6ZJ3

Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis

PDB DOI: https://doi.org/10.2210/pdb6ZJ3/pdb
NAKB: 6ZJ3
EM Map EMD-11232: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Euglena gracilis
Mutation(s): No

Deposited: 2020-06-27 Released: 2020-10-07
Deposition Author(s): Matzov, D., Halfon, H., Zimmerman, E., Rozenberg, H., Bashan, A., Gray, M.W., Yonath, A.E., Shalev-Benami, M.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.15 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis.

Matzov, D., Taoka, M., Nobe, Y., Yamauchi, Y., Halfon, Y., Asis, N., Zimermann, E., Rozenberg, H., Bashan, A., Bhushan, S., Isobe, T., Gray, M.W., Yonath, A., Shalev-Benami, M.

(2020) Nucleic Acids Res 48: 11750-11761

PubMed: 33091122 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1093/nar/gkaa893
Primary Citation of Related Structures:
6ZJ3

PubMed Abstract:
Ribosomal RNA is the central component of the ribosome, mediating its functional and architectural properties. Here, we report the cryo-EM structure of a highly divergent cytoplasmic ribosome from the single-celled eukaryotic alga Euglena gracilis. The Euglena large ribosomal subunit is distinct in that it contains 14 discrete rRNA fragments that are assembled non-covalently into the canonical ribosome structure. The rRNA is substantially enriched in post-transcriptional modifications that are spread far beyond the catalytic RNA core, contributing to the stabilization of this highly fragmented ribosome species. A unique cluster of five adenosine base methylations is found in an expansion segment adjacent to the protein exit tunnel, such that it is positioned for interaction with the nascent peptide. As well as featuring distinctive rRNA expansion segments, the Euglena ribosome contains four novel ribosomal proteins, localized to the ribosome surface, three of which do not have orthologs in other eukaryotes.

Organizational Affiliation

Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.

Macromolecule Content

Total Structure Weight: 3,672.47 kDa
Atom Count: 223,607
Modelled Residue Count: 17,647
Deposited Residue Count: 19,888
Unique protein chains: 78
Unique nucleic acid chains: 20

