Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 79-mer - A2BCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 79-mer -A2B2C2DEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWX 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 75-mer - ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVW Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 75-mer -A2B2CDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTU 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6310017.50 
• Atom Count: 411589 
• Residue Count: 33525 
• Unique protein chains: 84
• Unique nucleic acid chains: 7

5TGM

Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro

• DOI: 10.2210/pdb5TGM/pdb
• NDB: 5TGM

• Classification: RIBOSOME
• Organism(s): Saccharomyces cerevisiae, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Lachancea kluyveri, Naumovozyma castellii (strain ATCC 76901 / CBS 4309 / NBRC 1992 / NRRL Y-12630), Homo sapiens, Saccharomyces cerevisiae (strain RM11-1a)


• Deposited: 2016-09-28 Released: 2017-01-18 
• Deposition Author(s): Melnikov, S., Mailliot, J., Yusupov, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.5 Å
• R-Value Free: 0.312 
• R-Value Work: 0.261 

Literature

Molecular insights into protein synthesis with proline residues.

Melnikov, S., Mailliot, J., Rigger, L., Neuner, S., Shin, B.S., Yusupova, G., Dever, T.E., Micura, R., Yusupov, M.

(2016) EMBO Rep. 17: 1776-1784

• PubMed: 27827794 
• DOI: 10.15252/embr.201642943
• Primary Citation of Related Structures:  
  5TGA, 5LYB


• PubMed Abstract: 
  

Proline is an amino acid with a unique cyclic structure that facilitates the folding of many proteins, but also impedes the rate of peptide bond formation by the ribosome. As a ribosome substrate, proline reacts markedly slower when compared with other amino acids both as a donor and as an acceptor of the nascent peptide. Furthermore, synthesis of peptides with consecutive proline residues triggers ribosome stalling. Here, we report crystal structures of the eukaryotic ribosome bound to analogs of mono- and diprolyl-tRNAs. These structures provide a high-resolution insight into unique properties of proline as a ribosome substrate. They show that the cyclic structure of proline residue prevents proline positioning in the amino acid binding pocket and affects the nascent peptide chain position in the ribosomal peptide exit tunnel. These observations extend current knowledge of the protein synthesis mechanism. They also revise an old dogma that amino acids bind the ribosomal active site in a uniform way by showing that proline has a binding mode distinct from other amino acids.

---

Organizational Affiliation: 

Institute of Genetics and Molecular and Cellular Biology CNRS UMR7104 INSERM UMR964, Illkirch, France.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S0-A	S0, s0	206	Saccharomyces cerevisiae (strain RM11-1a)	Mutation(s): 0  Gene Names: RPS0A (NAB1, NAB1A, YST1)
Find proteins for B3LI22 (Saccharomyces cerevisiae (strain RM11-1a)) Go to UniProtKB:  B3LI22

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S1-A	S1, s1	216	Saccharomyces cerevisiae (strain RM11-1a)	Mutation(s): 0  Gene Names: RPS1A
Find proteins for B3RHV0 (Saccharomyces cerevisiae (strain RM11-1a)) Go to UniProtKB:  B3RHV0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S2	S2, s2	217	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS2 (RPS4, SUP38, SUP44)
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPS2 Go to UniProtKB:  P25443

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S3	S3, s3	223	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS3 (SUF14)
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPS3 Go to UniProtKB:  P05750

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S4-A	S4, s4	260	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS4A (RPS7B)
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0CX35

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S5	S5, s5	206	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS5 (RPS2)
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPS5 Go to UniProtKB:  P26783

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S6-A	S6, s6	226	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS6A (RPS101, RPS10B)
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0CX37

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S7-A	S7, s7	186	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS7A (RPS30)
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P26786

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S8	S8, s8	188	Lachancea kluyveri	Mutation(s): 0
Find proteins for A0A0J9X221 (Lachancea kluyveri) Go to UniProtKB:  A0A0J9X221

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S9-A	S9, s9	185	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS9A (RPS13A, YS11A)
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  O13516

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S10-A,40S Ribosomal Protein S10	C0	96	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS10A
Find proteins for Q08745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q08745

