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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

7OYD

Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1xRibosomal protein uL1polymer21724875.41UniProt (G1SKZ8)
Pfam (PF00687)
In PDB		Oryctolagus cuniculus (rabbit)
2528S rRNApolymer37401213395.51Oryctolagus cuniculus (rabbit)
385.8S rRNApolymer15650157.71GenBank (4CXE_3)Oryctolagus cuniculus (rabbit)
4918S rRNApolymer1786576826.81Oryctolagus cuniculus (rabbit)
5A60S ribosomal protein L8polymer25728088.91Oryctolagus cuniculus (rabbit)
6AA40S ribosomal protein SApolymer29532958.01UniProt (G1TLT8)
Pfam (PF00318)
Pfam (PF16122)
In PDB		Oryctolagus cuniculus (rabbit)37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40
7Aa40S ribosomal protein S26-likepolymer11513047.51Oryctolagus cuniculus (rabbit)
8BRibosomal protein L3polymer40346108.01UniProt (G1TL06)
Pfam (PF00297)
In PDB		Oryctolagus cuniculus (rabbit)uL3
9BB40S ribosomal protein S3apolymer26430002.11UniProt (G1SS70)
Pfam (PF01015)
In PDB		Oryctolagus cuniculus (rabbit)RPS3A
10Bb40S ribosomal protein S27polymer849480.21UniProt (G1TZ76)
Pfam (PF01667)
In PDB		Oryctolagus cuniculus (rabbit)
11C60S ribosomal protein L4polymer41346401.91UniProt (G1SVW5)
Pfam (PF00573)
Pfam (PF14374)
In PDB		Oryctolagus cuniculus (rabbit)
12CC40S ribosomal protein S2polymer29331287.41Oryctolagus cuniculus (rabbit)
13Cc40S ribosomal protein S28polymer697855.11UniProt (G1TIB4)
Pfam (PF01200)
In PDB		Oryctolagus cuniculus (rabbit)
14D60S ribosomal protein L5polymer29734481.81UniProt (G1SYJ6)
UniProt (by SIFTS) (P19949)
In PDB		Oryctolagus cuniculus (rabbit)
15DDRibosomal protein S3polymer24326715.31UniProt (G1TNM3)
Pfam (PF07650)
Pfam (PF00189)
In PDB		Oryctolagus cuniculus (rabbit)
16Dd40S ribosomal protein S29polymer566690.81UniProt (G1U7M4)
Pfam (PF00253)
In PDB		Oryctolagus cuniculus (rabbit)uS14
17E60S ribosomal protein L6polymer29133028.31UniProt (G1SKF7)
Pfam (PF03868)
Pfam (PF01159)
In PDB		Oryctolagus cuniculus (rabbit)
18EE40S ribosomal protein S4polymer26329654.91UniProt (G1TK17)
Pfam (PF08071)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
In PDB		Oryctolagus cuniculus (rabbit)
19Ee40S ribosomal protein S30polymer13314498.91UniProt (G1T8A2)
Pfam (PF00240)
Pfam (PF04758)
In PDB		Oryctolagus cuniculus (rabbit)
20F60S ribosomal protein L7polymer24929514.31UniProt (G1SV32)
Pfam (PF08079)
Pfam (PF00327)
In PDB		Oryctolagus cuniculus (rabbit)uL30
21FFRibosomal protein S5polymer20422913.51UniProt (G1TFM5)
Pfam (PF00177)
In PDB		Oryctolagus cuniculus (rabbit)
22G60S ribosomal protein L7apolymer26630089.81Oryctolagus cuniculus (rabbit)
23GG40S ribosomal protein S6polymer24928751.91UniProt (G1TM55)
Pfam (PF01092)
In PDB		Oryctolagus cuniculus (rabbit)
24GgRACK1polymer31735115.71UniProt (G1SJB4)
Pfam (PF00400)
In PDB		Oryctolagus cuniculus (rabbit)WD_REPEATS_REGION domain-containing protein
25H60S ribosomal protein L9polymer19221871.41UniProt (G1SWI6)
Pfam (PF00347)
In PDB		Oryctolagus cuniculus (rabbit)
26HH40S ribosomal protein S7polymer43247356.21UniProt (G1SVB0)
In PDB		Oryctolagus cuniculus (rabbit)
27I60S ribosomal protein L10polymer21424643.11UniProt (B7NZQ2)
