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5DGE

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

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A, BC
(2, 6)
18S ribosomal RNApolymer1800579761.92GenBank (874346701)Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
2B, CC
(S0, s0)
40S ribosomal protein S0-Apolymer25127920.12UniProt (P32905)
Pfam (PF00318)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nucleic acid-binding protein NAB1A
3C, DC
(S1, s1)
40S ribosomal protein S1-Apolymer25428667.32UniProt (P33442)
Pfam (PF01015)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP10A
4D, EC
(S2, s2)
40S ribosomal protein S2polymer25327359.62UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Omnipotent suppressor protein SUP44,RP12,S4,YS5
5E, FC
(S3, s3)
40S ribosomal protein S3polymer23926411.62UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP13,YS3
6F, GC
(S4, s4)
40S ribosomal protein S4-Apolymer26029338.12UniProt (P0CX35)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
Pfam (PF08071)
Pfam (PF01479)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP5,S7,YS6
7G, HC
(S5, s5)
40S ribosomal protein S5polymer22424941.42UniProt (P26783)
Pfam (PF00177)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP14,S2,YS8
8H, IC
(S6, s6)
40S ribosomal protein S6-Apolymer23627054.52UniProt (P0CX37)
Pfam (PF01092)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP9,S10,YS4
9I, JC
(S7, s7)
40S ribosomal protein S7-Apolymer18921527.02UniProt (P26786)
Pfam (PF01251)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP30,RP40
10J, KC
(S8, s8)
40S ribosomal protein S8-Apolymer20022537.82UniProt (P0CX39)
Pfam (PF01201)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP19,S14,YS9
11K, LC
(S9, s9)
40S ribosomal protein S9-Apolymer19622356.72UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP21,S13,YP28,YS11
12L, MC
(C0, c0)
40S ribosomal protein S10-Apolymer10512771.52UniProt (Q08745)
Pfam (PF03501)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
13M, NC
(C1, c1)
40S ribosomal protein S11-Apolymer15517668.82UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP41,S18,YS12
14N, OC
(C2, c2)
40S ribosomal protein S12polymer14215385.52UniProt (P48589)
Pfam (PF01248)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
15O, PC
(C3, c3)
40S ribosomal protein S13polymer15016928.72UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S27a,YS15
16P, QC
(C4, c4)
40S ribosomal protein S14-Apolymer13614431.52UniProt (P06367)
Pfam (PF00411)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP59A
17Q, RC
(C5, c5)
40S ribosomal protein S15polymer14115900.72UniProt (Q01855)
Pfam (PF00203)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RIG protein,RP52,S21,YS21
18R, SC
(C6, c6)
40S ribosomal protein S16-Apolymer14215746.32UniProt (P0CX51)
Pfam (PF00380)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP61R
19S, TC
(C7, c7)
40S ribosomal protein S17-Apolymer13615820.42UniProt (P02407)
Pfam (PF00833)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP51A
20T, UC
(C8, c8)
40S ribosomal protein S18-Apolymer14516940.42UniProt (P0CX55)
Pfam (PF00416)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
21U, VC
(C9, c9)
40S ribosomal protein S19-Apolymer14315810.92UniProt (P07280)
Pfam (PF01090)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP55A,S16a,YP45,YS16A
22V, WC
(D0, d0)
40S ribosomal protein S20polymer12013797.92UniProt (P38701)
Pfam (PF00338)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
23W, XC
(D1, d1)
40S ribosomal protein S21-Apolymer879758.82UniProt (P0C0V8)
Pfam (PF01249)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S26,YS25
