4V7R

Yeast 80S ribosome.

• PDB DOI: https://doi.org/10.2210/pdb4V7R/pdb
• Entry: 4V7R supersedes: 3O2Z, 3O30, 3O58, 3O5H
• NAKB: 4V7R

• Classification: RIBOSOME
• Organism(s): Saccharomyces cerevisiae, Saccharomyces cerevisiae S288C
• Mutation(s): No 


• Deposited: 2010-07-23 Released: 2014-07-09 
• Deposition Author(s): Ben-Shem, A., Jenner, L., Yusupova, G., Yusupov, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 0.341 
• R-Value Work: 0.278 
• R-Value Observed: 0.280 

Literature

Crystal structure of the eukaryotic ribosome.

Ben-Shem, A., Jenner, L., Yusupova, G., Yusupov, M.

(2010) Science 330: 1203-1209

• PubMed: 21109664 
• DOI: https://doi.org/10.1126/science.1194294
• Primary Citation of Related Structures:  
  4V7R


• PubMed Abstract: 
  

  Crystal structures of prokaryotic ribosomes have described in detail the universally conserved core of the translation mechanism. However, many facets of the translation process in eukaryotes are not shared with prokaryotes. The crystal structure of the yeast 80S ribosome determined at 4.15 angstrom resolution reveals the higher complexity of eukaryotic ribosomes, which are 40% larger than their bacterial counterparts. Our model shows how eukaryote-specific elements considerably expand the network of interactions within the ribosome and provides insights into eukaryote-specific features of protein synthesis. Our crystals capture the ribosome in the ratcheted state, which is essential for translocation of mRNA and transfer RNA (tRNA), and in which the small ribosomal subunit has rotated with respect to the large subunit. We describe the conformational changes in both ribosomal subunits that are involved in ratcheting and their implications in coordination between the two associated subunits and in mRNA and tRNA translocation.

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Organizational Affiliation: 

IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), 1 rue Laurent Fries, BP10142, Illkirch F-67400, France. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 69-mer - AA7AB3AC3AD2AE2AF1AG1AH1AI1AJ1AK1AL1AM1AN1AO1AP1AQ1AR1AS1AT1AU1AV1AW1AX1AY1AZ1Aa1Ab1Ac1Ad1Ae1Af1Ag1Ah1Ai1Aj1Ak1Al1Am1An1Ao1Ap1Aq1Ar1As1At1Au1Av1Aw1Ax1Ay1Az1BA1BB1BC1BD1BE1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 69-mer - AA1AB1AC1AD1AE1AF1AG1AH1AI1AJ1AK1AL1AM1AN1AO1AP1AQ1AR1AS1AT1AU1AV1AW1AX1AY1AZ1Aa1Ab1Ac1Ad1Ae1Af1Ag1Ah1Ai1Aj1Ak1Al1Am1An1Ao1Ap1Aq1Ar1As1At1Au1Av1Aw1Ax1Ay1Az1BA1BB1BC1BD1BE1BF1BG1BH1BI1BJ1BK1BL1BM1BN1BO1BP1BQ1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 62-mer - AA3AB3AC2AD1AE1AF1AG1AH1AI1AJ1AK1AL1AM1AN1AO1AP1AQ1AR1AS1AT1AU1AV1AW1AX1AY1AZ1Aa1Ab1Ac1Ad1Ae1Af1Ag1Ah1Ai1Aj1Ak1Al1Am1An1Ao1Ap1Aq1Ar1As1At1Au1Av1Aw1Ax1Ay1Az1BA1BB1BC1BD1BE1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 62-mer - AA1AB1AC1AD1AE1AF1AG1AH1AI1AJ1AK1AL1AM1AN1AO1AP1AQ1AR1AS1AT1AU1AV1AW1AX1AY1AZ1Aa1Ab1Ac1Ad1Ae1Af1Ag1Ah1Ai1Aj1Ak1Al1Am1An1Ao1Ap1Aq1Ar1As1At1Au1Av1Aw1Ax1Ay1Az1BA1BB1BC1BD1BE1BF1BG1BH1BI1BJ1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5,851.65 kDa 
• Atom Count: 309,610 
• Modelled Residue Count: 26,657 
• Deposited Residue Count: 30,002 
• Unique protein chains: 69
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S0-A	B [auth AA], WB [auth CA]	252	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P32905

