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6WOO

CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(5)
25S ribosomal RNApolymer32711057318.61Saccharomyces cerevisiae (Baker's yeast)
2B
(7)
5S ribosomal RNApolymer12138951.11GenBank (1039024045)Saccharomyces cerevisiae (Baker's yeast)
3C
(8)
5.8S ribosomal rRNApolymer15750376.81GenBank (1675231216)Saccharomyces cerevisiae (Baker's yeast)
4D
(A)
uL2polymer24926858.91UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)
Saccharomyces cerevisiae (Baker's yeast)
5E
(B)
uL3polymer38443491.41UniProt (P14126)
Pfam (PF00297)
Saccharomyces cerevisiae (Baker's yeast)
6F
(C)
uL4polymer35938825.81UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)
Saccharomyces cerevisiae (Baker's yeast)
7G
(D)
uL18polymer29533562.61UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)
Saccharomyces cerevisiae (Baker's yeast)
8H
(E)
eL6polymer17519869.41UniProt (Q02326)
Pfam (PF01159)
Saccharomyces cerevisiae (Baker's yeast)
9I
(F)
uL30polymer22225240.41UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)
Saccharomyces cerevisiae (Baker's yeast)
10J
(G)
eL8polymer23325815.01UniProt (P17076)
Pfam (PF01248)
Saccharomyces cerevisiae (Baker's yeast)
11K
(H)
uL6polymer19121691.11UniProt (P51401)
Pfam (PF00347)
Saccharomyces cerevisiae (Baker's yeast)
12L
(I)
uL16polymer21624937.91UniProt (P41805)
Pfam (PF00252)
Saccharomyces cerevisiae (Baker's yeast)
13M
(J)
uL5polymer16819136.91UniProt (Q3E757)
Pfam (PF00281)
Pfam (PF00673)
Saccharomyces cerevisiae (Baker's yeast)
14N
(L)
eL13polymer19822473.01UniProt (Q12690)
Pfam (PF01294)
Saccharomyces cerevisiae (Baker's yeast)
15O
(M)
eL14polymer13614992.81UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)
Saccharomyces cerevisiae (Baker's yeast)
16P
(N)
eL15polymer20224222.01UniProt (P05748)
Pfam (PF00827)
Saccharomyces cerevisiae (Baker's yeast)
17Q
(O)
uL13polymer19722029.01UniProt (P26784)
Pfam (PF00572)
Saccharomyces cerevisiae (Baker's yeast)
18R
(P)
uL22polymer18020245.11UniProt (P05740)
Pfam (PF00237)
Saccharomyces cerevisiae (Baker's yeast)
19S
(Q)
eL18polymer18420421.01UniProt (P0CX49)
Pfam (PF17135)
Saccharomyces cerevisiae (Baker's yeast)
20T
(R)
eL19polymer18821631.11UniProt (P0CX82)
Pfam (PF01280)
Saccharomyces cerevisiae (Baker's yeast)
21U
(S)
eL20polymer16920138.41UniProt (P0CX23)
Pfam (PF01775)
Saccharomyces cerevisiae (Baker's yeast)
22V
(T)
eL21polymer15818034.91UniProt (Q02753)
Pfam (PF01157)
Saccharomyces cerevisiae (Baker's yeast)
23W
(U)
eL22polymer10011263.91UniProt (P05749)
Pfam (PF01776)
Saccharomyces cerevisiae (Baker's yeast)
24X
(V)
uL14polymer13214005.41UniProt (P0CX41)
Pfam (PF00238)
Saccharomyces cerevisiae (Baker's yeast)
25Y
(W)
eL24polymer627253.51UniProt (P04449)
Pfam (PF01246)
Saccharomyces cerevisiae (Baker's yeast)
26Z
(X)
uL23polymer12113771.21UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)
Saccharomyces cerevisiae (Baker's yeast)
27AA
(Y)
uL24polymer12514063.51UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)
Saccharomyces cerevisiae (Baker's yeast)
28BA
(Z)
eL27polymer13415366.11UniProt (P0C2H6)
Pfam (PF01777)
Saccharomyces cerevisiae (Baker's yeast)
29CA
(a)
uL15polymer14716559.41UniProt (P02406)
Pfam (PF00828)
Saccharomyces cerevisiae (Baker's yeast)
30DA
(b)
eL29polymer576489.61UniProt (P05747)
Pfam (PF01779)
Saccharomyces cerevisiae (Baker's yeast)
31EA
(c)
eL30polymer9710558.31UniProt (P14120)
Pfam (PF01248)
