5DGE

Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic 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	2, 6	18S ribosomal RNA	polymer	1800	579761.9	2	GenBank (874346701)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
2	S0, s0	40S ribosomal protein S0-A	polymer	251	27920.1	2	UniProt (P32905) Pfam (PF00318) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Nucleic acid-binding protein NAB1A
3	S1, s1	40S ribosomal protein S1-A	polymer	254	28667.3	2	UniProt (P33442) Pfam (PF01015) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP10A
4	S2, s2	40S ribosomal protein S2	polymer	253	27359.6	2	UniProt (P25443) Pfam (PF00333) Pfam (PF03719) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Omnipotent suppressor protein SUP44,RP12,S4,YS5
5	S3, s3	40S ribosomal protein S3	polymer	239	26411.6	2	UniProt (P05750) Pfam (PF07650) Pfam (PF00189) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP13,YS3
6	S4, s4	40S ribosomal protein S4-A	polymer	260	29338.1	2	UniProt (P0CX35) Pfam (PF08071) Pfam (PF01479) Pfam (PF00900) Pfam (PF00467) Pfam (PF16121) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP5,S7,YS6
7	S5, s5	40S ribosomal protein S5	polymer	224	24941.4	2	UniProt (P26783) Pfam (PF00177) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP14,S2,YS8
8	S6, s6	40S ribosomal protein S6-A	polymer	236	27054.5	2	UniProt (P0CX37) Pfam (PF01092) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP9,S10,YS4
9	S7, s7	40S ribosomal protein S7-A	polymer	189	21527.0	2	UniProt (P26786) Pfam (PF01251) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP30,RP40
10	S8, s8	40S ribosomal protein S8-A	polymer	200	22537.8	2	UniProt (P0CX39) Pfam (PF01201) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP19,S14,YS9
11	S9, s9	40S ribosomal protein S9-A	polymer	196	22356.7	2	UniProt (O13516) Pfam (PF00163) Pfam (PF01479) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP21,S13,YP28,YS11
12	C0, c0	40S ribosomal protein S10-A	polymer	105	12771.5	2	UniProt (Q08745) Pfam (PF03501) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
13	C1, c1	40S ribosomal protein S11-A	polymer	155	17668.8	2	UniProt (P0CX47) Pfam (PF16205) Pfam (PF00366) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP41,S18,YS12
14	C2, c2	40S ribosomal protein S12	polymer	142	15385.5	2	UniProt (P48589) Pfam (PF01248) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
15	C3, c3	40S ribosomal protein S13	polymer	150	16928.7	2	UniProt (P05756) Pfam (PF08069) Pfam (PF00312) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	S27a,YS15
16	C4, c4	40S ribosomal protein S14-A	polymer	136	14431.5	2	UniProt (P06367) Pfam (PF00411) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP59A
17	C5, c5	40S ribosomal protein S15	polymer	141	15900.7	2	UniProt (Q01855) Pfam (PF00203) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RIG protein,RP52,S21,YS21
18	C6, c6	40S ribosomal protein S16-A	polymer	142	15746.3	2	UniProt (P0CX51) Pfam (PF00380) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP61R
19	C7, c7	40S ribosomal protein S17-A	polymer	136	15820.4	2	UniProt (P02407) Pfam (PF00833) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP51A
20	C8, c8	40S ribosomal protein S18-A	polymer	145	16940.4	2	UniProt (P0CX55) Pfam (PF00416) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
21	C9, c9	40S ribosomal protein S19-A	polymer	143	15810.9	2	UniProt (P07280) Pfam (PF01090) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP55A,S16a,YP45,YS16A
22	D0, d0	40S ribosomal protein S20	polymer	120	13797.9	2	UniProt (P38701) Pfam (PF00338) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