24X, YC
(D2, d2)
40S ribosomal protein S22-Apolymer12914518.92UniProt (P0C0W1)
Pfam (PF00410)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP50,S24,YP58,YS22
25Y, ZC
(D3, d3)
40S ribosomal protein S23-Apolymer14415942.72UniProt (P0CX29)
Pfam (PF00164)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP37,S28,YS14
26AD, Z
(D4, d4)
40S ribosomal protein S24-Apolymer13415231.62UniProt (P0CX31)
Pfam (PF01282)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP50
27AA, BD
(D5, d5)
40S ribosomal protein S25-Apolymer10711936.12UniProt (Q3E792)
Pfam (PF03297)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP45,S31,YS23
28BA, CD
(D6, d6)
40S ribosomal protein S26-Apolymer9711023.02UniProt (P39938)
Pfam (PF01283)
UniProt (by SIFTS) (P39939)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
29CA, DD
(D7, d7)
40S ribosomal protein S27-Apolymer818762.22UniProt (P35997)
Pfam (PF01667)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP61,YS20
30DA, ED
(D8, d8)
40S ribosomal protein S28-Apolymer667474.72UniProt (Q3E7X9)
Pfam (PF01200)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S33,YS27
31EA, FD
(D9, d9)
40S ribosomal protein S29-Apolymer556544.52UniProt (P41057)
Pfam (PF00253)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S36,YS29
32FA, GD
(E0, e0)
40S ribosomal protein S30-Apolymer637137.52UniProt (P0CX33)
Pfam (PF04758)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Small ribosomal subunit protein eS30-A
33GA, HD
(E1, e1)
Ubiquitin-40S ribosomal protein S31polymer768703.52UniProt (P05759)
Pfam (PF01599)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
34HA, ID
(SR, sR)
Guanine nucleotide-binding protein subunit beta-like proteinpolymer31834710.02UniProt (P38011)
Pfam (PF00400)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1
35IA, JD
(SM, sM)
Suppressor protein STM1polymer27330048.02UniProt (P39015)
Pfam (PF09598)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)3BP1,GU4 nucleic-binding protein 2,G4p2 protein,POP2 multicopy suppressor protein 4,Ribosomal subunits association factor,AF,TOM1 suppressor protein 1,Triplex-binding protein 1
36JA, KD
(1, 5)
25S ribosomal RNApolymer33961097493.92GenBank (834774822)Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
37KA, LD
(3, 7)
5S ribosomal RNApolymer12138951.12GenBank (834774822)Saccharomyces cerevisiae S288c
38LA, MD
(4, 8)
5.8S ribosomal RNApolymer15850682.92GenBank (940534893)Saccharomyces cerevisiae S288c
39MA, ND
(L2, l2)
60S ribosomal protein L2-Apolymer25327332.42UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L5,RP8,YL6
40NA, OD
(L3, l3)
60S ribosomal protein L3polymer38643719.62UniProt (P14126)
Pfam (PF00297)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
41OA, PD
(L4, l4)
60S ribosomal protein L4-Apolymer36139027.92UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L2,RP2,YL2
42PA, QD
(L5, l5)
60S ribosomal protein L5polymer29633633.62UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1,L1a,Ribosomal 5S RNA-binding protein,YL3
43QA, RD
(L6, l6)
60S ribosomal protein L6-Apolymer17519869.42UniProt (Q02326)
Pfam (PF01159)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17,RP18,YL16
44RA, SD
(L7, l7)
60S ribosomal protein L7-Apolymer24327555.12UniProt (P05737)
Pfam (PF00327)
Pfam (PF08079)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L6,RP11,YL8
45SA, TD
(L8, l8)
60S ribosomal protein L8-Apolymer25528058.62UniProt (P17076)
Pfam (PF01248)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5
46TA, UD
(L9, l9)
60S ribosomal protein L9-Apolymer19121605.12UniProt (P05738)
Pfam (PF00347)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L8,RP24,YL11
