Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome

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

doi:10.2210/pdb5dge/pdb

Macromolecule Content

Total Structure Weight: 6671823.00
Atom Count: 413109
Residue Count: 35633
Unique protein chains: 80
Unique nucleic acid chains: 5

5DGE

Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome

DOI: 10.2210/pdb5DGE/pdb
NDB: 5DGE

Classification: RIBOSOME
Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae S288C

Deposited: 2015-08-27 Released: 2017-01-25
Deposition Author(s): Melnikov, S., Mailliot, J., Shin, B.-S., Rigger, L., Yusupova, G., Micura, R., Dever, T.E., Yusupov, M.
Funding Organization(s): Fondation pour la Recherche Medicale; French National Research Agency; Austrian Science Fund; European Research Council; Human Frontier Science Program; Russian Government Program of Competitive Growh of Kazan Federal University; Intramural Research Program of the National Institutes of Health

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.45 Å
R-Value Free: 0.263
R-Value Work: 0.207

wwPDB Validation3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome

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

To be published.

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S0-A	S0, s0	251	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPS0A (NAB1, NAB1A, YST1)
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P32905
Protein Feature View Full Protein Feature View for P32905

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S1-A	S1, s1	254	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPS1A (PLC1, RPS10A)
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P33442
Protein Feature View Full Protein Feature View for P33442

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S2	S2, s2	253	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
Protein Feature View Full Protein Feature View for P25443

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S3	S3, s3	239	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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for P0CX35

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S5	S5, s5	224	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
Protein Feature View Full Protein Feature View for P26783

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S6-A	S6, s6	236	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
Protein Feature View Full Protein Feature View for P0CX37

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S7-A	S7, s7	189	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
Protein Feature View Full Protein Feature View for P26786

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S8-A	S8, s8	200	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPS8A (RPS14A)
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P0CX39
Protein Feature View Full Protein Feature View for P0CX39

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S9-A	S9, s9	196	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
Protein Feature View Full Protein Feature View for O13516

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S10-A	C0, c0	105	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
Protein Feature View Full Protein Feature View for Q08745

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S11-A	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
Protein Feature View Full Protein Feature View for P0CX47

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S12	C2, c2	142	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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for P05756

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S14-A	C4, c4	136	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
Protein Feature View Full Protein Feature View for P06367

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S15	C5, c5	141	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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for P0CX51

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S17-A	C7, c7	136	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPS17A (RP51A)
Find proteins for P02407 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P02407
Protein Feature View Full Protein Feature View for P02407

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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for P07280

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S20	D0, d0	120	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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for P0C0W1

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S23-A	D3, d3	144	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPS23A (RPS28A)
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P0CX29
Protein Feature View Full Protein Feature View for P0CX29

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
Protein Feature View Full Protein Feature View for P0CX31

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S25-A	D5, d5	107	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
Protein Feature View Full Protein Feature View for Q3E792

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S26-A	D6, d6	97	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPS26A (RPS26)
Find proteins for P39938 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P39938
Protein Feature View Full Protein Feature View for P39938

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
Protein Feature View Full Protein Feature View for P35997

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S28-A	D8, d8	66	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
Protein Feature View Full Protein Feature View for Q3E7X9

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S29-A	D9, d9	55	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
Protein Feature View Full Protein Feature View for P41057

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S30-A	E0	60	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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for P05759

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details
Guanine nucleotide-binding protein subunit beta-like protein	SR, 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
Protein Feature View Full Protein Feature View for P38011

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details
Suppressor protein STM1	SM, sM	273	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
Protein Feature View Full Protein Feature View for P39015

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L2-A	L2, l2	253	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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for Q02326

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L7-A	L7, l7	243	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
Protein Feature View Full Protein Feature View for P05737

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L8-A	L8, l8	255	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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for P41805

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L11-A	M1, m1	173	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPL11A (RP39A, RPL16A)
Find proteins for P0C0W9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P0C0W9
Protein Feature View Full Protein Feature View for P0C0W9

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L13-A	M3, m3	198	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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for P05748

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L16-A	M6, m6	198	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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for Q02753

Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L22-A	N2, n2	120	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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for P0CX41

Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L24-A	N4, n4	155	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
Protein Feature View Full Protein Feature View for P04449

Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L25	N5, n5	141	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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for P05747

Entity ID: 66
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L30	O0, o0	104	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
Protein Feature View Full Protein Feature View for P14120

Entity ID: 67
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L31-A	O1, o1	112	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
Protein Feature View Full Protein Feature View for P0C2H8

Entity ID: 68
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L32	O2, o2	129	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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for P05744

Entity ID: 70
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L34-A	O4, o4	119	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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for 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
Protein Feature View Full Protein Feature View for P0CX25

Entity ID: 80
Molecule	Chains	Sequence Length	Organism	Details
40S ribosomal protein S30-A	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
Protein Feature View Full Protein Feature View for P0CX33

Entity ID: 81
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L12-A	m2	165	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPL12A (RPL15B)
Find proteins for P0CX53 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P0CX53
Protein Feature View Full Protein Feature View for P0CX53

Entity ID: 82
Molecule	Chains	Sequence Length	Organism	Details
60S acidic ribosomal protein P0	p0	311	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPP0 (L10E, RPA0, RPL10E, RPLA0)
Find proteins for P05317 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P05317
Protein Feature View Full Protein Feature View for P05317

Entity ID: 83
Molecule	Chains	Sequence Length	Organism	Details
60S acidic ribosomal protein P1-alpha	p1, p2	106	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: RPP1A (L12EIIA, RPA1, RPLA1)
Find proteins for P05318 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P05318
Protein Feature View Full Protein Feature View for P05318