23	D1, d1	40S ribosomal protein S21-A	polymer	87	9758.8	2	UniProt (P0C0V8) Pfam (PF01249) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	S26,YS25
24	D2, d2	40S ribosomal protein S22-A	polymer	129	14518.9	2	UniProt (P0C0W1) Pfam (PF00410) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP50,S24,YP58,YS22
25	D3, d3	40S ribosomal protein S23-A	polymer	144	15942.7	2	UniProt (P0CX29) Pfam (PF00164) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP37,S28,YS14
26	D4, d4	40S ribosomal protein S24-A	polymer	134	15231.6	2	UniProt (P0CX31) Pfam (PF01282) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP50
27	D5, d5	40S ribosomal protein S25-A	polymer	107	11936.1	2	UniProt (Q3E792) Pfam (PF03297) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP45,S31,YS23
28	D6, d6	40S ribosomal protein S26-A	polymer	97	11023.0	2	UniProt (P39938) Pfam (PF01283) UniProt (by SIFTS) (P39939) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
29	D7, d7	40S ribosomal protein S27-A	polymer	81	8762.2	2	UniProt (P35997) Pfam (PF01667) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP61,YS20
30	D8, d8	40S ribosomal protein S28-A	polymer	66	7474.7	2	UniProt (Q3E7X9) Pfam (PF01200) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	S33,YS27
31	D9, d9	40S ribosomal protein S29-A	polymer	55	6544.5	2	UniProt (P41057) Pfam (PF00253) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	S36,YS29
32	E0, e0	40S ribosomal protein S30-A	polymer	63	7137.5	2	UniProt (P0CX33) Pfam (PF04758) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Small ribosomal subunit protein eS30-A
33	E1, e1	Ubiquitin-40S ribosomal protein S31	polymer	76	8703.5	2	UniProt (P05759) Pfam (PF01599) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
34	SR, sR	Guanine nucleotide-binding protein subunit beta-like protein	polymer	318	34710.0	2	UniProt (P38011) Pfam (PF00400) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1
35	SM, sM	Suppressor protein STM1	polymer	273	30048.0	2	UniProt (P39015) Pfam (PF09598) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	3BP1,GU4 nucleic-binding protein 2,G4p2 protein,POP2 multicopy suppressor protein 4,Ribosomal subunits association factor,AF,TOM1 suppressor protein 1,Triplex-binding protein 1
36	1, 5	25S ribosomal RNA	polymer	3396	1097493.9	2	GenBank (834774822)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
37	3, 7	5S ribosomal RNA	polymer	121	38951.1	2	GenBank (834774822)	Saccharomyces cerevisiae S288c
38	4, 8	5.8S ribosomal RNA	polymer	158	50682.9	2	GenBank (940534893)	Saccharomyces cerevisiae S288c
39	L2, l2	60S ribosomal protein L2-A	polymer	253	27332.4	2	UniProt (P0CX45) Pfam (PF00181) Pfam (PF03947) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L5,RP8,YL6
40	L3, l3	60S ribosomal protein L3	polymer	386	43719.6	2	UniProt (P14126) Pfam (PF00297) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
41	L4, l4	60S ribosomal protein L4-A	polymer	361	39027.9	2	UniProt (P10664) Pfam (PF00573) Pfam (PF14374) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L2,RP2,YL2
42	L5, l5	60S ribosomal protein L5	polymer	296	33633.6	2	UniProt (P26321) Pfam (PF17144) Pfam (PF14204) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L1,L1a,Ribosomal 5S RNA-binding protein,YL3
43	L6, l6	60S ribosomal protein L6-A	polymer	175	19869.4	2	UniProt (Q02326) Pfam (PF01159) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L17,RP18,YL16
44	L7, l7	60S ribosomal protein L7-A	polymer	243	27555.1	2	UniProt (P05737) Pfam (PF08079) Pfam (PF00327) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L6,RP11,YL8
45	L8, l8	60S ribosomal protein L8-A	polymer	255	28058.6	2	UniProt (P17076) Pfam (PF01248) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5
