Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6YXX

State A of the Trypanosoma brucei mitoribosomal large subunit assembly intermediate

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 (A1)	bL28m	polymer	241	28051.4	1	UniProt (Q586A2)	Trypanosoma brucei brucei
2	B (E1)	mt-LAF21	polymer	482	56574.4	1	UniProt (Q57WG6)	Trypanosoma brucei brucei
3	C (A2)	uL29m	polymer	471	54045.4	1	UniProt (Q38EM7) Pfam (PF06984)	Trypanosoma brucei brucei
4	D (E2)	DUF4379 domain-containing protein	polymer	568	63645.2	1	UniProt (C9ZTN9) Pfam (PF14311)	Trypanosoma brucei brucei
5	E (A3)	uL30m	polymer	218	25218.4	1	UniProt (C9ZY77)	Trypanosoma brucei brucei
6	F (E3)	mt-LAF23	polymer	557	63989.4	1	UniProt (D0A795)	Trypanosoma brucei brucei
7	G (E4)	mt-LAF24	polymer	439	49278.2	1	UniProt (Q585A0)	Trypanosoma brucei brucei
8	H (A5)	bL32m	polymer	80	9745.7	1	UniProt (Q584F4)	Trypanosoma brucei brucei
9	I (E5)	mt-LAF25	polymer	376	32017.4	1		Trypanosoma brucei brucei
10	J (E6)	KRIPP3	polymer	531	58601.6	1	UniProt (Q4GZA2)	Trypanosoma brucei brucei
11	K (A8)	bL35m	polymer	181	21661.5	1	UniProt (D0A1K1)	Trypanosoma brucei brucei
12	L (AA)	12S ribosomal RNA	polymer	1176	365178.3	1		Trypanosoma brucei brucei
13	M (BA)	mL67	polymer	831	93569.3	1	UniProt (D0A5V6)	Trypanosoma brucei brucei
14	N (EA)	mt-EngA	polymer	576	65528.3	1	UniProt (Q57TZ4) Pfam (PF01926) Pfam (PF14714)	Trypanosoma brucei brucei
15	O, TB (UA, Uf)	UNK	polymer	10	869.1	2		Trypanosoma brucei brucei
16	P (BB)	mL68	polymer	541	62806.3	1	UniProt (D0A135)	Trypanosoma brucei brucei
17	Q (EB)	DEAD-box helicase, putative	polymer	754	85715.3	1	UniProt (D0A9G9) Pfam (PF00270) Pfam (PF00271)	Trypanosoma brucei brucei
18	R (EC)	Pseudouridylate synthase, putative	polymer	406	46374.7	1	UniProt (Q38FJ3) Pfam (PF00849)	Trypanosoma brucei brucei
19	S (BD)	mL70	polymer	547	62442.4	1		Trypanosoma brucei brucei
20	T (ED)	mt-LAF4	polymer	616	69432.4	1	UniProt (Q385G9)	Trypanosoma brucei brucei
21	U (AE)	Ribosomal protein L3 mitochondrial, putative	polymer	473	55073.7	1	UniProt (Q580R4) Pfam (PF00297)	Trypanosoma brucei brucei
22	V (BE)	mL71	polymer	449	50313.8	1	UniProt (Q57WG1)	Trypanosoma brucei brucei
23	W (EE)	SpoU_methylase domain-containing protein	polymer	586	67167.3	1	UniProt (C9ZZ65) Pfam (PF00588)	Trypanosoma brucei brucei
24	X (AF)	Ribosomal protein L4/L1 family, putative	polymer	459	53156.7	1	UniProt (A0A1G4HYD1) Pfam (PF00573)	Trypanosoma brucei brucei
25	Y (BF)	Tetratricopeptide repeat	polymer	426	49407.0	1	UniProt (A0A3L6LA84)	Trypanosoma brucei brucei
26	Z (EF)	SpoU_methylase domain-containing protein	polymer	373	40223.1	1	UniProt (C9ZWD9) Pfam (PF00588)	Trypanosoma brucei brucei
27	AA (EG)	mt-LAF7	polymer	156	18645.3	1	UniProt (Q387S8)	Trypanosoma brucei brucei
28	BA (BH)	mL74	polymer	349	39765.2	1	UniProt (Q38AM5)	Trypanosoma brucei brucei