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S2	C [auth AB], XB [auth CB]	254	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P25443

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S3	D [auth AC], YB [auth CC]	240	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05750

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S5	E [auth AD], ZB [auth CD]	225	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P26783

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S9-A	AC [auth CE], F [auth AE]	197	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  O13516

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S11	BC [auth CF], G [auth AF]	156	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S13	CC [auth CG], H [auth AG]	151	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05756

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S14-A	DC [auth CH], I [auth AH]	137	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P06367

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S15	EC [auth CI], J [auth AI]	142	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q01855

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S16	FC [auth CJ], K [auth AJ]	143	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S17-A	GC [auth CK], L [auth AK]	136	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P02407 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P02407

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S18	HC [auth CL], M [auth AL]	146	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S19-A	IC [auth CM], N [auth AM]	144	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P07280

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S20	JC [auth CN], O [auth AN]	121	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P38701

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S22-A	KC [auth CO], P [auth AO]	130	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0C0W1

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S23	LC [auth CP], Q [auth AP]	145	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S25-A	MC [auth CQ], R [auth AQ]	108	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q3E792

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S28-A	NC [auth CR], S [auth AR]	67	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q3E7X9

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S29-A	OC [auth CS], T [auth AS]	56	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P41057

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein subunit beta-like protein; RACK-1	PC [auth CT], U [auth AT]	319	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P38011

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure	QC [auth Ca], RB [auth Bo], V [auth Aa]	20	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure	RC [auth Cb], W [auth Ab]	105	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure	SC [auth Cc], X [auth Ac]	93	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure	TC [auth Cd], Y [auth Ad]	35	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure	HE [auth Dj], MB [auth Bj], Z [auth Ae]	21	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure	AA [auth Af]	11	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure	BA [auth Ah], UC [auth Ch]	41	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L1	FA [auth BA], YC [auth DA]	217	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L2	GA [auth BB], ZC [auth DB]	254	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L3	AD [auth DC], HA [auth BC]	387	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P14126

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L4-A	BD [auth DD], IA [auth BD]	362	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P10664

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L5	CD [auth DE], JA [auth BE]	297	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P26321

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L6-A	DD [auth DF], KA [auth BF]	176	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q02326

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L7-A	ED [auth DG], LA [auth BG]	244	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05737

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L8-A	FD [auth DH], MA [auth BH]	256	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P17076

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L9-A	GD [auth DI], NA [auth BI]	191	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05738

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L10	HD [auth DJ], OA [auth BJ]	221	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P41805

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L11-A	ID [auth DK], PA [auth BK]	174	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0C0W9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0C0W9

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L14-A	LD [auth DN], QA [auth BN]	138	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P36105

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L15-A	MD [auth DO], RA [auth BO]	204	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05748

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L16-A	ND [auth DP], SA [auth BP]	199	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P26784

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L17-A	OD [auth DQ], TA [auth BQ]	184	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05740

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L18	PD [auth DR], UA [auth BR]	186	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L19	QD [auth DS], VA [auth BS]	189	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L21-A	RD [auth DT], WA [auth BT]	160	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q02753

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L23	SD [auth DU], XA [auth BU]	137	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L24-A	TD [auth DV], YA [auth BV]	155	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P04449

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L25	UD [auth DW], ZA [auth BW]	142	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P04456

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L26-A	AB [auth BX], VD [auth DX]	127	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05743

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L28	BB [auth BY], WD [auth DY]	149	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P02406

Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L30	CB [auth BZ], XD [auth DZ]	105	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P14120

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L31-A	DB [auth Ba], YD [auth Da]	113	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0C2H8

Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L32	EB [auth Bb], ZD [auth Db]	130	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P38061

Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L35	AE [auth Dc], FB [auth Bc]	120	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L37-A	BE [auth Dd], GB [auth Bd]	88	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P49166

Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L39	CE [auth De], HB [auth Be]	51	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P04650

Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L42	DE [auth Df], IB [auth Bf]	106	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 62
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L43	EE [auth Dg], JB [auth Bg]	92	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 63
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure	FE [auth Dh], KB [auth Bh]	44	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 64
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure	GE [auth Di], LB [auth Bi]	12	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 65
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure	IE [auth Dk], NB [auth Bk]	16	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 66
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure	OB [auth Bl]	19	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 67
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure	PB [auth Bm]	9	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 68
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure	QB [auth Bn]	27	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 69
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure	SB [auth Bp]	8	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 70
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure	TB [auth Bq]	17	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 71
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned secondary structure	UB [auth Br]	23	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 72
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L12	JD [auth DL]	165	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 73
Molecule	Chains	Sequence Length	Organism	Details	Image
60S acidic ribosomal protein P0	KD [auth DM]	312	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05317 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05317

Entity ID: 1
Molecule	Chains	Length	Organism	Image
18S ribosomal RNA	A [auth A1], VB [auth C1]	1,800	Saccharomyces cerevisiae

Entity ID: 29
Molecule	Chains	Length	Organism	Image
25S ribosomal RNA	CA [auth B1], VC [auth D1]	3,396	Saccharomyces cerevisiae S288C

Entity ID: 30
Molecule	Chains	Length	Organism	Image
5S ribosomal RNA	DA [auth B2], WC [auth D2]	121	Saccharomyces cerevisiae

Entity ID: 31
Molecule	Chains	Length	Organism	Image
5.8S ribosomal RNA	EA [auth B3], XC [auth D3]	158	Saccharomyces cerevisiae

