ribosomal protein L30	polymer	59	6650.8	1	UniProt (P19947) Pfam (PF00327)	Bacillus subtilis subsp. subtilis str. 168	BL27
31	EA (0)	50S ribosomal protein L32	polymer	59	6745.1	1	UniProt (O34687) Pfam (PF01783)	Bacillus subtilis subsp. subtilis str. 168
32	FA (1)	50S ribosomal protein L33 1	polymer	49	5915.9	1	UniProt (P56849) Pfam (PF00471)	Bacillus subtilis subsp. subtilis str. 168
33	GA (2)	50S ribosomal protein L34	polymer	44	5271.3	1	UniProt (P05647) Pfam (PF00468)	Bacillus subtilis subsp. subtilis str. 168
34	HA (3)	50S ribosomal protein L35	polymer	66	7581.1	1	UniProt (P55874) Pfam (PF01632)	Bacillus subtilis subsp. subtilis str. 168
35	IA (4)	50S ribosomal protein L36	polymer	37	4318.4	1	UniProt (P20278) Pfam (PF00444)	Bacillus subtilis subsp. subtilis str. 168	BL38,Ribosomal protein B,Ribosomal protein II
36	JA (6)	50S ribosomal protein L31	polymer	66	7458.6	1	UniProt (Q03223) Pfam (PF01197)	Bacillus subtilis subsp. subtilis str. 168
37	KA (A)	16S rRNA (1533-MER)	polymer	1533	496854.2	1	GenBank (225184640)	Bacillus subtilis subsp. subtilis str. 168
38	LA (B)	30S ribosomal protein S2	polymer	246	28009.3	1	UniProt (P21464) Pfam (PF00318)	Bacillus subtilis subsp. subtilis str. 168	BS1,Vegetative protein 209,VEG209
39	MA (C)	30S ribosomal protein S3	polymer	218	24351.9	1	UniProt (P21465) Pfam (PF07650) Pfam (PF00189)	Bacillus subtilis subsp. subtilis str. 168	BS3,BS2
40	NA (D)	30S ribosomal protein S4	polymer	200	22874.3	1	UniProt (P21466) Pfam (PF00163) Pfam (PF01479)	Bacillus subtilis subsp. subtilis str. 168	BS4
41	OA (E)	30S ribosomal protein S5	polymer	166	17650.6	1	UniProt (P21467) Pfam (PF00333) Pfam (PF03719)	Bacillus subtilis subsp. subtilis str. 168	BS5
42	PA (F)	30S ribosomal protein S6	polymer	95	11140.5	1	UniProt (P21468) Pfam (PF01250)	Bacillus subtilis subsp. subtilis str. 168	BS9
43	QA (G)	30S ribosomal protein S7	polymer	156	17915.9	1	UniProt (P21469) Pfam (PF00177)	Bacillus subtilis subsp. subtilis str. 168	BS7
44	RA (H)	30S ribosomal protein S8	polymer	132	14901.4	1	UniProt (P12879) Pfam (PF00410)	Bacillus subtilis subsp. subtilis str. 168	BS8
45	SA (I)	30S ribosomal protein S9	polymer	130	14335.5	1	UniProt (P21470) Pfam (PF00380)	Bacillus subtilis subsp. subtilis str. 168	BS10
46	TA (J)	30S ribosomal protein S10	polymer	102	11687.7	1	UniProt (P21471) Pfam (PF00338)	Bacillus subtilis subsp. subtilis str. 168	BS13
47	UA (K)	30S ribosomal protein S11	polymer	131	13993.1	1	UniProt (P04969) Pfam (PF00411)	Bacillus subtilis subsp. subtilis str. 168	BS11
48	VA (L)	30S ribosomal protein S12	polymer	138	15248.7	1	UniProt (P21472) Pfam (PF00164)	Bacillus subtilis subsp. subtilis str. 168	BS12
49	WA (M)	30S ribosomal protein S13	polymer	121	13818.1	1	UniProt (P20282) Pfam (PF00416)	Bacillus subtilis subsp. subtilis str. 168	BS14
50	XA (N)	30S ribosomal protein S14	polymer	61	7263.8	1	UniProt (P12878) Pfam (PF00253)	Bacillus subtilis subsp. subtilis str. 168	30S ribosomal protein S14 type Z,30S ribosomal protein S14-1,BS-A
51	YA (O)	30S ribosomal protein S15	polymer	89	10597.2	1	UniProt (P21473) Pfam (PF00312)	Bacillus subtilis subsp. subtilis str. 168	BS18
52	ZA (P)	30S ribosomal protein S16	polymer	90	10153.8	1	UniProt (P21474) Pfam (PF00886)	Bacillus subtilis subsp. subtilis str. 168	BS17
53	AB (Q)	30S ribosomal protein S17	polymer	87	10221.0	1	UniProt (P12874) Pfam (PF00366)	Bacillus subtilis subsp. subtilis str. 168	BS16
54	BB (R)	30S ribosomal protein S18	polymer	79	8990.6	1	UniProt (P21475) Pfam (PF01084)	Bacillus subtilis subsp. subtilis str. 168	BS21
55	CB (S)	30S ribosomal protein S19	polymer	92	10607.3	1	UniProt (P21476) Pfam (PF00203)	Bacillus subtilis subsp. subtilis str. 168	BS19
56	DB (T)	30S ribosomal protein S20	polymer	88	9622.2	1	UniProt (P21477) Pfam (PF01649)	Bacillus subtilis subsp. subtilis str. 168	BS20
57	EB (g)	GUANOSINE-5',3'-TETRAPHOSPHATE	non-polymer		603.2	1	Chemie (G4P)

Sequence modifications

W: 4 - 269 (GenBank: 1837880844)

PDB	External Database	Details
-	U 26655	deletion

g: 1 - 446 (UniProt: P37105)

PDB	External Database	Details
His -2	-	expression tag
Met -1	-	expression tag
Gly 0	-	expression tag

p: 1 - 166 (UniProt: P42923)

PDB	External Database	Details
Thr 154	Ala 154	conflict

X: 2 - 2926 (GenBank: 1491848961)

PDB	External Database	Details
G 243	A 946795	conflict
-	U 946727	deletion
-	G 946726	deletion
-	U 946725	deletion
-	A 946724	deletion
-	C 946723	deletion
-	G 946722	deletion
-	G 946721	deletion
-	A 946720	deletion
-	U 946718	deletion
-	U 946717	deletion
-	A 946716	deletion
-	C 946715	deletion
-	A 946714	deletion
-	U 946642	deletion
-	C 946641	deletion
-	U 946640	deletion
-	C 946639	deletion
-	C 946638	deletion
-	U 946637	deletion
U 640	C 946402	conflict
-	U 945825	deletion
-	U 945824	deletion
-	C 945823	deletion
-	U 945488	deletion
-	A 945463	deletion
-	A 945462	deletion
-	A 945461	deletion
-	U 945460	deletion
-	A 945459	deletion
-	U 945458	deletion
-	A 945457	deletion
-	G 945456	deletion
-	U 945455	deletion
-	A 945454	deletion
-	G 945453	deletion

C: 1 - 218 (UniProt: P21465)

PDB	External Database	Details
Thr 213	Asn 213	conflict

K: 1 - 131 (UniProt: P04969)

PDB	External Database	Details
Gln 7	Ser 7	conflict

Sequence viewer

Contents of the asymmetric unit

Polymers	Number of chains	56
Polymers	Total formula weight	2294872.3
Non-Polymers*	Number of molecules	1
Non-Polymers*	Total formula weight	603.2
All*	Total formula weight	2295475.4

*Water molecules are not included.

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