Saccharomyces cerevisiae (Baker's yeast)
32FA
(d)
eL31polymer10612292.41UniProt (P0C2H8)
Pfam (PF01198)
Saccharomyces cerevisiae (Baker's yeast)
33GA
(e)
eL32polymer12214022.51UniProt (P38061)
Pfam (PF01655)
Saccharomyces cerevisiae (Baker's yeast)
34HA
(f)
eL33polymer10511932.81UniProt (P05744)
Pfam (PF01247)
Saccharomyces cerevisiae (Baker's yeast)
35IA
(g)
eL34polymer12113671.21UniProt (P87262)
Pfam (PF01199)
Saccharomyces cerevisiae (Baker's yeast)
36JA
(h)
uL29polymer11613540.11UniProt (P0CX84)
Pfam (PF00831)
Saccharomyces cerevisiae (Baker's yeast)
37KA
(i)
eL36polymer9810919.01UniProt (P05745)
Pfam (PF01158)
Saccharomyces cerevisiae (Baker's yeast)
38LA
(j)
eL37polymer859629.11UniProt (P49166)
Pfam (PF01907)
Saccharomyces cerevisiae (Baker's yeast)
39MA
(k)
eL38polymer768643.31UniProt (P49167)
Pfam (PF01781)
Saccharomyces cerevisiae (Baker's yeast)
40NA
(l)
eL39polymer496114.31UniProt (P04650)
Pfam (PF00832)
Saccharomyces cerevisiae (Baker's yeast)
41OA
(m)
eL40polymer515919.21UniProt (P0CH08)
Pfam (PF01020)
Saccharomyces cerevisiae (Baker's yeast)
42PA
(n)
eL41polymer233138.01Saccharomyces cerevisiae (Baker's yeast)
43QA
(o)
eL42polymer10111655.91UniProt (P0CX27)
Pfam (PF00935)
Saccharomyces cerevisiae (Baker's yeast)
44RA
(p)
eL43polymer879611.41UniProt (P0CX25)
Pfam (PF01780)
Saccharomyces cerevisiae (Baker's yeast)
45SA
(q)
uL1polymer21724524.81UniProt (P0CX43)
Pfam (PF00687)
Saccharomyces cerevisiae (Baker's yeast)
46TA
(r)
uL10polymer19521474.71UniProt (P05317)
Pfam (PF00466)
Pfam (PF17777)
Saccharomyces cerevisiae (Baker's yeast)
47UA
(K)
L10polymer15212954.01Saccharomyces cerevisiae (Baker's yeast)
48VA
(AA)
uS2polymer20622852.21UniProt (P46654)
Pfam (PF00318)
Saccharomyces cerevisiae (Baker's yeast)
49WA
(BB)
eS1polymer21424410.31UniProt (P23248)
Pfam (PF01015)
Saccharomyces cerevisiae (Baker's yeast)
50XA
(CC)
uS5polymer21723213.01UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)
Saccharomyces cerevisiae (Baker's yeast)
51YA
(DD)
uS3polymer22324702.81UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)
Saccharomyces cerevisiae (Baker's yeast)
52ZA
(EE)
eS4polymer25729039.81UniProt (P0CX35)
Pfam (PF08071)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
Saccharomyces cerevisiae (Baker's yeast)
53AB
(FF)
uS7polymer20622908.31UniProt (A0A1L4AA68)
Pfam (PF00177)
Saccharomyces cerevisiae (Baker's yeast)
54BB
(GG)
eS6polymer22625895.11UniProt (P0CX37)
Pfam (PF01092)
Saccharomyces cerevisiae (Baker's yeast)
55CB
(HH)
eS7polymer18421000.51UniProt (P26786)
Pfam (PF01251)
Saccharomyces cerevisiae (Baker's yeast)
56DB
(II)
eS8polymer19922406.61UniProt (P0CX39)
Pfam (PF01201)
Saccharomyces cerevisiae (Baker's yeast)
57EB
(JJ)
uS4polymer18220965.41UniProt (P05755)
Pfam (PF00163)
Pfam (PF01479)
Saccharomyces cerevisiae (Baker's yeast)
58FB
(KK)
eS10polymer9611585.11UniProt (Q08745)
Pfam (PF03501)
Saccharomyces cerevisiae (Baker's yeast)
59GB
(LL)
uS17polymer14516561.41UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)
Saccharomyces cerevisiae (Baker's yeast)
60HB
(MM)
eS12polymer12413327.31UniProt (P48589)
Pfam (PF01248)
Saccharomyces cerevisiae (Baker's yeast)
61IB
(NN)
uS15polymer15016928.71UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)
Saccharomyces cerevisiae (Baker's yeast)
62JB
(OO)
uS11polymer12713446.41UniProt (P39516)
Pfam (PF00411)
Saccharomyces cerevisiae (Baker's yeast)
63KB
(PP)
uS19polymer10311651.81UniProt (Q01855)