Macromolecules

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eS1	F [auth SA]	249	Euglena gracilis	Mutation(s): 0
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uS2	G [auth SB]	261	Euglena gracilis	Mutation(s): 0
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uS3	H [auth SC]	220	Euglena gracilis	Mutation(s): 0
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uS4	I [auth SD]	196	Euglena gracilis	Mutation(s): 0
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eS4	J [auth SE]	271	Euglena gracilis	Mutation(s): 0
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uS5	K [auth SF]	257	Euglena gracilis	Mutation(s): 0
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eS6	L [auth SG]	283	Euglena gracilis	Mutation(s): 0
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uS7	M [auth SH]	190	Euglena gracilis	Mutation(s): 0
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eS7	N [auth SI]	200	Euglena gracilis	Mutation(s): 0
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uS8	O [auth SJ]	130	Euglena gracilis	Mutation(s): 0
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eS8	P [auth SK]	304	Euglena gracilis	Mutation(s): 0
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uS9	Q [auth SL]	151	Euglena gracilis	Mutation(s): 0
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uS10	R [auth SM]	121	Euglena gracilis	Mutation(s): 0
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eS10	S [auth SN]	152	Euglena gracilis	Mutation(s): 0
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uS11	T [auth SO]	152	Euglena gracilis	Mutation(s): 0
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uS12	U [auth SP]	143	Euglena gracilis	Mutation(s): 0
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eS12	V [auth SQ]	139	Euglena gracilis	Mutation(s): 0
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uS13	W [auth SR]	153	Euglena gracilis	Mutation(s): 0
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uS14	X [auth SS]	55	Euglena gracilis	Mutation(s): 0
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uS15	Y [auth ST]	151	Euglena gracilis	Mutation(s): 0
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uS17	Z [auth SU]	164	Euglena gracilis	Mutation(s): 0
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eS17	AA [auth SV]	145	Euglena gracilis	Mutation(s): 0
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uS19	BA [auth SW]	150	Euglena gracilis	Mutation(s): 0
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eS19	CA [auth SX]	148	Euglena gracilis	Mutation(s): 0
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eS21	DA [auth SY]	96	Euglena gracilis	Mutation(s): 0
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eS24	EA [auth SZ]	137	Euglena gracilis	Mutation(s): 0
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eS25	FA [auth Sa]	119	Euglena gracilis	Mutation(s): 0
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eS26	GA [auth Sb]	120	Euglena gracilis	Mutation(s): 0
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eS27	HA [auth Sc]	86	Euglena gracilis	Mutation(s): 0
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eS28	IA [auth Sd]	76	Euglena gracilis	Mutation(s): 0
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eS30	JA [auth Se]	67	Euglena gracilis	Mutation(s): 0
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eS31	KA [auth Sf]	157	Euglena gracilis	Mutation(s): 0
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eSEug1	LA [auth Sg]	295	Euglena gracilis	Mutation(s): 0
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
RACK1	MA [auth Sh]	317	Euglena gracilis	Mutation(s): 0
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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uL2	CB [auth LP]	264	Euglena gracilis	Mutation(s): 0
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Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uL3	DB [auth LQ]	410	Euglena gracilis	Mutation(s): 0
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Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uL4	EB [auth LR]	375	Euglena gracilis	Mutation(s): 0
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Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uL5	FB [auth LS]	191	Euglena gracilis	Mutation(s): 0
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Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uL6	GB [auth LT]	193	Euglena gracilis	Mutation(s): 0
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Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL6	HB [auth LU]	195	Euglena gracilis	Mutation(s): 0
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Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L7a	IB [auth LV]	295	Euglena gracilis	Mutation(s): 0
UniProt
Find proteins for Q4VH13 (Euglena gracilis) Explore Q4VH13 Go to UniProtKB: Q4VH13
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UniProt Group	Q4VH13
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Entity ID: 62
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uL13	JB [auth LW]	209	Euglena gracilis	Mutation(s): 0
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Entity ID: 63
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL13	KB [auth LX]	226	Euglena gracilis	Mutation(s): 0
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Entity ID: 64
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uL14	LB [auth LY]	140	Euglena gracilis	Mutation(s): 0
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Entity ID: 65
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL14	MB [auth LZ]	219	Euglena gracilis	Mutation(s): 0
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Entity ID: 66
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uL15	NB [auth La]	152	Euglena gracilis	Mutation(s): 0
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Entity ID: 67
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL15	OB [auth Lb]	204	Euglena gracilis	Mutation(s): 0
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Entity ID: 68
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L10	PB [auth Lc]	215	Euglena gracilis	Mutation(s): 0
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Find proteins for Q39724 (Euglena gracilis) Explore Q39724 Go to UniProtKB: Q39724
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UniProt Group	Q39724
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Entity ID: 69
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uL18	QB [auth Ld]	260	Euglena gracilis	Mutation(s): 0
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Entity ID: 70
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL18	RB [auth Le]	193	Euglena gracilis	Mutation(s): 0
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Entity ID: 71
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL19	SB [auth Lf]	250	Euglena gracilis	Mutation(s): 0
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Entity ID: 72
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL20	TB [auth Lg]	182	Euglena gracilis	Mutation(s): 0
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Entity ID: 73
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL21	UB [auth Lh]	159	Euglena gracilis	Mutation(s): 0
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Entity ID: 74
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uL22	VB [auth Li]	164	Euglena gracilis	Mutation(s): 0
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Entity ID: 75
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL22	WB [auth Lj]	170	Euglena gracilis	Mutation(s): 0
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Entity ID: 76
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uL23	XB [auth Lk]	163	Euglena gracilis	Mutation(s): 0