29	CA (EH)	mt-LAF8	polymer	634	68905.0	1	UniProt (A0A1G4IEQ9)	Trypanosoma brucei brucei
30	DA (AI)	RIBOSOMAL_L9 domain-containing protein	polymer	263	30729.3	1	UniProt (Q57UC5) Pfam (PF01281)	Trypanosoma brucei brucei
31	EA (BI)	mL75	polymer	342	39770.5	1	UniProt (D0A108)	Trypanosoma brucei brucei
32	FA, FC (UI, Ur)	UNK	polymer	21	1805.2	2		Trypanosoma brucei brucei
33	GA (BJ)	mL76	polymer	333	39638.9	1	UniProt (Q383M2)	Trypanosoma brucei brucei
34	HA (AK)	Ribosomal protein L11, putative	polymer	342	40266.8	1	UniProt (Q586R9) Pfam (PF03946) Pfam (PF00298)	Trypanosoma brucei brucei
35	IA (BK)	Chaperone protein DNAj, putative	polymer	386	43754.6	1	UniProt (C9ZQR6) Pfam (PF00226)	Trypanosoma brucei brucei
36	JA (UK)	UNK	polymer	25	2145.6	1		Trypanosoma brucei brucei
37	KA (BL)	mL78	polymer	312	35104.5	1	UniProt (D0A4P5)	Trypanosoma brucei brucei
38	LA (EL)	mt-LAF12	polymer	691	77908.4	1	UniProt (C9ZVC0)	Trypanosoma brucei brucei
39	MA (EM)	GTP-binding protein, putative	polymer	451	50416.5	1	UniProt (Q38E75) Pfam (PF01926)	Trypanosoma brucei brucei
40	NA (UM)	UNK	polymer	8	698.9	1		Trypanosoma brucei brucei
41	OA (AN)	50S ribosomal protein L13, putative	polymer	202	24341.3	1	UniProt (Q580D5) Pfam (PF00572)	Trypanosoma brucei brucei
42	PA (BN)	mL80	polymer	302	34883.3	1	UniProt (C9ZQF0)	Trypanosoma brucei brucei
43	QA (EN)	mt-LAF14	polymer	731	82109.0	1	UniProt (C9ZPS0)	Trypanosoma brucei brucei
44	RA (BO)	mL81	polymer	262	29284.5	1	UniProt (D0A755)	Trypanosoma brucei brucei
45	SA, UA (EO, EP)	mt-LAF15a	polymer	319	34621.4	2	UniProt (C9ZMA6)	Trypanosoma brucei brucei
46	TA (AP)	Ribosomal_L18e/L15P domain-containing protein	polymer	374	43780.0	1	UniProt (Q57U68) Pfam (PF00828)	Trypanosoma brucei brucei
47	VA (BQ)	Peptidyl-prolyl cis-trans isomerase	polymer	231	25579.0	1	UniProt (Q57WF8) Pfam (PF00160)	Trypanosoma brucei brucei	PPIase
48	WA (AR)	50S ribosomal protein L17, putative	polymer	301	35117.8	1	UniProt (Q57YI7) Pfam (PF01196)	Trypanosoma brucei brucei
49	XA (BR)	mL84	polymer	205	24773.6	1	UniProt (Q586A6)	Trypanosoma brucei brucei
50	YA (ER)	Acyl carrier protein	polymer	148	16550.8	1	UniProt (Q57WW9) Pfam (PF00550)	Trypanosoma brucei brucei
51	ZA (BS)	mL85	polymer	198	22658.0	1	UniProt (Q38FG8)	Trypanosoma brucei brucei
52	AB (ES)	Lipase (Class 3)	polymer	524	58830.7	1	UniProt (A0A3L6L1Y4) Pfam (PF01764)	Trypanosoma brucei brucei
53	BB (AT)	bL19m	polymer	144	16931.5	1	UniProt (Q4GZ98)	Trypanosoma brucei brucei
54	CB (BT)	mL86	polymer	191	22376.2	1	UniProt (A0A3L6L8W0)	Trypanosoma brucei brucei
55	DB (ET)	mt-LAF19	polymer	102	12076.1	1	UniProt (Q383S4)	Trypanosoma brucei brucei
56	EB (AU)	bL20m	polymer	213	24393.9	1	UniProt (Q383R2)	Trypanosoma brucei brucei
57	FB (BU)	mL87	polymer	185	22337.5	1	UniProt (D0A7Z9)	Trypanosoma brucei brucei