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S11-A,40S Ribosomal Protein S11	C1, c1	155	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS11A (RPS18A)
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0CX47

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
40S Ribosomal Protein S12,40S ribosomal protein S12	C2, c2	124	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS12
Find proteins for P48589 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPS12 Go to UniProtKB:  P48589

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S13	C3, c3	150	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS13 (RPS13C)
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPS13 Go to UniProtKB:  P05756

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S14-A	C4, c4	128	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS14A (CRY1, RPL59)
Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P06367

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
40S Ribosomal Protein S15,40S ribosomal protein S15,40S Ribosomal Protein S15	C5, c5	135	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS15 (RPS21)
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPS15 Go to UniProtKB:  Q01855

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S16-A	C6, c6	142	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS16A (RP61R)
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0CX51

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
ES17	C7	120	Lachancea kluyveri	Mutation(s): 0
Find proteins for A0A0J9X224 (Lachancea kluyveri) Go to UniProtKB:  A0A0J9X224

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S18-A	C8, c8	145	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS18A
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0CX55

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S19-A	C9, c9	143	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS19A (RP55A, RPS16AA)
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P07280

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S20	D0, d0	110	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS20 (URP2)
Find proteins for P38701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPS20 Go to UniProtKB:  P38701

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S21-A	D1, d1	87	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS21A (RPS25, RPS25A, RPS26A)
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0C0V8

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S22-A	D2, d2	129	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS22A (RPS24, RPS24A)
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0C0W1

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S23-A	D3, d3	144	Naumovozyma castellii (strain ATCC 76901 / CBS 4309 / NBRC 1992 / NRRL Y-12630)	Mutation(s): 0  Gene Names: RPS23A
Find proteins for P0CY39 (Naumovozyma castellii (strain ATCC 76901 / CBS 4309 / NBRC 1992 / NRRL Y-12630)) Go to UniProtKB:  P0CY39

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S24-A	D4, d4	134	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS24A (RPS24EA)
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0CX31

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S25-A	D5, d5	70	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS25A (RPS31A)
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q3E792

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S26-B	D6, d6	97	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS26B
Find proteins for P39939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P39939

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S27-A	D7, d7	81	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS27A
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPS27A Go to UniProtKB:  P35997

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S28-A	D8, d8	63	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS28A (RPS33, RPS33A)
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q3E7X9

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S29-A	D9, d9	53	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS29A (RPS36A, YS29A)
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P41057

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S30-A	E0, e0	62	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS30A
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0CX33

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-40S ribosomal protein S31	E1, e1	76	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS31 (RPS37, UBI3)
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05759

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details
Guanine nucleotide-binding protein subunit beta-like protein	SR	318	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: ASC1 (CPC2)
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P38011

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details
Ribosome-bound protein Stm1,Suppressor protein STM1,Ribosome-bound protein Stm1	SM	159	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: STM1 (MPT4, STO1)
Find proteins for P39015 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P39015

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L2-A	L2, l2	252	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL2A (RPL5B)
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0CX45

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L3	L3, l3	386	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL3 (MAK8, TCM1)
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL3 Go to UniProtKB:  P14126

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L4-A	L4, l4	361	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL4A (RPL2, RPL2A)
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P10664

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L5	L5, l5	296	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL5 (RPL1, RPL1A)
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL5 Go to UniProtKB:  P26321

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L6-A	L6, l6	175	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL6A (RPL17A, YL16A)
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q02326

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L7-A	L7, l7	223	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL7A (RPL6A, RPL8A, YL8A)
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL7A Go to UniProtKB:  P05737

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L8-A	L8	233	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL8A (MAK7, RPL4A)
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P17076

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L9-A	L9, l9	191	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL9A (RPL8A, RPL9)
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05738

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L10	M0, m0	220	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL10 (GRC5, QSR1)
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL10 Go to UniProtKB:  P41805

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L11-B	M1, m1	169	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL11B (RP39B, RPL16B)
Find proteins for Q3E757 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q3E757

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L13-A	M3, m3	194	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL13A
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL13A Go to UniProtKB:  Q12690

