7OSM

Intermediate translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands

• PDB DOI: https://doi.org/10.2210/pdb7OSM/pdb
• NAKB: 7OSM

• Classification: RIBOSOME
• Organism(s): Saccharomyces cerevisiae, Escherichia coli
• Mutation(s): No 


• Deposited: 2021-06-09 Released: 2021-12-08 
• Deposition Author(s): Djumagulov, M., Jenner, L., Rozov, A., Demeshkina, N., Yusupov, M., Yusupova, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.284 
• R-Value Work: 0.228 
• R-Value Observed: 0.228 

Literature

Accuracy mechanism of eukaryotic ribosome translocation.

Djumagulov, M., Demeshkina, N., Jenner, L., Rozov, A., Yusupov, M., Yusupova, G.

(2021) Nature 600: 543-546

• PubMed: 34853469 
• DOI: https://doi.org/10.1038/s41586-021-04131-9
• Primary Citation of Related Structures:  
  7OSA, 7OSM


• PubMed Abstract: 
  

  Translation of the genetic code into proteins is realized through repetitions of synchronous translocation of messenger RNA (mRNA) and transfer RNAs (tRNA) through the ribosome. In eukaryotes translocation is ensured by elongation factor 2 (eEF2), which catalyses the process and actively contributes to its accuracy ¹ . Although numerous studies point to critical roles for both the conserved eukaryotic posttranslational modification diphthamide in eEF2 and tRNA modifications in supporting the accuracy of translocation, detailed molecular mechanisms describing their specific functions are poorly understood. Here we report a high-resolution X-ray structure of the eukaryotic 80S ribosome in a translocation-intermediate state containing mRNA, naturally modified eEF2 and tRNAs. The crystal structure reveals a network of stabilization of codon-anticodon interactions involving diphthamide ¹ and the hypermodified nucleoside wybutosine at position 37 of phenylalanine tRNA, which is also known to enhance translation accuracy ² . The model demonstrates how the decoding centre releases a codon-anticodon duplex, allowing its movement on the ribosome, and emphasizes the function of eEF2 as a 'pawl' defining the directionality of translocation ³ . This model suggests how eukaryote-specific elements of the 80S ribosome, eEF2 and tRNAs undergo large-scale molecular reorganizations to ensure maintenance of the mRNA reading frame during the complex process of translocation.

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Organizational Affiliation: 

Institute of Genetics and Molecular and Cellular Biology, CNRS UMR7104, INSERM U1258, University of Strasbourg, Illkirch, Strasbourg, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 76-mer - AA1AB1AC1AD1AE1AF1AG1AH1AI1AJ1AK1AL1AM1AN1AO1AP1AQ1AR1AS1AT1AU1AV1AW1AX1AY1AZ1Aa1Ab1Ac1Ad1Ae1Af1Ag1Ah1Ai1Aj1Ak1Al1Am1An1Ao1Ap1Aq1Ar1As1At1Au1Av1Aw1Ax1Ay1Az1BA1BB1BC1BD1BE1BF1BG1BH1BI1BJ1BK1BL1BM1BN1BO1BP1BQ1BR1BS1BT1BU1BV1BW1BX1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 3,300.08 kDa 
• Atom Count: 207,073 
• Modelled Residue Count: 17,095 
• Deposited Residue Count: 18,690 
• Unique protein chains: 76
• Unique nucleic acid chains: 7

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
60S acidic ribosomal protein P0	D [auth uL10]	312	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L2-B	E [auth uL2]	254	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L3	F [auth uL3]	387	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5Q627 (Saccharomyces cerevisiae) Explore A0A6A5Q627  Go to UniProtKB:  A0A6A5Q627

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
BJ4_G0008850.mRNA.1.CDS.1	G [auth uL4]	362	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5Q3W0 (Saccharomyces cerevisiae) Explore A0A6A5Q3W0  Go to UniProtKB:  A0A6A5Q3W0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L5	H [auth uL18]	297	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5Q0W8 (Saccharomyces cerevisiae) Explore A0A6A5Q0W8  Go to UniProtKB:  A0A6A5Q0W8

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L6	I [auth eL6]	176	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L7-A	J [auth uL30]	244	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L8-A	K [auth eL8]	256	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P17076  Go to UniProtKB:  P17076