58	GB (AV)	bL21m	polymer	188	20895.3	1	UniProt (C9ZT11) Pfam (PF00829)	Trypanosoma brucei brucei
59	HB (BV)	mL88	polymer	190	22255.6	1	UniProt (C9ZUW3)	Trypanosoma brucei brucei
60	IB (AW)	uL22m	polymer	278	32083.3	1	UniProt (C9ZSI8) Pfam (PF00237)	Trypanosoma brucei brucei
61	JB (BW)	mL89	polymer	188	22213.4	1	UniProt (Q57WW5)	Trypanosoma brucei brucei
62	KB (AX)	uL23m	polymer	246	28848.0	1	UniProt (Q387G3)	Trypanosoma brucei brucei
63	LB (AY)	uL24m	polymer	378	43999.0	1	UniProt (C9ZK52)	Trypanosoma brucei brucei
64	MB (BZ)	Peptidyl-prolyl cis-trans isomerase	polymer	190	20542.3	1	UniProt (Q383Y4) Pfam (PF00160)	Trypanosoma brucei brucei	PPIase
65	NB (Ba)	mL93	polymer	153	18929.7	1	UniProt (D0A4T0)	Trypanosoma brucei brucei
66	OB (Bb)	mL94	polymer	162	17831.0	1	UniProt (Q38EP7)	Trypanosoma brucei brucei
67	PB (Bc)	mL95	polymer	146	17803.4	1	UniProt (Q389K3)	Trypanosoma brucei brucei
68	QB (Ae)	mL41	polymer	197	22610.9	1	UniProt (Q383U6)	Trypanosoma brucei brucei
69	RB (Af)	mL42	polymer	189	21602.6	1	UniProt (Q383S1)	Trypanosoma brucei brucei
70	SB (Bf)	mL98	polymer	113	12968.6	1	UniProt (Q388M2)	Trypanosoma brucei brucei
71	UB (Ag)	L51_S25_CI-B8 domain-containing protein	polymer	260	31300.4	1	UniProt (Q583E5) Pfam (PF05047)	Trypanosoma brucei brucei
72	VB (E7)	mt-LAF27	polymer	97	11609.3	1		Trypanosoma brucei brucei
73	WB (E8)	KRIPP9	polymer	786	89421.0	1	UniProt (Q57YZ6) Pfam (PF13812)	Trypanosoma brucei brucei
74	XB (E9)	mt-LAF29	polymer	343	38526.0	1	UniProt (A0A3L6L206)	Trypanosoma brucei brucei
75	YB (Al)	mL49	polymer	218	24501.5	1	UniProt (Q57Z82)	Trypanosoma brucei brucei
76	ZB (Ul)	UNK	polymer	238	20272.9	1		Trypanosoma brucei brucei
77	AC (Um)	UNK	polymer	27	2315.8	1		Trypanosoma brucei brucei
78	BC (Un)	UNK	polymer	28	2401.0	1		Trypanosoma brucei brucei
79	CC (Ao)	mL52	polymer	1520	167692.8	1		Trypanosoma brucei brucei
80	DC (Ap)	mL53	polymer	309	35656.4	1	UniProt (A0A3L6L3K9)	Trypanosoma brucei brucei
81	EC (Up)	UNK	polymer	87	7422.1	1		Trypanosoma brucei brucei
82	GC (Us)	UNK	polymer	79	6741.3	1		Trypanosoma brucei brucei
83	HC (At)	mL63	polymer	154	18213.9	1	UniProt (C9ZU82)	Trypanosoma brucei brucei
84	IC (Av)	mL64	polymer	242	28546.0	1	UniProt (D0A934)	Trypanosoma brucei brucei
85	JC, KC, KD, LC, MC... (E2, EG, E9, A5)	ZINC ION	non-polymer		65.4	7	Chemie (ZN)
86	AD, BD, DD, GD, JD... (AA, EA, EB, A8)	MAGNESIUM ION	non-polymer		24.3	17	Chemie (MG)
87	CD, FD (EA)	GUANOSINE-5'-TRIPHOSPHATE	non-polymer		523.2	2	Chemie (GTP)
88	ED, HD (EA)	SODIUM ION	non-polymer		23.0	2	Chemie (NA)
89	ID (EB)	ADENOSINE-5'-TRIPHOSPHATE	non-polymer		507.2	1	Chemie (ATP)
90	LD (ER)	S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE	non-polymer		496.6	1	Chemie (PM8)
91	ND (Av)	NICOTINAMIDE-ADENINE-DINUCLEOTIDE	non-polymer		663.4	1	Chemie (NAD)
92	OD, PD (EA, EB)	water	water		18.0	8	Chemie (HOH)