Entity ID: 84
Molecule	Chains	Sequence Length	Organism	Details
Eukaryotic translation initiation factor 5A-1	f	157	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0 Gene Names: HYP2 (TIF51A)
Find proteins for P23301 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB: P23301
Protein Feature View Full Protein Feature View for P23301

Entity ID: 1
Molecule	Chains	Length	Organism
18S ribosomal RNA	2,6	1800	Saccharomyces cerevisiae S288C

Entity ID: 36
Molecule	Chains	Length	Organism
25S ribosomal RNA	1,5	3396	Saccharomyces cerevisiae S288C

Entity ID: 37
Molecule	Chains	Length	Organism
5S ribosomal RNA	3,7	121	Saccharomyces cerevisiae S288C

Entity ID: 38
Molecule	Chains	Length	Organism
5.8S ribosomal RNA	4,8	158	Saccharomyces cerevisiae S288C

Entity ID: 85
Molecule	Chains	Length	Organism
DNA (5'-R(CPCP*(NA))-3')	B,C	4	Saccharomyces cerevisiae S288C

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
ZN Query on ZN Download SDF File Download CCD File	D6, d6, d7, D7, D9, d9, E1, e1, O7, o7, q0, Q0, Q2, q2, q3, Q3	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
OHX Query on OHX Download SDF File Download CCD File	1, 2, 3, 4, 5, 6, 7, 8, c3, C3, C5, c5, C8, c8, d4, D9, d9, l3, L3, L4, l4, l5, L5, l9, m0, M0, m1, m4, m5, M5, m6, M6, M7, m7, M8, m8, m9, M9, n3, N8, N9, n9, O1, O3, o3, O4, o6, o7, O7, O9, Q2, q2, S1, s1, s4, S6, s8, S8, s9, S9, SR, sR	osmium (III) hexammine osmium(6+) hexaazanide H₁₂ N₆ Os OWCQTVJQFLTQTE-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download SDF File Download CCD File	1, 2, 3, 4, 5, 6, 7, 8, B, C, c8, d2, d3, D3, d6, f, L2, l2, l3, L3, l4, l5, L6, L7, l7, M0, m3, M5, m5, M6, m7, M7, M9, n0, N3, n3, N6, n6, n8, N8, o2, O3, o3, O4, o4, O7, q1, Q2, q3, S2, s4, s8, sM, SM	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction
PRO Query on PRO Download SDF File Download CCD File	B, C	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Ligand Interaction
SPS Query on SPS Download SDF File Download CCD File	5, B	SPARSOMYCIN C₁₃ H₁₉ N₃ O₅ S₂ XKLZIVIOZDNKEQ-CLQLPEFOSA-N		Ligand Interaction

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
8AN Query on 8AN	B, C	RNA LINKING	C₁₀ H₁₅ N₆ O₆ P		A
5CT Query on 5CT	f	peptide linking	C₁₀ H₂₃ N₃ O₃		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.45 Å
R-Value Free: 0.263
R-Value Work: 0.207
Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 438.000	α = 90.00
b = 289.050	β = 98.95
c = 305.260	γ = 90.00

Software Package:

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

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History & Funding Information

Deposition Data

Deposited Date: 2015-08-27
Released Date: 2017-01-25
Deposition Author(s): Melnikov, S., Mailliot, J., Shin, B.-S., Rigger, L., Yusupova, G., Micura, R., Dever, T.E., Yusupov, M.

Funding Organization	Location	Grant Number
Fondation pour la Recherche Medicale	France	--
French National Research Agency	France	ANR-11-BSV8-006 01
Austrian Science Fund	Austria	P21641
Austrian Science Fund	Austria	I1040
European Research Council		294312
Human Frontier Science Program		RGP0062
Human Frontier Science Program		RGP2012
Russian Government Program of Competitive Growh of Kazan Federal University	Russian Federation	--
Intramural Research Program of the National Institutes of Health	United States	--

Revision History

Version 1.0: 2017-01-25
Type: Initial release
Version 1.1: 2017-08-30
Type: Advisory, Author supporting evidence, Derived calculations

Prepare Data

Validate Data

Deposit Data

Deposition Help & Resources

154939 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

5DGE

Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome

Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome

Entity ID: 2

Entity ID: 3

Entity ID: 4

Entity ID: 5

Entity ID: 6

Entity ID: 7

Entity ID: 8

Entity ID: 9

Entity ID: 10

Entity ID: 11

Entity ID: 12

Entity ID: 13

Entity ID: 14

Entity ID: 15

Entity ID: 16

Entity ID: 17

Entity ID: 18

Entity ID: 19

Entity ID: 20

Entity ID: 21

Entity ID: 22

Entity ID: 23

Entity ID: 24

Entity ID: 25

Entity ID: 26

Entity ID: 27

Entity ID: 28

Entity ID: 29

Entity ID: 30

Entity ID: 31

Entity ID: 32

Entity ID: 33

Entity ID: 34

Entity ID: 35

Entity ID: 39

Entity ID: 40

Entity ID: 41

Entity ID: 42

Entity ID: 43

Entity ID: 44

Entity ID: 45

Entity ID: 46

Entity ID: 47

Entity ID: 48

Entity ID: 49

Entity ID: 50

Entity ID: 51

Entity ID: 52

Entity ID: 53

Entity ID: 54

Entity ID: 55

Entity ID: 56

Entity ID: 57

Entity ID: 58

Entity ID: 59

Entity ID: 60

Entity ID: 61

Entity ID: 62

Entity ID: 63

Entity ID: 64

Entity ID: 65

Entity ID: 66

Entity ID: 67

Entity ID: 68

Entity ID: 69

Entity ID: 70

Entity ID: 71

Entity ID: 72

Entity ID: 73

Entity ID: 74

Entity ID: 75

Entity ID: 76