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L9-A	L [auth uL6]	191	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05738  Go to UniProtKB:  P05738

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L10	M [auth uL16]	221	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5PUZ5 (Saccharomyces cerevisiae) Explore A0A6A5PUZ5  Go to UniProtKB:  A0A6A5PUZ5

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
BJ4_G0027750.mRNA.1.CDS.1	N [auth uL5]	174	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5Q7I9 (Saccharomyces cerevisiae) Explore A0A6A5Q7I9  Go to UniProtKB:  A0A6A5Q7I9

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L13	O [auth eL13]	199	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L14-A	P [auth eL14]	138	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36105  Go to UniProtKB:  P36105

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L15-A	Q [auth eL15]	204	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05748  Go to UniProtKB:  P05748

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L16-A	R [auth uL13]	199	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
BJ4_G0005750.mRNA.1.CDS.1	S [auth uL22]	184	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
BJ4_G0033900.mRNA.1.CDS.1	T [auth eL18]	186	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L19-A	U [auth eL19]	189	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX82  Go to UniProtKB:  P0CX82

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L20	V [auth eL20]	172	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
BJ4_G0003770.mRNA.1.CDS.1	W [auth eL21]	160	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L22-A	X [auth eL22]	121	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L23-B	Y [auth uL14]	137	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L24-A	Z [auth eL24]	155	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5PY83 (Saccharomyces cerevisiae) Explore A0A6A5PY83  Go to UniProtKB:  A0A6A5PY83

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L25	AA [auth uL23]	142	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L26-A	BA [auth uL24]	127	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05743  Go to UniProtKB:  P05743

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L27	CA [auth eL27]	136	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L28	DA [auth uL15]	149	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L29	EA [auth eL29]	59	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5PWR1 (Saccharomyces cerevisiae) Explore A0A6A5PWR1  Go to UniProtKB:  A0A6A5PWR1

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
BJ4_G0020000.mRNA.1.CDS.1	FA [auth eL30]	105	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
BJ4_G0008090.mRNA.1.CDS.1	GA [auth eL31]	113	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
HN1_G0013350.mRNA.1.CDS.1	HA [auth eL32]	130	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
BJ4_G0025510.mRNA.1.CDS.1	IA [auth eL33]	107	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L34-A	JA [auth eL34]	121	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
BJ4_G0044250.mRNA.1.CDS.1	KA [auth uL29]	120	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L36-A	LA [auth eL36]	100	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05745  Go to UniProtKB:  P05745

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L37	MA [auth eL37]	88	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
BJ4_G0032190.mRNA.1.CDS.1	NA [auth eL38]	78	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5PUL8 (Saccharomyces cerevisiae) Explore A0A6A5PUL8  Go to UniProtKB:  A0A6A5PUL8

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L39	OA [auth eL39]	51	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	PA [auth eL40]	128	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
eL41	QA [auth eL41]	25	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
BJ4_G0001880.mRNA.1.CDS.1	RA [auth eL42]	106	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L43-A	SA [auth eL43]	92	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX25  Go to UniProtKB:  P0CX25

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S0	UA [auth uS2]	252	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S1	VA [auth eS1]	255	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5PRY4 (Saccharomyces cerevisiae) Explore A0A6A5PRY4  Go to UniProtKB:  A0A6A5PRY4

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S2	WA [auth uS5]	254	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5PWF7 (Saccharomyces cerevisiae) Explore A0A6A5PWF7  Go to UniProtKB:  A0A6A5PWF7

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
BJ4_G0045400.mRNA.1.CDS.1	XA [auth uS3]	240	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S4	YA [auth eS4]	261	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
Rps5p	ZA [auth uS7]	225	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A1L4AA68 (Saccharomyces cerevisiae) Explore A0A1L4AA68  Go to UniProtKB:  A0A1L4AA68

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S6	AB [auth eS6]	236	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S7	BB [auth eS7]	190	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S8	CB [auth eS8]	200	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5Q1H1 (Saccharomyces cerevisiae) Explore A0A6A5Q1H1  Go to UniProtKB:  A0A6A5Q1H1