47UA, VD
(M0, m0)
60S ribosomal protein L10polymer22025279.32UniProt (P41805)
Pfam (PF00252)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
48VA, WD
(M1, m1)
60S ribosomal protein L11-Apolymer17319654.52UniProt (P0C0W9)
Pfam (PF00281)
Pfam (PF00673)
UniProt (by SIFTS) (Q3E757)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L16,RP39,YL22
49WA, YD
(M3, m3)
60S ribosomal protein L13-Apolymer19822473.02UniProt (Q12690)
Pfam (PF01294)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
50XA, ZD
(M4, m4)
60S ribosomal protein L14-Apolymer13715063.92UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
51AE, YA
(M5, m5)
60S ribosomal protein L15-Apolymer20324351.22UniProt (P05748)
Pfam (PF00827)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13,RP15R,YL10,YP18
52BE, ZA
(M6, m6)
60S ribosomal protein L16-Apolymer19822116.02UniProt (P26784)
Pfam (PF00572)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13a,L21,RP22,YL15
53AB, CE
(M7, m7)
60S ribosomal protein L17-Apolymer18320458.32UniProt (P05740)
Pfam (PF00237)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L20A,YL17
54BB, DE
(M8, m8)
60S ribosomal protein L18-Apolymer18520478.12UniProt (P0CX49)
Pfam (PF17135)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP28
55CB, EE
(M9, m9)
60S ribosomal protein L19-Apolymer18821631.12UniProt (P0CX82)
Pfam (PF01280)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L23,RP15L,RP33,YL14
56DB, FE
(N0, n0)
60S ribosomal protein L20-Apolymer17220478.92UniProt (P0CX23)
Pfam (PF01775)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L18a
57EB, GE
(N1, n1)
60S ribosomal protein L21-Apolymer15918148.12UniProt (Q02753)
Pfam (PF01157)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
58FB, HE
(N2, n2)
60S ribosomal protein L22-Apolymer12013580.22UniProt (P05749)
Pfam (PF01776)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1c,RP4,YL31
59GB, IE
(N3, n3)
60S ribosomal protein L23-Apolymer13614362.82UniProt (P0CX41)
Pfam (PF00238)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17a,YL32
60HB, JE
(N4, n4)
60S ribosomal protein L24-Apolymer15517661.72UniProt (P04449)
Pfam (PF01246)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L30,RP29,YL21
61IB, KE
(N5, n5)
60S ribosomal protein L25polymer14115656.42UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP16L,YL25,YP42'
62JB, LE
(N6, n6)
60S ribosomal protein L26-Apolymer12614134.62UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L33,YL33
63KB, ME
(N7, n7)
60S ribosomal protein L27-Apolymer13515437.22UniProt (P0C2H6)
Pfam (PF01777)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
64LB, NE
(N8, n8)
60S ribosomal protein L28polymer14816630.52UniProt (P02406)
Pfam (PF00828)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L27a,L29,RP44,RP62,YL24
65MB, OE
(N9, n9)
60S ribosomal protein L29polymer586560.72UniProt (P05747)
Pfam (PF01779)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)YL43
66NB, PE
(O0, o0)
60S ribosomal protein L30polymer10411299.22UniProt (P14120)
Pfam (PF01248)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L32,RP73,YL38
67OB, QE
(O1, o1)
60S ribosomal protein L31-Apolymer11212849.02UniProt (P0C2H8)
Pfam (PF01198)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L34,YL28
68PB, RE
(O2, o2)
60S ribosomal protein L32polymer12914678.22UniProt (P38061)
Pfam (PF01655)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
69QB, SE
(O3, o3)
60S ribosomal protein L33-Apolymer10612045.92UniProt (P05744)
Pfam (PF01247)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37,RP47,YL37
70RB, TE
(O4, o4)
60S ribosomal protein L34-Apolymer12113673.22UniProt (P87262)