46	L9, l9	60S ribosomal protein L9-A	polymer	191	21605.1	2	UniProt (P05738) Pfam (PF00347) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L8,RP24,YL11
47	M0, m0	60S ribosomal protein L10	polymer	220	25279.3	2	UniProt (P41805) Pfam (PF00252) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
48	M1, m1	60S ribosomal protein L11-A	polymer	173	19654.5	2	UniProt (P0C0W9) Pfam (PF00281) Pfam (PF00673) UniProt (by SIFTS) (Q3E757) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L16,RP39,YL22
49	M3, m3	60S ribosomal protein L13-A	polymer	198	22473.0	2	UniProt (Q12690) Pfam (PF01294) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
50	M4, m4	60S ribosomal protein L14-A	polymer	137	15063.9	2	UniProt (P36105) Pfam (PF00467) Pfam (PF01929) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
51	M5, m5	60S ribosomal protein L15-A	polymer	203	24351.2	2	UniProt (P05748) Pfam (PF00827) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L13,RP15R,YL10,YP18
52	M6, m6	60S ribosomal protein L16-A	polymer	198	22116.0	2	UniProt (P26784) Pfam (PF00572) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L13a,L21,RP22,YL15
53	M7, m7	60S ribosomal protein L17-A	polymer	183	20458.3	2	UniProt (P05740) Pfam (PF00237) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L20A,YL17
54	M8, m8	60S ribosomal protein L18-A	polymer	185	20478.1	2	UniProt (P0CX49) Pfam (PF17135) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP28
55	M9, m9	60S ribosomal protein L19-A	polymer	188	21631.1	2	UniProt (P0CX82) Pfam (PF01280) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L23,RP15L,RP33,YL14
56	N0, n0	60S ribosomal protein L20-A	polymer	172	20478.9	2	UniProt (P0CX23) Pfam (PF01775) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L18a
57	N1, n1	60S ribosomal protein L21-A	polymer	159	18148.1	2	UniProt (Q02753) Pfam (PF01157) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
58	N2, n2	60S ribosomal protein L22-A	polymer	120	13580.2	2	UniProt (P05749) Pfam (PF01776) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L1c,RP4,YL31
59	N3, n3	60S ribosomal protein L23-A	polymer	136	14362.8	2	UniProt (P0CX41) Pfam (PF00238) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L17a,YL32
60	N4, n4	60S ribosomal protein L24-A	polymer	155	17661.7	2	UniProt (P04449) Pfam (PF01246) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L30,RP29,YL21
61	N5, n5	60S ribosomal protein L25	polymer	141	15656.4	2	UniProt (P04456) Pfam (PF03939) Pfam (PF00276) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	RP16L,YL25,YP42'
62	N6, n6	60S ribosomal protein L26-A	polymer	126	14134.6	2	UniProt (P05743) Pfam (PF16906) Pfam (PF00467) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L33,YL33
63	N7, n7	60S ribosomal protein L27-A	polymer	135	15437.2	2	UniProt (P0C2H6) Pfam (PF01777) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
64	N8, n8	60S ribosomal protein L28	polymer	148	16630.5	2	UniProt (P02406) Pfam (PF00828) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L27a,L29,RP44,RP62,YL24
65	N9, n9	60S ribosomal protein L29	polymer	58	6560.7	2	UniProt (P05747) Pfam (PF01779) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	YL43
66	O0, o0	60S ribosomal protein L30	polymer	104	11299.2	2	UniProt (P14120) Pfam (PF01248) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L32,RP73,YL38
67	O1, o1	60S ribosomal protein L31-A	polymer	112	12849.0	2	UniProt (P0C2H8) Pfam (PF01198) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L34,YL28
68	O2, o2	60S ribosomal protein L32	polymer	129	14678.2	2	UniProt (P38061) Pfam (PF01655) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