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
BJ4_G0026100.mRNA.1.CDS.1	DB [auth uS4]	197	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S10-A	EB [auth eS10]	105	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S11-B	FB [auth uS17]	156	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S13	GB [auth uS15]	151	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S14-A	HB [auth uS11]	137	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S15	IB [auth uS19]	142	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5Q6F2 (Saccharomyces cerevisiae) Explore A0A6A5Q6F2  Go to UniProtKB:  A0A6A5Q6F2

Entity ID: 62
Molecule	Chains	Sequence Length	Organism	Details	Image
BJ4_G0008010.mRNA.1.CDS.1	JB [auth uS9]	143	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 63
Molecule	Chains	Sequence Length	Organism	Details	Image
BJ4_G0020710.mRNA.1.CDS.1	KB [auth eS17]	136	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 64
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S18-B	LB [auth uS13]	146	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 65
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S19-A	MB [auth eS19]	144	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 66
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S20	NB [auth uS10]	121	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5PVE9 (Saccharomyces cerevisiae) Explore A0A6A5PVE9  Go to UniProtKB:  A0A6A5PVE9

Entity ID: 67
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S21	OB [auth eS21]	87	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 68
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S22-A	PB [auth uS8]	130	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5PSE9 (Saccharomyces cerevisiae) Explore A0A6A5PSE9  Go to UniProtKB:  A0A6A5PSE9

Entity ID: 69
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S23	QB [auth uS12]	145	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 70
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S24	RB [auth eS24]	135	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 71
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S25	SB [auth eS25]	108	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5PZ18 (Saccharomyces cerevisiae) Explore A0A6A5PZ18  Go to UniProtKB:  A0A6A5PZ18

Entity ID: 72
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S26	TB [auth eS26]	119	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5PUG0 (Saccharomyces cerevisiae) Explore A0A6A5PUG0  Go to UniProtKB:  A0A6A5PUG0

Entity ID: 73
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S27-A	UB [auth eS27]	82	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P35997  Go to UniProtKB:  P35997

Entity ID: 74
Molecule	Chains	Sequence Length	Organism	Details	Image
eS28	VB [auth eS28]	67	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5Q700 (Saccharomyces cerevisiae) Explore A0A6A5Q700  Go to UniProtKB:  A0A6A5Q700

Entity ID: 75
Molecule	Chains	Sequence Length	Organism	Details	Image
HLJ1_G0030400.mRNA.1.CDS.1	WB [auth uS14]	56	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5PV92 (Saccharomyces cerevisiae) Explore A0A6A5PV92  Go to UniProtKB:  A0A6A5PV92

Entity ID: 76
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S30	XB [auth eS30]	63	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 77
Molecule	Chains	Sequence Length	Organism	Details	Image
BJ4_G0022010.mRNA.1.CDS.1	YB [auth RACK]	319	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 78
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-40S ribosomal protein S31	ZB [auth eS31]	152	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5PU37 (Saccharomyces cerevisiae) Explore A0A6A5PU37  Go to UniProtKB:  A0A6A5PU37

Entity ID: 79
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor 2	AC [auth eEF2]	842	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5Q7K2 (Saccharomyces cerevisiae) Explore A0A6A5Q7K2  Go to UniProtKB:  A0A6A5Q7K2

Entity ID: 83
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L12-B	EC [auth uL11]	165	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for A0A6A5Q275 (Saccharomyces cerevisiae) Explore A0A6A5Q275  Go to UniProtKB:  A0A6A5Q275

Entity ID: 1
Molecule	Chains	Length	Organism	Image
25S rRNA	A [auth 25S]	3,396	Saccharomyces cerevisiae

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5S rRNA	B [auth AB]	121	Saccharomyces cerevisiae

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5.8S rRNA	C [auth 58S]	158	Saccharomyces cerevisiae

Entity ID: 46
Molecule	Chains	Length	Organism	Image
18S rRNA	TA [auth 18S]	1,798	Saccharomyces cerevisiae

Entity ID: 80
Molecule	Chains	Length	Organism	Image
PHE tRNA	BC [auth ASIT]	76	Saccharomyces cerevisiae

Entity ID: 81
Molecule	Chains	Length	Organism	Image
FMET tRNA	CC [auth PSIT]	77	Escherichia coli