Pfam (PF01199)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein eL34-A
71SB, UE
(O5, o5)
60S ribosomal protein L35-Apolymer11913811.42UniProt (P0CX84)
Pfam (PF00831)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
72TB, VE
(O6, o6)
60S ribosomal protein L36-Apolymer9911020.12UniProt (P05745)
Pfam (PF01158)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L39,YL39
73UB, WE
(O7, o7)
60S ribosomal protein L37-Apolymer879746.22UniProt (P49166)
Pfam (PF01907)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L43,YL35,YP55
74VB, XE
(O8, o8)
60S ribosomal protein L38polymer778714.42UniProt (P49167)
Pfam (PF01781)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
75WB, YE
(O9, o9)
60S ribosomal protein L39polymer506227.42UniProt (P04650)
Pfam (PF00832)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L46,YL40
76XB, ZE
(Q0, q0)
Ubiquitin-60S ribosomal protein L40polymer526032.32UniProt (P0CH08)
Pfam (PF01020)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
77AF, YB
(Q1, q1)
60S ribosomal protein L41-Apolymer253354.22UniProt (P0CX86)
Pfam (PF05162)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L47,YL41
78BF, ZB
(Q2, q2)
60S ribosomal protein L42-Apolymer10512115.52UniProt (P0CX27)
Pfam (PF00935)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L41,YL27,YP44
79AC, CF
(Q3, q3)
60S ribosomal protein L43-Apolymer919981.82UniProt (P0CX25)
Pfam (PF01780)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37a,YL35
80XD
(m2)
60S ribosomal protein L12-Apolymer16517850.61UniProt (P0CX53)
Pfam (PF03946)
Pfam (PF00298)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L15,YL23
81DF
(p0)
60S acidic ribosomal protein P0polymer31133617.91UniProt (P05317)
Pfam (PF00428)
Pfam (PF00466)
Pfam (PF17777)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)A0,L10E
82EF, FF
(p1, p2)
60S acidic ribosomal protein P1-alphapolymer10610912.92UniProt (P05318)
Pfam (PF00428)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)P1A,A1,L12EIIA,YP1alpha
83GF
(f)
Eukaryotic translation initiation factor 5A-1polymer15717222.41UniProt (P23301)
Pfam (PF21485)
Pfam (PF01287)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)eIF-5A-1,Hypusine-containing protein HP2,eIF-4D
84HF, IF
(B, C)
DNA (5'-R(*CP*CP*(NA))-3')polymer3893.62Saccharomyces cerevisiae S288c
85AAA, ABA, ACA, ADA, AG...
(1, 2, 5, 7, 8...)
MAGNESIUM IONnon-polymer24.31093Chemie (MG)
86AAB, AAC, ABB, ABC, ACB...
(6, 5, 1, 2, l3...)
osmium (III) hexamminenon-polymer286.41169Chemie (OHX)
87AVA, DVA, KP, LP, MP...
(Q2, Q3, D6, D7, D9...)
ZINC IONnon-polymer65.416Chemie (ZN)
88BRA, CHB
(1, 5)
SPARSOMYCINnon-polymer361.42Chemie (SPS)
89BPC, CRA, DPC, SKC
(B, 1, C, 5)
PROLINEnon-polymer115.14Chemie (PRO)Saccharomyces cerevisiae S288c
90FPC, GPC
(5, f)
waterwater18.012Chemie (HOH)
Sequence modifications
C0, c0: 1 - 105 (UniProt: Q08745)
PDBExternal DatabaseDetails
Ala 89Gly 89conflict
C1, c1: 2 - 156 (UniProt: P0CX47)
PDBExternal DatabaseDetails
Ala 147Gly 147conflict
C2, c2: 2 - 143 (UniProt: P48589)
PDBExternal DatabaseDetails
Ala 104Gly 104conflict
Ala 110Gly 110conflict
L8, l8: 2 - 256 (UniProt: P17076)
PDBExternal DatabaseDetails
Ala 119Gly 119conflict
M1, m1: 2 - 174 (UniProt: P0C0W9)
PDBExternal DatabaseDetails
Thr 3Ala 3conflict
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains165
Total formula weight6309313.5
Non-Polymers*Number of molecules2284
Total formula weight363556.0
All*Total formula weight6672869.5
*Water molecules are not included.

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PDB entries from 2025-06-18

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