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5DAT

Complex of yeast 80S ribosome with hypusine-containing eIF5A

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 RNApolymer1800579761.92REF (831416132)Saccharomyces cerevisiae S288c (Baker's yeast)
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 (PF08071)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
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-Apolymer10512757.42UniProt (Q08745)
Pfam (PF03501)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
13M, NC
(C1, c1)
40S ribosomal protein S11-Apolymer15517654.72UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)
Saccharomyces cerevisiae (Baker's yeast)RP41,S18,YS12
14N, OC
(C2, c2)
40S ribosomal protein S12polymer12413327.32UniProt (P48589)
Pfam (PF01248)
Saccharomyces cerevisiae (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 S15polymer13715448.12UniProt (Q01855)
Pfam (PF00203)
Saccharomyces cerevisiae (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
(D2)
40S ribosomal protein S22-Apolymer12914518.91UniProt (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-Bpolymer9711023.02UniProt (P39939)
Pfam (PF01283)
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-Apolymer627006.32UniProt (P0CX33)
Pfam (PF04758)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
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 RNApolymer33961097493.92REF (831416132)Saccharomyces cerevisiae S288c (Baker's yeast)
37KA, LD
(3, 7)
5S ribosomal RNApolymer12138951.12GenBank (834774822)Saccharomyces cerevisiae S288c (Baker's yeast)
38LA, MD
(4, 8)
5.8S ribosomal RNApolymer15850682.92GenBank (940534893)Saccharomyces cerevisiae S288c (Baker's yeast)
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 (PF08079)
Pfam (PF00327)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L6,RP11,YL8
45SA, TD
(L8, l8)
60S ribosomal protein L8-Apolymer25528044.62UniProt (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-Bpolymer17319654.52UniProt (Q3E757)
Pfam (PF00281)
Pfam (PF00673)
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)
51YA
(M5)
60S ribosomal protein L15-Apolymer20424480.31UniProt (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-A (eL34)polymer11913412.82UniProt (P87262)
Pfam (PF01199)
Saccharomyces cerevisiae S288c (Baker's yeast)
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
80YC
(d2)
40S ribosomal protein S22-Apolymer13014682.01UniProt (P0C0W1)
Pfam (PF00410)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP50,S24,YP58,YS22
81XD
(m2)
60S ribosomal protein L12-A (uL11)polymer15012783.81Saccharomyces cerevisiae S288c (Baker's yeast)
82AE
(m5)
60S ribosomal protein L15-Apolymer20324351.21UniProt (P05748)
Pfam (PF00827)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13,RP15R,YL10,YP18
83DF
(p0)
60S acidic ribosomal protein P0polymer22024101.71UniProt (P05317)
Pfam (PF00466)
Pfam (PF17777)
Saccharomyces cerevisiae S288c (Baker's yeast)A0,L10E
84EF, FF
(p1, p2)
60S ribosomal protein P1 alpha/P2 betapolymer474017.92Saccharomyces cerevisiae S288c (Baker's yeast)
85GF
(f)
Eukaryotic translation initiation factor 5A-1polymer15717222.41UniProt (P23301)
Pfam (PF21485)
Pfam (PF01287)
Saccharomyces cerevisiae S288c (Baker's yeast)eIF-5A-1,Hypusine-containing protein HP2,eIF-4D
86HF
(l1)
60S ribosomal protein L1-A (uL1)polymer21318145.31Saccharomyces cerevisiae S288c (Baker's yeast)
87AAA, ABA, ACA, ADA, AG...
(1, 2, c7, 5, 7...)
MAGNESIUM IONnon-polymer24.31108Chemie (MG)
88AAB, AAC, ABB, ABC, ACB...
(6, 5, 1, 2, 8...)
osmium (III) hexamminenon-polymer286.41166Chemie (OHX)
89APC, EHB, EPC, EVA, GHB...
(q0, d6, q2, O7, d7...)
ZINC IONnon-polymer65.416Chemie (ZN)
90KPC, LPC
(5, f)
waterwater18.012Chemie (HOH)
Sequence modifications
M5: 2 - 205 (UniProt: P05748)
PDBExternal DatabaseDetails
Lys 170-insertion
d2: 2 - 131 (UniProt: P0C0W1)
PDBExternal DatabaseDetails
Tyr 47-insertion
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains164
Total formula weight6291702.2
Non-Polymers*Number of molecules2290
Total formula weight361878.1
All*Total formula weight6653580.2
*Water molecules are not included.

240291

PDB entries from 2025-08-13

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