6SW9

IC2A model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	2	16S ribosomal RNA	polymer	1497	487700.3	1		Pyrococcus abyssi GE5
2	A	30S ribosomal protein S3Ae	polymer	199	22888.1	1	UniProt (Q9V2K7) Pfam (PF01015) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)	Ribosomal protein S1e
3	B	30S ribosomal protein S2	polymer	202	23026.9	1	UniProt (Q9V191) Pfam (PF00318) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
4	C	Zn-ribbon RNA-binding protein involved in translation	polymer	63	7163.4	1	UniProt (G8ZFK7) Pfam (PF07754) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
5	D	30S ribosomal protein S4	polymer	180	21381.9	1	UniProt (P61992) Pfam (PF00163) Pfam (PF01479) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
6	E	30S ribosomal protein S4e	polymer	243	28246.1	1	UniProt (Q9V1U8) Pfam (PF08071) Pfam (PF01479) Pfam (PF00900) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
7	F	30S ribosomal protein S5	polymer	236	26523.9	1	UniProt (Q9V1V5) Pfam (PF00333) Pfam (PF03719) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
8	G	30S ribosomal protein S6e	polymer	125	14029.5	1	UniProt (Q9UYS3) Pfam (PF01092) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
9	H	30S ribosomal protein S7	polymer	215	24662.8	1	UniProt (Q9V109) Pfam (PF00177) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
10	I	30S ribosomal protein S8	polymer	130	14772.2	1	UniProt (Q9V1V0) Pfam (PF00410) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
11	J	30S ribosomal protein S8e	polymer	127	14293.7	1	UniProt (Q9UZL4) Pfam (PF01201) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
12	K	30S ribosomal protein S9	polymer	135	15293.9	1	UniProt (Q9V195) Pfam (PF00380) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
13	L	30S ribosomal protein S10	polymer	102	11795.8	1	UniProt (Q9V0V6) Pfam (PF00338) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
14	M	30S ribosomal protein S11	polymer	137	14773.0	1	UniProt (P62010) Pfam (PF00411) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
15	N	30S ribosomal protein S12	polymer	147	16477.6	1	UniProt (P61994) Pfam (PF00164) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
16	O	30S ribosomal protein S13	polymer	148	16992.9	1	UniProt (Q9V1A0) Pfam (PF00416) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
17	P	30S ribosomal protein S14 type Z	polymer	56	6644.1	1	UniProt (P62012) Pfam (PF00253) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
18	Q	30S ribosomal protein S15	polymer	158	18697.1	1	UniProt (Q9V2K9) Pfam (PF08069) Pfam (PF00312) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
19	R	30S ribosomal protein S17	polymer	113	13364.6	1	UniProt (Q9V1U5) Pfam (PF00366) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
20	S	30S ribosomal protein S17e	polymer	67	8059.5	1	UniProt (Q9V0G0) Pfam (PF00833) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
21	T	30S ribosomal protein S19	polymer	132	15307.3	1	UniProt (Q9V1T9) Pfam (PF00203) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
22	U	30S ribosomal protein S19e	polymer	150	17422.3	1	UniProt (Q9V0G8) Pfam (PF01090) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
23	V	30S ribosomal protein S24e	polymer	99	11798.6	1	UniProt (Q9UY20) Pfam (PF01282) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
24	W	30S ribosomal protein S27e	polymer	65	7186.6	1	UniProt (Q9UXZ3) Pfam (PF01667) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
25	X	30S ribosomal protein S28e	polymer	71	8102.3	1	UniProt (P61029) Pfam (PF01200) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
26	Y	30S ribosomal protein S27ae	polymer	51	5992.2	1	UniProt (P61238) Pfam (PF01599) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
27	Z	30S ribosomal protein S3	polymer	210	23472.3	1	UniProt (Q9V1U1) Pfam (PF07650) Pfam (PF00189) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)
28	0	50S ribosomal protein L41e	polymer	36	4910.2	1	UniProt (by SIFTS) (Q8U232) In PDB	Pyrococcus abyssi GE5
29	3	50S ribosomal protein L7Ae	polymer	123	13442.7	1	UniProt (P62008) Pfam (PF01248) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)	Ribosomal protein L8e
30	5	mRNA	polymer	20	6448.9	1		Pyrococcus abyssi GE5
31	4	initiator Met-tRNA fMet from E. coli (A1U72 variant)	polymer	76	24504.7	1		Escherichia coli
32	6	Translation initiation factor 1A	polymer	113	13078.3	1	UniProt (Q9V138) Pfam (PF01176) In PDB	Pyrococcus abyssi (strain GE5 / Orsay)	aIF-1A
33	7	Translation initiation factor 2 subunit gamma	polymer	414	45718.0	1	UniProt (Q980A5) Pfam (PF00009) Pfam (PF09173) In PDB	Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)	aIF2-gamma,eIF-2-gamma
34	8	Translation initiation factor 2 subunit beta	polymer	129	14835.5	1	UniProt (Q97W59) Pfam (PF01873) In PDB	Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)	aIF2-beta,eIF-2-beta
35	9	Translation initiation factor 2 subunit alpha	polymer	254	28946.6	1	UniProt (Q97Z79) Pfam (PF00575) Pfam (PF07541) In PDB	Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)	aIF2-alpha,eIF-2-alpha
36	2, 5, 4, 7	MAGNESIUM ION	non-polymer		24.3	34	Chemie (MG)
37	C, F, P, R, W	ZINC ION	non-polymer		65.4	6	Chemie (ZN)
38	7	METHIONINE	non-polymer		149.2	1	Chemie (MET)
39	7	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	non-polymer		522.2	1	Chemie (GNP)
40		water	water		18.0	42	Chemie (HOH)

Sequence modifications

8: 3 - 139 (UniProt: Q97W59)

PDB	External Database	Details
-	Glu 20	deletion
-	Lys 21	deletion
-	Gly 22	deletion
-	Arg 23	deletion
-	Lys 24	deletion
-	Glu 25	deletion
-	Gly 26	deletion
-	Thr 27	deletion

9: 1 - 264 (UniProt: Q97Z79)

PDB	External Database	Details
-	Ser 48	deletion
-	Lys 49	deletion
-	Trp 50	deletion
-	Val 51	deletion
-	Lys 52	deletion
-	Lys 170	deletion
-	His 171	deletion
-	Ala 172	deletion
-	Glu 173	deletion
-	Glu 174	deletion

Contents of the asymmetric unit

Polymers	Number of chains	35
	Total formula weight	1047953.7
Non-Polymers*	Number of molecules	42
	Total formula weight	1890.2
All*	Total formula weight	1049844.0

*Water molecules are not included.