Sequence modifications

E1: 1 - 482 (UniProt: Q57WG6)

PDB	External Database	Details
Ser 379	Ala 379	conflict

A2: 1 - 471 (UniProt: Q38EM7)

PDB	External Database	Details
Gly 238	Ala 238	conflict

E2: -68 - 499 (UniProt: C9ZTN9)

PDB	External Database	Details
Thr 167	Lys 236	conflict

A3: 1 - 218 (UniProt: C9ZY77)

PDB	External Database	Details
Unk 198	Ala 198	conflict

E3: 2 - 557 (UniProt: D0A795)

PDB	External Database	Details
Met 1	-	initiating methionine

E6: -1 - 529 (UniProt: Q4GZA2)

PDB	External Database	Details
Ser 360	Ala 362	conflict

EA: 1 - 576 (UniProt: Q57TZ4)

PDB	External Database	Details
Unk 12	Arg 12	conflict

EB: 1 - 754 (UniProt: D0A9G9)

PDB	External Database	Details
Ala 301	Thr 301	conflict

EC: 1 - 406 (UniProt: Q38FJ3)

PDB	External Database	Details
Unk 25	His 25	conflict

ED: 1 - 616 (UniProt: Q385G9)

PDB	External Database	Details
Arg 252	Lys 252	conflict

EE: 1 - 586 (UniProt: C9ZZ65)

PDB	External Database	Details
Asp 337	Gly 337	conflict

EH: 1 - 634 (UniProt: A0A1G4IEQ9)

PDB	External Database	Details
Unk 166	Gly 166	conflict
Arg 495	Lys 495	conflict

AI: 1 - 263 (UniProt: Q57UC5)

PDB	External Database	Details
Unk 249	Lys 249	conflict
Unk 250	Gly 250	conflict
Unk 251	Pro 251	conflict
Unk 252	Val 252	conflict
Unk 253	Lys 253	conflict
Unk 254	Gln 254	conflict
Unk 255	Arg 255	conflict
Unk 256	Lys 256	conflict
Unk 257	Ala 257	conflict
Unk 258	Arg 258	conflict

BI: 1 - 342 (UniProt: D0A108)

PDB	External Database	Details
Asn 227	Asp 227	conflict

BJ: 1 - 333 (UniProt: Q383M2)

PDB	External Database	Details
Glu 329	Ala 329	conflict

AK: 1 - 342 (UniProt: Q586R9)

PDB	External Database	Details
Unk 327	Ala 327	conflict

BK: 1 - 386 (UniProt: C9ZQR6)

PDB	External Database	Details
Unk 33	His 33	conflict
Unk 60	Pro 60	conflict
Val 348	Leu 348	conflict

EL: 1 - 691 (UniProt: C9ZVC0)

PDB	External Database	Details
Unk 104	Ile 104	conflict
Glu 108	Gly 108	conflict
Val 126	Leu 126	conflict
Ser 188	Phe 188	conflict

EM: 1 - 451 (UniProt: Q38E75)

PDB	External Database	Details
Unk 407	Pro 407	conflict

EN: 1 - 731 (UniProt: C9ZPS0)

PDB	External Database	Details
Glu 18	Gly 18	conflict
Lys 310	Asn 310	conflict
Cys 676	Tyr 676	conflict

BS: 1 - 198 (UniProt: Q38FG8)

PDB	External Database	Details
Ile 45	Val 45	conflict
Unk 173	Leu 173	conflict

AX: 1 - 246 (UniProt: Q387G3)

PDB	External Database	Details
Tyr 126	His 126	conflict

AY: 1 - 378 (UniProt: C9ZK52)

PDB	External Database	Details
Glu 345	Val 345	conflict

E8: 1 - 786 (UniProt: Q57YZ6)

PDB	External Database	Details
Lys 208	Glu 218	conflict
Gln 250	Arg 260	conflict
Ile 345	Met 355	conflict
Unk 630	Leu 640	conflict

Sequence viewer

Contents of the asymmetric unit

Polymers	Number of chains	87
Polymers	Total formula weight	3474784.4
Non-Polymers*	Number of molecules	31
Non-Polymers*	Total formula weight	3630.6
All*	Total formula weight	3478415.0

*Water molecules are not included.

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