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Entity ID: 77
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uL24	YB [auth Ll]	146	Euglena gracilis	Mutation(s): 0
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Entity ID: 78
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL24	ZB [auth Lm]	157	Euglena gracilis	Mutation(s): 0
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Entity ID: 79
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL27	AC [auth Ln]	134	Euglena gracilis	Mutation(s): 0
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Entity ID: 80
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eLEgr1	BC [auth Lo]	72	Euglena gracilis	Mutation(s): 0
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Entity ID: 81
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uL29	CC [auth Lp]	123	Euglena gracilis	Mutation(s): 0
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Entity ID: 82
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL29	DC [auth Lq]	117	Euglena gracilis	Mutation(s): 0
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Entity ID: 83
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uL30	EC [auth Lr]	242	Euglena gracilis	Mutation(s): 0
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Entity ID: 84
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL30	FC [auth Ls]	109	Euglena gracilis	Mutation(s): 0
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Entity ID: 85
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL31	GC [auth Lt]	151	Euglena gracilis	Mutation(s): 0
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Entity ID: 86
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL32	HC [auth Lu]	139	Euglena gracilis	Mutation(s): 0
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Entity ID: 87
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL33	IC [auth Lv]	115	Euglena gracilis	Mutation(s): 0
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Entity ID: 88
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL34	JC [auth Lw]	128	Euglena gracilis	Mutation(s): 0
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Entity ID: 89
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL36	KC [auth Lx]	106	Euglena gracilis	Mutation(s): 0
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Entity ID: 90
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL37	LC [auth Ly]	117	Euglena gracilis	Mutation(s): 0
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Entity ID: 91
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL38	MC [auth Lz]	82	Euglena gracilis	Mutation(s): 0
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Entity ID: 92
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL39	NC [auth L1]	51	Euglena gracilis	Mutation(s): 0
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Entity ID: 93
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL40	OC [auth L2]	126	Euglena gracilis	Mutation(s): 0
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Entity ID: 94
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL41	PC [auth L3]	34	Euglena gracilis	Mutation(s): 0
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Entity ID: 95
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL42	QC [auth L5]	92	Euglena gracilis	Mutation(s): 0
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Entity ID: 96
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eL43	RC [auth L4]	106	Euglena gracilis	Mutation(s): 0
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Entity ID: 97
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eLEgr2	SC [auth L6]	69	Euglena gracilis	Mutation(s): 0
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Entity ID: 98
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein eLEgr3	TC [auth L7]	64	Euglena gracilis	Mutation(s): 0
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Entity ID: 1
Molecule	Chains	Length	Organism	Image
18S rRNA	A [auth S1]	2,315	Euglena gracilis
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Entity ID: 2
Molecule	Chains	Length	Organism	Image
A-tRNA	B [auth S2]	76	Euglena gracilis
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Entity ID: 3
Molecule	Chains	Length	Organism	Image
P-tRNA	C [auth S3]	76	Euglena gracilis
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Entity ID: 4
Molecule	Chains	Length	Organism	Image
E-tRNA	D [auth S4]	76	Euglena gracilis
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Entity ID: 5
Molecule	Chains	Length	Organism	Image
A-site tRNA	E [auth S5]	12	Euglena gracilis
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Entity ID: 40
Molecule	Chains	Length	Organism	Image
5.8S rRNA	NA [auth LA]	163	Euglena gracilis
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Entity ID: 41
Molecule	Chains	Length	Organism	Image
LSU rRNA chain 1	OA [auth LB]	133	Euglena gracilis
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Entity ID: 42
Molecule	Chains	Length	Organism	Image
LSU rRNA chain 2	PA [auth LC]	350	Euglena gracilis
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Entity ID: 43
Molecule	Chains	Length	Organism	Image
LSU rRNA chain 3	QA [auth LD]	116	Euglena gracilis
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Entity ID: 44
Molecule	Chains	Length	Organism	Image
LSU rRNA chain 4	RA [auth LE]	698	Euglena gracilis
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Entity ID: 45
Molecule	Chains	Length	Organism	Image
LSU rRNA chain 5	SA [auth LF]	527	Euglena gracilis
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Entity ID: 46
Molecule	Chains	Length	Organism	Image
LSU rRNA chain 6	TA [auth LG]	234	Euglena gracilis
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Entity ID: 47
Molecule	Chains	Length	Organism	Image
LSU rRNA chain 7	UA [auth LH]	744	Euglena gracilis
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Entity ID: 48
Molecule	Chains	Length	Organism	Image
LSU rRNA chain 8	VA [auth LI]	617	Euglena gracilis
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Entity ID: 49
Molecule	Chains	Length	Organism	Image
LSU rRNA chain 9	WA [auth LJ]	164	Euglena gracilis
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Entity ID: 50
Molecule	Chains	Length	Organism	Image
LSU rRNA chain 10	XA [auth LK]	64	Euglena gracilis
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Entity ID: 51
Molecule	Chains	Length	Organism	Image
LSU rRNA chain 11	YA [auth LL]	95	Euglena gracilis
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Entity ID: 52
Molecule	Chains	Length	Organism	Image
LSU rRNA chain 12	ZA [auth LM]	58	Euglena gracilis
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Entity ID: 53
Molecule	Chains	Length	Organism	Image
LSU rRNA chain 13	AB [auth LN]	86	Euglena gracilis
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Entity ID: 54
Molecule	Chains	Length	Organism	Image
5S rRNA	BB [auth LO]	120	Euglena gracilis
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Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain UC [auth Sb] SDF format, chain VC [auth Ly] SDF format, chain WC [auth L2] SDF format, chain XC [auth L5] SDF format, chain YC [auth L4] MOL2 format, chain UC [auth Sb] MOL2 format, chain VC [auth Ly] MOL2 format, chain WC [auth L2] MOL2 format, chain XC [auth L5] MOL2 format, chain YC [auth L4]	UC [auth Sb], VC [auth Ly], WC [auth L2], XC [auth L5], YC [auth L4]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain UC [auth Sb] Focus chain VC [auth Ly] Focus chain WC [auth L2] Focus chain XC [auth L5] Focus chain YC [auth L4] Interactions & Density Focus chain UC [auth Sb] Focus chain VC [auth Ly] Focus chain WC [auth L2] Focus chain XC [auth L5] Focus chain YC [auth L4]