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L14-A	M4, m4	137	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL14A
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P36105

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L15-A	M5, m5	203	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL15A (RPL10A, RPL13A, YL10A)
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05748

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L16-A	M6, m6	197	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL16A (RPL13, RPL21A)
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P26784

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L17-A	M7, m7	183	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL17A (RPL17, RPL20A)
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05740

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L18-A	M8, m8	185	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL18A (RP28A)
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL18A Go to UniProtKB:  P0CX49

Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L19-A	M9, m9	188	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL19A (RPL23A, YL14A)
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0CX82

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L20-A	N0, n0	172	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL20A (RPL18A, RPL18A2)
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0CX23

Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L21-A	N1, n1	159	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL21A (URP1)
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q02753

Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L22-A	N2, n2	100	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL22A
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05749

Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L23-A	N3, n3	136	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL23A (RPL17A, RPL17AA)
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL23A Go to UniProtKB:  P0CX41

Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L24-A	N4	98	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL24A (RP29, RPL30A)
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P04449

Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L25	N5, n5	121	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL25
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P04456

Entity ID: 62
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L26-A	N6, n6	126	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL26A (RPL26, RPL33A)
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05743

Entity ID: 63
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L27-A	N7, n7	135	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL27A (RPL27)
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL27A Go to UniProtKB:  P0C2H6

Entity ID: 64
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L28	N8, n8	148	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL28 (CYH2)
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL28 Go to UniProtKB:  P02406

Entity ID: 65
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L29	N9, n9	58	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL29 (YL43)
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL29 Go to UniProtKB:  P05747

Entity ID: 66
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L30	O0, o0	100	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL30 (RPL32)
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL30 Go to UniProtKB:  P14120

Entity ID: 67
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L31-A	O1, o1	109	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL31A (RPL34, RPL34A)
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0C2H8

Entity ID: 68
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L32	O2, o2	127	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL32
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL32 Go to UniProtKB:  P38061

Entity ID: 69
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L33-A	O3, o3	106	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL33A (RPL37A)
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05744

Entity ID: 70
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L34-A	O4, o4	112	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL34A
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P87262

Entity ID: 71
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L35-A	O5, o5	119	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL35A (SOS1)
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL35A Go to UniProtKB:  P0CX84

Entity ID: 72
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L36-A	O6, o6	99	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL36A (RPL39A)
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL36A Go to UniProtKB:  P05745

Entity ID: 73
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L37-A	O7, o7	87	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL37A (RPL35A)
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL37A Go to UniProtKB:  P49166

Entity ID: 74
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L38	O8, o8	77	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL38
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL38 Go to UniProtKB:  P49167

Entity ID: 75
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L39	O9, o9	50	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL39 (RPL46, SPB2)
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL39 Go to UniProtKB:  P04650

Entity ID: 76
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-60S ribosomal protein L40	Q0, q0	52	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL40A (UBI1)
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0CH08

Entity ID: 77
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L41-A	Q1, q1	25	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL41A (RPL47A, YL41A)
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0CX86

Entity ID: 78
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L42-A	Q2, q2	105	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL42A (RPL41A, SCL41A)
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0CX27

Entity ID: 79
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L43-A	Q3, q3	91	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL43A
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0CX25

Entity ID: 81
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S10-A,40S Ribosomal Protein S10	c0	96	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPS10A
Find proteins for Q08745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q08745

Entity ID: 82
Molecule	Chains	Sequence Length	Organism	Details
ES17	c7	121	Lachancea kluyveri	Mutation(s): 0
Find proteins for A0A0J9X224 (Lachancea kluyveri) Go to UniProtKB:  A0A0J9X224

Entity ID: 83
Molecule	Chains	Sequence Length	Organism	Details
Guanine nucleotide-binding protein subunit beta-like protein	sR	318	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: ASC1 (CPC2)
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P38011

Entity ID: 84
Molecule	Chains	Sequence Length	Organism	Details
Suppressor protein STM1,Ribosome-bound protein Stm1	sM	104	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: STM1 (MPT4, STO1)
Find proteins for P39015 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P39015

Entity ID: 86
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L8-A,60S Ribosomal Protein L8	l8	231	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL8A (MAK7, RPL4A)
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P17076