Pfam (PF00203)
Saccharomyces cerevisiae (Baker's yeast)
64LB
(QQ)
uS19polymer14115659.21UniProt (P0CX51)
Pfam (PF00380)
Saccharomyces cerevisiae (Baker's yeast)
65MB
(RR)
eS17polymer12314110.41UniProt (P14127)
Pfam (PF00833)
Saccharomyces cerevisiae (Baker's yeast)
66NB
(SS)
uS13polymer13615928.31UniProt (P0CX55)
Pfam (PF00416)
Saccharomyces cerevisiae (Baker's yeast)
67OB
(TT)
eS19polymer14315810.91UniProt (P07280)
Pfam (PF01090)
Saccharomyces cerevisiae (Baker's yeast)
68PB
(UU)
uS10polymer10612076.11UniProt (P38701)
Pfam (PF00338)
Saccharomyces cerevisiae (Baker's yeast)
69QB
(VV)
eS21polymer879758.81UniProt (P0C0V8)
Pfam (PF01249)
Saccharomyces cerevisiae (Baker's yeast)
70RB
(WW)
uS8polymer12914518.91UniProt (P0C0W1)
Pfam (PF00410)
Saccharomyces cerevisiae (Baker's yeast)
71SB
(XX)
uS12polymer14415986.81UniProt (P0CX29)
Pfam (PF00164)
Saccharomyces cerevisiae (Baker's yeast)
72TB
(YY)
eS24polymer13415231.61UniProt (P0CX31)
Pfam (PF01282)
Saccharomyces cerevisiae (Baker's yeast)
73UB
(ZZ)
eS25polymer708001.41UniProt (Q3E792)
Pfam (PF03297)
Saccharomyces cerevisiae (Baker's yeast)
74VB
(aa)
eS26polymer9711023.01UniProt (P39939)
Pfam (PF01283)
Saccharomyces cerevisiae (Baker's yeast)
75WB
(bb)
eS27polymer818762.21UniProt (P35997)
Pfam (PF01667)
Saccharomyces cerevisiae (Baker's yeast)
76XB
(cc)
eS28polymer637116.31UniProt (Q3E7X9)
Pfam (PF01200)
Saccharomyces cerevisiae (Baker's yeast)
77YB
(dd)
uS14polymer536335.31UniProt (P41057)
Pfam (PF00253)
Saccharomyces cerevisiae (Baker's yeast)
78ZB
(ee)
eS30polymer536084.31UniProt (P0CX33)
Pfam (PF04758)
Saccharomyces cerevisiae (Baker's yeast)
79AC
(ff)
eS31polymer576457.71UniProt (P05759)
Pfam (PF01599)
Saccharomyces cerevisiae (Baker's yeast)
80BC
(gg)
RACK1polymer31834710.01UniProt (P38011)
Pfam (PF00400)
Saccharomyces cerevisiae (Baker's yeast)
81CC
(2)
18S ribosomal RNApolymer1796578475.11GenBank (1329886537)Saccharomyces cerevisiae (Baker's yeast)
82DC
(1)
eIF5Bpolymer60067068.31UniProt (P39730)
Pfam (PF00009)
Pfam (PF11987)
Pfam (PF14578)
Saccharomyces cerevisiae (Baker's yeast)
83EC
(3)
Met-tRNA-iMetpolymer7624583.71GenBank (176433)Saccharomyces cerevisiae (Baker's yeast)
84FC
(4)
mRNApolymer61923.21Saccharomyces cerevisiae
85GC, HC, IC, JC, KC...
(j, m, o, aa, bb...)
ZINC IONnon-polymer65.46Chemie (ZN)
86MC
(1)
GUANOSINE-5'-DIPHOSPHATEnon-polymer443.21Chemie (GDP)
87NC
(3)
N-carboxy-L-threoninenon-polymer163.11Chemie (U6A)
88OC
(3)
METHIONINEnon-polymer149.21Chemie (MET)
Sequence modifications
H: 1 - 190 (UniProt: P51401)
PDBExternal DatabaseDetails
Glu 191-insertion
g: 2 - 121 (UniProt: P87262)
PDBExternal DatabaseDetails
Lys 122-insertion
j: 2 - 83 (UniProt: P49166)
PDBExternal DatabaseDetails
Lys 84-insertion
Ala 85-insertion
Gln 86-insertion
KK: 1 - 96 (UniProt: Q08745)
PDBExternal DatabaseDetails
Ala 89Gly 89conflict
LL: 2 - 145 (UniProt: P0CX47)
PDBExternal DatabaseDetails
Thr 146-insertion
2: 1 - 1798 (GenBank: 1329886537)
PDBExternal DatabaseDetails
A 677G 469479conflict
U 678A 469478conflict
3: 1 - 76 (GenBank: 176433)
PDBExternal DatabaseDetails
G 17-insertion
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains84
Total formula weight3120152.6
Non-Polymers*Number of molecules9
Total formula weight1148.0
All*Total formula weight3121300.6
*Water molecules are not included.

237735

PDB entries from 2025-06-18

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