69	O3, o3	60S ribosomal protein L33-A	polymer	106	12045.9	2	UniProt (P05744) Pfam (PF01247) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L37,RP47,YL37
70	O4, o4	60S ribosomal protein L34-A	polymer	121	13673.2	2	UniProt (P87262) Pfam (PF01199) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Large ribosomal subunit protein eL34-A
71	O5, o5	60S ribosomal protein L35-A	polymer	119	13811.4	2	UniProt (P0CX84) Pfam (PF00831) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
72	O6, o6	60S ribosomal protein L36-A	polymer	99	11020.1	2	UniProt (P05745) Pfam (PF01158) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L39,YL39
73	O7, o7	60S ribosomal protein L37-A	polymer	87	9746.2	2	UniProt (P49166) Pfam (PF01907) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L43,YL35,YP55
74	O8, o8	60S ribosomal protein L38	polymer	77	8714.4	2	UniProt (P49167) Pfam (PF01781) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
75	O9, o9	60S ribosomal protein L39	polymer	50	6227.4	2	UniProt (P04650) Pfam (PF00832) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L46,YL40
76	Q0, q0	Ubiquitin-60S ribosomal protein L40	polymer	52	6032.3	2	UniProt (P0CH08) Pfam (PF01020) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
77	Q1, q1	60S ribosomal protein L41-A	polymer	25	3354.2	2	UniProt (P0CX86) Pfam (PF05162) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L47,YL41
78	Q2, q2	60S ribosomal protein L42-A	polymer	105	12115.5	2	UniProt (P0CX27) Pfam (PF00935) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L41,YL27,YP44
79	Q3, q3	60S ribosomal protein L43-A	polymer	91	9981.8	2	UniProt (P0CX25) Pfam (PF01780) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L37a,YL35
80	m2	60S ribosomal protein L12-A	polymer	165	17850.6	1	UniProt (P0CX53) Pfam (PF03946) Pfam (PF00298) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	L15,YL23
81	p0	60S acidic ribosomal protein P0	polymer	311	33617.9	1	UniProt (P05317) Pfam (PF00466) Pfam (PF17777) Pfam (PF00428) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	A0,L10E
82	p1, p2	60S acidic ribosomal protein P1-alpha	polymer	106	10912.9	2	UniProt (P05318) Pfam (PF00428) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	P1A,A1,L12EIIA,YP1alpha
83	f	Eukaryotic translation initiation factor 5A-1	polymer	157	17222.4	1	UniProt (P23301) Pfam (PF21485) Pfam (PF01287) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	eIF-5A-1,Hypusine-containing protein HP2,eIF-4D
84	B, C	DNA (5'-R(*CP*CP*(NA))-3')	polymer	3	893.6	2		Saccharomyces cerevisiae S288c
85	1, 2, 5, 7, 8...	MAGNESIUM ION	non-polymer		24.3	1093	Chemie (MG)
86	6, 5, 1, 2, l3...	osmium (III) hexammine	non-polymer		286.4	1169	Chemie (OHX)
87	Q2, Q3, D6, D7, D9...	ZINC ION	non-polymer		65.4	16	Chemie (ZN)
88	1, 5	SPARSOMYCIN	non-polymer		361.4	2	Chemie (SPS)
89	B, 1, C, 5	PROLINE	non-polymer		115.1	4	Chemie (PRO)	Saccharomyces cerevisiae S288c
90		water	water		18.0	12	Chemie (HOH)

Sequence modifications

C0, c0: 1 - 105 (UniProt: Q08745)

PDB	External Database	Details
Ala 89	Gly 89	conflict

C1, c1: 2 - 156 (UniProt: P0CX47)

PDB	External Database	Details
Ala 147	Gly 147	conflict

C2, c2: 2 - 143 (UniProt: P48589)

PDB	External Database	Details
Ala 104	Gly 104	conflict
Ala 110	Gly 110	conflict

L8, l8: 2 - 256 (UniProt: P17076)

PDB	External Database	Details
Ala 119	Gly 119	conflict

M1, m1: 2 - 174 (UniProt: P0C0W9)

PDB	External Database	Details
Thr 3	Ala 3	conflict

Contents of the asymmetric unit

Polymers	Number of chains	165
	Total formula weight	6309313.5
Non-Polymers*	Number of molecules	2284
	Total formula weight	363556.0
All*	Total formula weight	6672869.5

*Water molecules are not included.