Entity ID: 82
Molecule	Chains	Length	Organism	Image
MRNA	DC [auth mRNA]	8	Saccharomyces cerevisiae

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	KV [auth eEF2]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN	AV [auth eS26], CV [auth uS14], DV [auth eS31], NP [auth eL34], OP [auth eL37], QP [auth eL40], UP [auth eL42], VP [auth eL43]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	AD [auth 25S], AE [auth 25S], AF [auth 25S], AG [auth 25S], AH [auth 25S], AI [auth 25S], AJ [auth 25S], AK [auth 25S], AL [auth 25S], AM [auth 25S], AN [auth 25S], AO [auth 25S], AP [auth uL18], AQ [auth 18S], AR [auth 18S], AS [auth 18S], AT [auth 18S], AU [auth 18S], BD [auth 25S], BE [auth 25S], BF [auth 25S], BG [auth 25S], BH [auth 25S], BI [auth 25S], BJ [auth 25S], BK [auth 25S], BL [auth 25S], BM [auth 25S], BN [auth 25S], BO [auth 25S], BP [auth uL18], BQ [auth 18S], BR [auth 18S], BS [auth 18S], BT [auth 18S], BU [auth 18S], BV [auth uS14], CD [auth 25S], CE [auth 25S], CF [auth 25S], CG [auth 25S], CH [auth 25S], CI [auth 25S], CJ [auth 25S], CK [auth 25S], CL [auth 25S], CM [auth 25S], CN [auth 25S], CO [auth 25S], CP [auth uL16], CQ [auth 18S], CR [auth 18S], CS [auth 18S], CT [auth 18S], CU [auth 18S], DD [auth 25S], DE [auth 25S], DF [auth 25S], DG [auth 25S], DH [auth 25S], DI [auth 25S], DJ [auth 25S], DK [auth 25S], DL [auth 25S], DM [auth 25S], DN [auth 25S], DO [auth 25S], DP [auth eL15], DQ [auth 18S], DR [auth 18S], DS [auth 18S], DT [auth 18S], DU [auth 18S], ED [auth 25S], EE [auth 25S], EF [auth 25S], EG [auth 25S], EH [auth 25S], EI [auth 25S], EJ [auth 25S], EK [auth 25S], EL [auth 25S], EM [auth 25S], EN [auth 25S], EO [auth 25S], EP [auth uL22], EQ [auth 18S], ER [auth 18S], ES [auth 18S], ET [auth 18S], EU [auth 18S], EV [auth eEF2], FC [auth 25S], FD [auth 25S], FE [auth 25S], FF [auth 25S], FG [auth 25S], FH [auth 25S], FI [auth 25S], FJ [auth 25S], FK [auth 25S], FL [auth 25S], FM [auth 25S], FN [auth 25S], FO [auth 25S], FP [auth eL18], FQ [auth 18S], FR [auth 18S], FS [auth 18S], FT [auth 18S], FU [auth 18S], FV [auth eEF2], GC [auth 25S], GD [auth 25S], GE [auth 25S], GF [auth 25S], GG [auth 25S], GH [auth 25S], GI [auth 25S], GJ [auth 25S], GK [auth 25S], GL [auth 25S], GM [auth 25S], GN [auth 25S], GO [auth 25S], GP [auth eL20], GQ [auth 18S], GR [auth 18S], GS [auth 18S], GT [auth 18S], GU [auth 18S], GV [auth eEF2], HC [auth 25S], HD [auth 25S], HE [auth 25S], HF [auth 25S], HG [auth 25S], HH [auth 25S], HI [auth 25S], HJ [auth 25S], HK [auth 25S], HL [auth 25S], HM [auth 25S], HN [auth 25S], HO [auth 25S], HP [auth uL14], HQ [auth 18S], HR [auth 18S], HS [auth 18S], HT [auth 18S], HU [auth 18S], HV [auth eEF2], IC [auth 25S], ID [auth 25S], IE [auth 25S], IF [auth 25S], IG [auth 25S], IH [auth 25S], II [auth 25S], IJ [auth 25S], IK [auth 25S], IL [auth 25S], IM [auth 25S], IN [auth 25S], IO [auth 25S], IP [auth eL30], IQ [auth 18S], IR [auth 18S], IS [auth 18S], IT [auth 18S], IU [auth 18S], IV [auth eEF2], JC [auth 25S], JD [auth 25S], JE [auth 25S], JF [auth 25S], JG [auth 25S], JH [auth 25S], JI [auth 25S], JJ [auth 25S], JK [auth 25S], JL [auth 25S], JM [auth 25S], JN [auth 25S], JO [auth 25S], JP [auth eL30], JQ [auth 18S], JR [auth 18S], JS [auth 18S], JT [auth 18S], JU [auth 18S], JV [auth eEF2], KC [auth 25S], KD [auth 25S], KE [auth 25S], KF [auth 25S], KG [auth 25S], KH [auth 25S], KI [auth 25S], KJ [auth 25S], KK [auth 25S], KL [auth 25S], KM [auth 25S], KN [auth 25S], KO [auth AB], KP [auth eL31], KQ [auth 18S], KR [auth 18S], KS [auth 18S], KT [auth 18S], KU [auth 18S], LC [auth 25S], LD [auth 25S], LE [auth 25S], LF [auth 25S], LG [auth 25S], LH [auth 25S], LI [auth 25S], LJ [auth 25S], LK [auth 25S], LL [auth 25S], LM [auth 25S], LN [auth 25S], LO [auth AB], LP [auth eL32], LQ [auth 18S], LR [auth 18S], LS [auth 18S], LT [auth 18S], LU [auth 18S], LV [auth ASIT], MC [auth 25S], MD [auth 25S], ME [auth 25S], MF [auth 25S], MG [auth 25S], MH [auth 25S], MI [auth 25S], MJ [auth 25S], MK [auth 25S], ML [auth 25S], MM [auth 25S], MN [auth 25S], MO [auth AB], MP [auth eL33], MQ [auth 18S], MR [auth 18S], MS [auth 18S], MT [auth 18S], MU [auth 18S], MV [auth PSIT], NC [auth 25S], ND [auth 25S], NE [auth 25S], NF [auth 25S], NG [auth 25S], NH [auth 25S], NI [auth 25S], NJ [auth 25S], NK [auth 25S], NL [auth 25S], NM [auth 25S], NN [auth 25S], NO [auth AB], NQ [auth 18S], NR [auth 18S], NS [auth 18S], NT [auth 18S], NU [auth 18S], NV [auth PSIT], OC [auth 25S], OD [auth 25S], OE [auth 25S], OF [auth 25S], OG [auth 25S], OH [auth 25S], OI [auth 25S], OJ [auth 25S], OK [auth 25S], OL [auth 25S], OM [auth 25S], ON [auth 25S], OO [auth AB], OQ [auth 18S], OR [auth 18S], OS [auth 18S], OT [auth 18S], OU [auth eS1], OV [auth PSIT], PC [auth 25S], PD [auth 25S], PE [auth 25S], PF [auth 25S], PG [auth 25S], PH [auth 25S], PI [auth 25S], PJ [auth 25S], PK [auth 25S], PL [auth 25S], PM [auth 25S], PN [auth 25S], PO [auth 58S], PP [auth eL40], PQ [auth 18S], PR [auth 18S], PS [auth 18S], PT [auth 18S], PU [auth eS4], PV [auth PSIT], QC [auth 25S], QD [auth 25S], QE [auth 25S], QF [auth 25S], QG [auth 25S], QH [auth 25S], QI [auth 25S], QJ [auth 25S], QK [auth 25S], QL [auth 25S], QM [auth 25S], QN [auth 25S], QO [auth 58S], QQ [auth 18S], QR [auth 18S], QS [auth 18S], QT [auth 18S], QU [auth eS4], QV [auth PSIT], RC [auth 25S], RD [auth 25S], RE [auth 25S], RF [auth 25S], RG [auth 25S], RH [auth 25S], RI [auth 25S], RJ [auth 25S], RK [auth 25S], RL [auth 25S], RM [auth 25S], RN [auth 25S], RO [auth 58S], RP [auth eL41], RQ [auth 18S], RR [auth 18S], RS [auth 18S], RT [auth 18S], RU [auth eS4], RV [auth PSIT], SC [auth 25S], SD [auth 25S], SE [auth 25S], SF [auth 25S], SG [auth 25S], SH [auth 25S], SI [auth 25S], SJ [auth 25S], SK [auth 25S], SL [auth 25S], SM [auth 25S], SN [auth 25S], SO [auth 58S], SP [auth eL42], SQ [auth 18S], SR [auth 18S], SS [auth 18S], ST [auth 18S], SU [auth eS6], SV [auth mRNA], TC [auth 25S], TD [auth 25S], TE [auth 25S], TF [auth 25S], TG [auth 25S], TH [auth 25S], TI [auth 25S], TJ [auth 25S], TK [auth 25S], TL [auth 25S], TM [auth 25S], TN [auth 25S], TO [auth 58S], TP [auth eL42], TQ [auth 18S], TR [auth 18S], TS [auth 18S], TT [auth 18S], TU [auth eS6], UC [auth 25S], UD [auth 25S], UE [auth 25S], UF [auth 25S], UG [auth 25S], UH [auth 25S], UI [auth 25S], UJ [auth 25S], UK [auth 25S], UL [auth 25S], UM [auth 25S], UN [auth 25S], UO [auth 58S], UQ [auth 18S], UR [auth 18S], US [auth 18S], UT [auth 18S], UU [auth uS15], VC [auth 25S], VD [auth 25S], VE [auth 25S], VF [auth 25S], VG [auth 25S], VH [auth 25S], VI [auth 25S], VJ [auth 25S], VK [auth 25S], VL [auth 25S], VM [auth 25S], VN [auth 25S], VO [auth 58S], VQ [auth 18S], VR [auth 18S], VS [auth 18S], VT [auth 18S], VU [auth uS19], WC [auth 25S], WD [auth 25S], WE [auth 25S], WF [auth 25S], WG [auth 25S], WH [auth 25S], WI [auth 25S], WJ [auth 25S], WK [auth 25S], WL [auth 25S], WM [auth 25S], WN [auth 25S], WO [auth uL2], WP [auth 18S], WQ [auth 18S], WR [auth 18S], WS [auth 18S], WT [auth 18S], WU [auth uS12], XC [auth 25S], XD [auth 25S], XE [auth 25S], XF [auth 25S], XG [auth 25S], XH [auth 25S], XI [auth 25S], XJ [auth 25S], XK [auth 25S], XL [auth 25S], XM [auth 25S], XN [auth 25S], XO [auth uL2], XP [auth 18S], XQ [auth 18S], XR [auth 18S], XS [auth 18S], XT [auth 18S], XU [auth uS12], YC [auth 25S], YD [auth 25S], YE [auth 25S], YF [auth 25S], YG [auth 25S], YH [auth 25S], YI [auth 25S], YJ [auth 25S], YK [auth 25S], YL [auth 25S], YM [auth 25S], YN [auth 25S], YO [auth uL2], YP [auth 18S], YQ [auth 18S], YR [auth 18S], YS [auth 18S], YT [auth 18S], YU [auth uS12], ZC [auth 25S], ZD [auth 25S], ZE [auth 25S], ZF [auth 25S], ZG [auth 25S], ZH [auth 25S], ZI [auth 25S], ZJ [auth 25S], ZK [auth 25S], ZL [auth 25S], ZM [auth 25S], ZN [auth 25S], ZO [auth uL3], ZP [auth 18S], ZQ [auth 18S], ZR [auth 18S], ZS [auth 18S], ZT [auth 18S], ZU [auth eS26]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DDE	AC [auth eEF2]	L-PEPTIDE LINKING	C13 H24 N5 O3		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.284 
• R-Value Work: 0.228 
• R-Value Observed: 0.228 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 233.49	α = 90
b = 299.85	β = 90
c = 513.84	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-12-08 
Deposition Author(s): Djumagulov, M., Jenner, L., Rozov, A., Demeshkina, N., Yusupov, M., Yusupova, G.

Revision History  

• Version 1.0: 2021-12-08
  Type: Initial release
  
• Version 1.1: 2021-12-22
  Changes: Database references
• Version 1.2: 2021-12-29
  Changes: Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Refinement description