Entity ID: 87
Molecule	Chains	Sequence Length	Organism	Details
60S Ribosomal Protein L12	m2	150	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 88
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L24-A	n4	135	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL24A (RP29, RPL30A)
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P04449

Entity ID: 89
Molecule	Chains	Sequence Length	Organism	Details
60S Ribosomal Protein P0	p0	143	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 90
Molecule	Chains	Sequence Length	Organism	Details
60S Ribosomal Protein P1/2	p1, p2	47	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 1
Molecule	Chains	Length	Organism
18S ribosomal RNA	2	1812	Saccharomyces cerevisiae

Entity ID: 36
Molecule	Chains	Length	Organism
25S ribosomal RNA	1	3149	Saccharomyces cerevisiae

Entity ID: 37
Molecule	Chains	Length	Organism
5S ribosomal RNA	3,7	121	Saccharomyces cerevisiae

Entity ID: 38
Molecule	Chains	Length	Organism
5.8S ribosomal RNA	4,8	158	Saccharomyces cerevisiae

Entity ID: 80
Molecule	Chains	Length	Organism
18S ribosomal RNA	6	1800	Saccharomyces cerevisiae

Entity ID: 85
Molecule	Chains	Length	Organism
25S ribosomal RNA	5	3150	Saccharomyces cerevisiae

Entity ID: 91
Molecule	Chains	Length	Organism
Peptidyl-tRNA analog ACCA-Leu-Phe	P,p	5	Homo sapiens

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	d6, D6, D7, d7, D9, d9, E1, e1, O7, o7, Q0, q0, q2, Q2, Q3, q3	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
LEU	1, 5	LEUCINE C6 H13 N O2 ROHFNLRQFUQHCH-YFKPBYRVSA-N
OHX	1, 2, 3, 4, 5, 6, 7, 8, c3, C3, c5, C5, C7, C8, c8, d4, D9, l3, L3, L4, l5, L6, l9, M0, m0, m5, M5, m6, M6, M7, M8, m8, M9, m9, n9, N9, o3, O3, O4, O7, o7, O9, Q2, q2, s1, s4, s8, S8, S9, s9, SR, sR	osmium (III) hexammine osmium(6+) hexaazanide H12 N6 Os OWCQTVJQFLTQTE-UHFFFAOYSA-N
PHE	1, 5	PHENYLALANINE C9 H11 N O2 COLNVLDHVKWLRT-QMMMGPOBSA-N
MG	1, 2, 3, 4, 5, 6, 7, 8, C1, c6, C8, c8, C9, c9, d3, d4, d6, d7, D9, l2, L2, L3, l3, L4, l5, l6, l7, L7, l9, M0, m0, M3, m4, M5, m5, m6, m7, M7, N0, n0, n3, N3, N5, N6, n6, n8, N8, n9, o2, o3, O4, o4, O5, O7, o9, p, P, q1, Q2, s4, S4, s6, sM	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
8AN	P, p	3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) C10 H15 N6 O6 P WIVGZDLLXCRANL-QYYRPYCUSA-N
SPS	1, 5	SPARSOMYCIN C13 H19 N3 O5 S2 XKLZIVIOZDNKEQ-CLQLPEFOSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NA	P, p	NON-POLYMER	Na		--
UNK	C0, c0, C1, c1, c2, C2, C5, c5, l8, m2, p, P, p0, p1, p2, sM, SM	L-PEPTIDE LINKING	C4 H9 N O2		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.5 Å
• R-Value Free: 0.312 
• R-Value Work: 0.261 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 434.730	α = 90.00
b = 286.770	β = 98.87
c = 303.150	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
PDB_EXTRACT	data extraction
PHENIX	phasing
XSCALE	data scaling
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-09-28 
• Released Date: 2017-01-18 
• Deposition Author(s): Melnikov, S., Mailliot, J., Yusupov, M.

Revision History 

• Version 1.0: 2017-01-18
  Type: Initial release
• Version 1.1: 2017-01-25
  Type: Derived calculations, Source and taxonomy, Structure summary