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OHX	AAA [auth D1], ABA [auth D1], ACA [auth D1], ADA [auth D1], AEA [auth D1], AF [auth A1], AFA [auth D2], AG [auth A1], AH [auth A1], AI [auth A1], AJ [auth B1], AK [auth B1], AL [auth B1], AM [auth B1], AN [auth B1], AO [auth B1], AP [auth B1], AQ [auth B1], AR [auth B2], AS [auth C1], AT [auth C1], AU [auth C1], AV [auth C1], AW [auth CT], AX [auth D1], AY [auth D1], AZ [auth D1], BAA [auth D1], BBA [auth D1], BCA [auth D1], BDA [auth D1], BEA [auth D1], BF [auth A1], BFA [auth D3], BG [auth A1], BH [auth A1], BI [auth A1], BJ [auth B1], BK [auth B1], BL [auth B1], BM [auth B1], BN [auth B1], BO [auth B1], BP [auth B1], BQ [auth B1], BR [auth B2], BS [auth C1], BT [auth C1], BU [auth C1], BV [auth C1], BW [auth D1], BX [auth D1], BY [auth D1], BZ [auth D1], CAA [auth D1], CBA [auth D1], CCA [auth D1], CDA [auth D1], CEA [auth D1], CF [auth A1], CFA [auth D3], CG [auth A1], CH [auth A1], CI [auth A1], CJ [auth B1], CK [auth B1], CL [auth B1], CM [auth B1], CN [auth B1], CO [auth B1], CP [auth B1], CQ [auth B1], CR [auth B2], CS [auth C1], CT [auth C1], CU [auth C1], CV [auth C1], CW [auth D1], CX [auth D1], CY [auth D1], CZ [auth D1], DAA [auth D1], DBA [auth D1], DCA [auth D1], DDA [auth D1], DEA [auth D1], DF [auth A1], DFA [auth D3], DG [auth A1], DH [auth A1], DI [auth A1], DJ [auth B1], DK [auth B1], DL [auth B1], DM [auth B1], DN [auth B1], DO [auth B1], DP [auth B1], DQ [auth B1], DR [auth B2], DS [auth C1], DT [auth C1], DU [auth C1], DV [auth C1], DW [auth D1], DX [auth D1], DY [auth D1], DZ [auth D1], EAA [auth D1], EBA [auth D1], ECA [auth D1], EDA [auth D1], EEA [auth D1], EF [auth A1], EFA [auth D3], EG [auth A1], EH [auth A1], EI [auth A1], EJ [auth B1], EK [auth B1], EL [auth B1], EM [auth B1], EN [auth B1], EO [auth B1], EP [auth B1], EQ [auth B1], ER [auth B2], ES [auth C1], ET [auth C1], EU [auth C1], EV [auth C1], EW [auth D1], EX [auth D1], EY [auth D1], EZ [auth D1], FAA [auth D1], FBA [auth D1], FCA [auth D1], FDA [auth D1], FEA [auth D1], FF [auth A1], FFA [auth D3], FG [auth A1], FH [auth A1], FI [auth A1], FJ [auth B1], FK [auth B1], FL [auth B1], FM [auth B1], FN [auth B1], FO [auth B1], FP [auth B1], FQ [auth B1], FR [auth B2], FS [auth C1], FT [auth C1], FU [auth C1], FV [auth C1], FW [auth D1], FX [auth D1], FY [auth D1], FZ [auth D1], GAA [auth D1], GBA [auth D1], GCA [auth D1], GDA [auth D1], GEA [auth D1], GF [auth A1], GFA [auth D3], GG [auth A1], GH [auth A1], GI [auth A1], GJ [auth B1], GK [auth B1], GL [auth B1], GM [auth B1], GN [auth B1], GO [auth B1], GP [auth B1], GQ [auth B1], GR [auth B2], GS [auth C1], GT [auth C1], GU [auth C1], GV [auth C1], GW [auth D1], GX [auth D1], GY [auth D1], GZ [auth D1], HAA [auth D1], HBA [auth D1], HCA [auth D1], HDA [auth D1], HEA [auth D1], HF [auth A1], HFA [auth D3], HG [auth A1], HH [auth A1], HI [auth AL], HJ [auth B1], HK [auth B1], HL [auth B1], HM [auth B1], HN [auth B1], HO [auth B1], HP [auth B1], HQ [auth B1], HR [auth B2], HS [auth C1], HT [auth C1], HU [auth C1], HV [auth C1], HW [auth D1], HX [auth D1], HY [auth D1], HZ [auth D1], IAA [auth D1], IBA [auth D1], ICA [auth D1], IDA [auth D1], IEA [auth D1], IF [auth A1], IFA [auth D3], IG [auth A1], IH [auth A1], II [auth AS], IJ [auth B1], IK [auth B1], IL [auth B1], IM [auth B1], IN [auth B1], IO [auth B1], IP [auth B1], IQ [auth B1], IR [auth B3], IS [auth C1], IT [auth C1], IU [auth C1], IV [auth C1], IW [auth D1], IX [auth D1], IY [auth D1], IZ [auth D1], JAA [auth D1], JBA [auth D1], JCA [auth D1], JDA [auth D1], JE [auth A1], JEA [auth D1], JF [auth A1], JFA [auth D3], JG [auth A1], JH [auth A1], JI [auth AT], JJ [auth B1], JK [auth B1], JL [auth B1], JM [auth B1], JN [auth B1], JO [auth B1], JP [auth B1], JQ [auth B1], JR [auth B3], JS [auth C1], JT [auth C1], JU [auth C1], JV [auth C1], JW [auth D1], JX [auth D1], JY [auth D1], JZ [auth D1], KAA [auth D1], KBA [auth D1], KCA [auth D1], KDA [auth D1], KE [auth A1], KEA [auth D1], KF [auth A1], KFA [auth D3], KG [auth A1], KH [auth A1], KI [auth Ac], KJ [auth B1], KK [auth B1], KL [auth B1], KM [auth B1], KN [auth B1], KO [auth B1], KP [auth B1], KQ [auth B1], KR [auth B3], KS [auth C1], KT [auth C1], KU [auth C1], KV [auth C1], KW [auth D1], KX [auth D1], KY [auth D1], KZ [auth D1], LAA [auth D1], LBA [auth D1], LCA [auth D1], LDA [auth D1], LE [auth A1], LEA [auth D1], LF [auth A1], LFA [auth D3], LG [auth A1], LH [auth A1], LI [auth B1], LJ [auth B1], LK [auth B1], LL [auth B1], LM [auth B1], LN [auth B1], LO [auth B1], LP [auth B1], LQ [auth B1], LR [auth B3], LS [auth C1], LT [auth C1], LU [auth C1], LV [auth C1], LW [auth D1], LX [auth D1], LY [auth D1], LZ [auth D1], MAA [auth D1], MBA [auth D1], MCA [auth D1], MDA [auth D1], ME [auth A1], MEA [auth D1], MF [auth A1], MFA [auth D3], MG [auth A1], MH [auth A1], MI [auth B1], MJ [auth B1], MK [auth B1], ML [auth B1], MM [auth B1], MN [auth B1], MO [auth B1], MP [auth B1], MQ [auth B1], MR [auth B3], MS [auth C1], MT [auth C1], MU [auth C1], MV [auth C1], MW [auth D1], MX [auth D1], MY [auth D1], MZ [auth D1], NAA [auth D1], NBA [auth D1], NCA [auth D1], NDA [auth D1], NE [auth A1], NEA [auth D1], NF [auth A1], NFA [auth DC], NG [auth A1], NH [auth A1], NI [auth B1], NJ [auth B1], NK [auth B1], NL [auth B1], NM [auth B1], NN [auth B1], NO [auth B1], NP [auth B1], NQ [auth B1], NR [auth B3], NS [auth C1], NT [auth C1], NU [auth C1], NV [auth C1], NW [auth D1], NX [auth D1], NY [auth D1], NZ [auth D1], OAA [auth D1], OBA [auth D1], OCA [auth D1], ODA [auth D1], OE [auth A1], OEA [auth D1], OF [auth A1], OFA [auth DE], OG [auth A1], OH [auth A1], OI [auth B1], OJ [auth B1], OK [auth B1], OL [auth B1], OM [auth B1], ON [auth B1], OO [auth B1], OP [auth B1], OQ [auth B1], OR [auth B3], OS [auth C1], OT [auth C1], OU [auth C1], OV [auth C1], OW [auth D1], OX [auth D1], OY [auth D1], OZ [auth D1], PAA [auth D1], PBA [auth D1], PCA [auth D1], PDA [auth D1], PE [auth A1], PEA [auth D1], PF [auth A1], PFA [auth DJ], PG [auth A1], PH [auth A1], PI [auth B1], PJ [auth B1], PK [auth B1], PL [auth B1], PM [auth B1], PN [auth B1], PO [auth B1], PP [auth B1], PQ [auth B1], PR [auth B3], PS [auth C1], PT [auth C1], PU [auth C1], PV [auth C1], PW [auth D1], PX [auth D1], PY [auth D1], PZ [auth D1], QAA [auth D1], QBA [auth D1], QCA [auth D1], QDA [auth D1], QE [auth A1], QEA [auth D1], QF [auth A1], QFA [auth DO], QG [auth A1], QH [auth A1], QI [auth B1], QJ [auth B1], QK [auth B1], QL [auth B1], QM [auth B1], QN [auth B1], QO [auth B1], QP [auth B1], QQ [auth B1], QR [auth B3], QS [auth C1], QT [auth C1], QU [auth C1], QV [auth C1], QW [auth D1], QX [auth D1], QY [auth D1], QZ [auth D1], RAA [auth D1], RBA [auth D1], RCA [auth D1], RDA [auth D1], RE [auth A1], REA [auth D1], RF [auth A1], RFA [auth DO], RG [auth A1], RH [auth A1], RI [auth B1], RJ [auth B1], RK [auth B1], RL [auth B1], RM [auth B1], RN [auth B1], RO [auth B1], RP [auth B1], RQ [auth B1], RR [auth B3], RS [auth C1], RT [auth C1], RU [auth C1], RV [auth C1], RW [auth D1], RX [auth D1], RY [auth D1], RZ [auth D1], SAA [auth D1], SBA [auth D1], SCA [auth D1], SDA [auth D1], SE [auth A1], SEA [auth D2], SF [auth A1], SFA [auth DT], SG [auth A1], SH [auth A1], SI [auth B1], SJ [auth B1], SK [auth B1], SL [auth B1], SM [auth B1], SN [auth B1], SO [auth B1], SP [auth B1], SQ [auth B1], SR [auth B3], SS [auth C1], ST [auth C1], SU [auth C1], SV [auth C1], SW [auth D1], SX [auth D1], SY [auth D1], SZ [auth D1], TAA [auth D1], TBA [auth D1], TCA [auth D1], TDA [auth D1], TE [auth A1], TEA [auth D2], TF [auth A1], TFA [auth Dd], TG [auth A1], TH [auth A1], TI [auth B1], TJ [auth B1], TK [auth B1], TL [auth B1], TM [auth B1], TN [auth B1], TO [auth B1], TP [auth B1], TQ [auth B1], TR [auth B3], TS [auth C1], TT [auth C1], TU [auth C1], TV [auth C1], TW [auth D1], TX [auth D1], TY [auth D1], TZ [auth D1], UAA [auth D1], UBA [auth D1], UCA [auth D1], UDA [auth D1], UE [auth A1], UEA [auth D2], UF [auth A1], UFA [auth Dd], UG [auth A1], UH [auth A1], UI [auth B1], UJ [auth B1], UK [auth B1], UL [auth B1], UM [auth B1], UN [auth B1], UO [auth B1], UP [auth B1], UQ [auth B1], UR [auth BC], US [auth C1], UT [auth C1], UU [auth C1], UV [auth C1], UW [auth D1], UX [auth D1], UY [auth D1], UZ [auth D1], VAA [auth D1], VBA [auth D1], VCA [auth D1], VDA [auth D1], VE [auth A1], VEA [auth D2], VF [auth A1], VFA [auth Dg], VG [auth A1], VH [auth A1], VI [auth B1], VJ [auth B1], VK [auth B1], VL [auth B1], VM [auth B1], VN [auth B1], VO [auth B1], VP [auth B1], VQ [auth B1], VR [auth BO], VS [auth C1], VT [auth C1], VU [auth C1], VV [auth C1], VW [auth D1], VX [auth D1], VY [auth D1], VZ [auth D1], WAA [auth D1], WBA [auth D1], WCA [auth D1], WDA [auth D1], WE [auth A1], WEA [auth D2], WF [auth A1], WG [auth A1], WH [auth A1], WI [auth B1], WJ [auth B1], WK [auth B1], WL [auth B1], WM [auth B1], WN [auth B1], WO [auth B1], WP [auth B1], WQ [auth B1], WR [auth BT], WS [auth C1], WT [auth C1], WU [auth C1], WV [auth C1], WW [auth D1], WX [auth D1], WY [auth D1], WZ [auth D1], XAA [auth D1], XBA [auth D1], XCA [auth D1], XDA [auth D1], XE [auth A1], XEA [auth D2], XF [auth A1], XG [auth A1], XH [auth A1], XI [auth B1], XJ [auth B1], XK [auth B1], XL [auth B1], XM [auth B1], XN [auth B1], XO [auth B1], XP [auth B1], XQ [auth B1], XR [auth Bd], XS [auth C1], XT [auth C1], XU [auth C1], XV [auth CI], XW [auth D1], XX [auth D1], XY [auth D1], XZ [auth D1], YAA [auth D1], YBA [auth D1], YCA [auth D1], YDA [auth D1], YE [auth A1], YEA [auth D2], YF [auth A1], YG [auth A1], YH [auth A1], YI [auth B1], YJ [auth B1], YK [auth B1], YL [auth B1], YM [auth B1], YN [auth B1], YO [auth B1], YP [auth B1], YQ [auth B2], YR [auth Bd], YS [auth C1], YT [auth C1], YU [auth C1], YV [auth CS], YW [auth D1], YX [auth D1], YY [auth D1], YZ [auth D1], ZAA [auth D1], ZBA [auth D1], ZCA [auth D1], ZDA [auth D1], ZE [auth A1], ZEA [auth D2], ZF [auth A1], ZG [auth A1], ZH [auth A1], ZI [auth B1], ZJ [auth B1], ZK [auth B1], ZL [auth B1], ZM [auth B1], ZN [auth B1], ZO [auth B1], ZP [auth B1], ZQ [auth B2], ZR [auth Bg], ZS [auth C1], ZT [auth C1], ZU [auth C1], ZV [auth CS], ZW [auth D1], ZX [auth D1], ZY [auth D1], ZZ [auth D1]	osmium (III) hexammine H12 N6 Os OWCQTVJQFLTQTE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 0.341 
• R-Value Work: 0.278 
• R-Value Observed: 0.280 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 437.11	α = 90
b = 288.38	β = 99.13
c = 306.56	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
DM	model building
DMMulti	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
DM	phasing
DMMulti	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Ben-Shem, A., Jenner, L., Yusupova, G., Yusupov, M.
• This entry supersedes: 3O2Z, 3O30, 3O58, 3O5H

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release
  
• Version 1.1: 2014-12-10
  Changes: Other
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references