Pfam (PF00252)
In PDB		Oryctolagus cuniculus (rabbit)Ribosomal protein L10
28II40S ribosomal protein S8polymer20824263.41UniProt (G1TJW1)
Pfam (PF01201)
In PDB		Oryctolagus cuniculus (rabbit)
29J60S ribosomal protein L11polymer17820288.51UniProt (G1TUB8)
Pfam (PF00281)
Pfam (PF00673)
In PDB		Oryctolagus cuniculus (rabbit)
30JJ40S ribosomal protein S9polymer19422641.61UniProt (B7NZS8)
Pfam (PF00163)
Pfam (PF01479)
In PDB		Oryctolagus cuniculus (rabbit)
31K5S rRNApolymer12038691.91GenBank (4CXE_4)Oryctolagus cuniculus (rabbit)
32KKS10_plectin domain-containing proteinpolymer16518933.81UniProt (G1TPV3)
Pfam (PF03501)
In PDB		Oryctolagus cuniculus (rabbit)eS10
33L60S ribosomal protein L13polymer21124331.71UniProt (G1TKB3)
Pfam (PF01294)
In PDB		Oryctolagus cuniculus (rabbit)L13
34LL40S ribosomal protein S11polymer15818468.81UniProt (G1TRM4)
Pfam (PF16205)
Pfam (PF00366)
In PDB		Oryctolagus cuniculus (rabbit)
35M60S ribosomal protein L14polymer21823810.41UniProt (U3KNW6)
Pfam (PF01929)
UniProt (by SIFTS) (G1SZ12)
In PDB		Oryctolagus cuniculus (rabbit)
36NRibosomal protein L15polymer20424207.31UniProt (G1T0C1)
Pfam (PF00827)
In PDB		Oryctolagus cuniculus (rabbit)
37NN40S ribosomal protein S13polymer15117259.41UniProt (G1SP51)
Pfam (PF08069)
Pfam (PF00312)
In PDB		Oryctolagus cuniculus (rabbit)uS15
38O60S ribosomal protein L13apolymer20323575.41Oryctolagus cuniculus (rabbit)
39OO40S ribosomal protein S14-likepolymer15116288.71Oryctolagus cuniculus (rabbit)
40P60S ribosomal protein L17polymer18721741.61UniProt (G1SCJ6)
Pfam (PF00237)
In PDB		Oryctolagus cuniculus (rabbit)
41PP40S ribosomal protein uS19polymer14517049.21UniProt (G1U0Q2)
Pfam (PF00203)
In PDB		Oryctolagus cuniculus (rabbit)
42QRibosomal protein L18polymer18821699.71Oryctolagus cuniculus (rabbit)
43QQRibosomal protein S16polymer14616477.41UniProt (G1SGX4)
Pfam (PF00380)
In PDB		Oryctolagus cuniculus (rabbit)
44RRibosomal protein L19polymer19623535.31UniProt (G1TYL6)
Pfam (PF01280)
In PDB		Oryctolagus cuniculus (rabbit)
45RR40S ribosomal protein eS17polymer13515552.11UniProt (G1TU13)
Pfam (PF00833)
In PDB		Oryctolagus cuniculus (rabbit)
46S60S ribosomal protein L18apolymer22426103.41Oryctolagus cuniculus (rabbit)
47SS40S ribosomal protein uS13polymer15217759.81UniProt (G1TPG3)
Pfam (PF00416)
In PDB		Oryctolagus cuniculus (rabbit)
48T60S ribosomal protein L21polymer16018610.01UniProt (G1SHQ2)
Pfam (PF01157)
In PDB		Oryctolagus cuniculus (rabbit)eL21
49TT40S ribosomal protein S19polymer14516106.61UniProt (G1TN62)
Pfam (PF01090)
In PDB		Oryctolagus cuniculus (rabbit)RPS19
50U60S ribosomal protein L22-likepolymer14116330.81Oryctolagus cuniculus (rabbit)
51UU40S ribosomal protein uS10polymer11913398.81UniProt (G1SIZ2)
Pfam (PF00338)
In PDB		Oryctolagus cuniculus (rabbit)
52VRibosomal protein L23polymer14014892.51UniProt (G1T6D1)
Pfam (PF00238)
In PDB		Oryctolagus cuniculus (rabbit)
53VV40S ribosomal protein S21polymer839124.41Oryctolagus cuniculus (rabbit)
54WRibosomal protein L24polymer15717825.11UniProt (G1SE28)
Pfam (PF01246)
In PDB		Oryctolagus cuniculus (rabbit)eL24
55WWRibosomal protein S15apolymer13014865.61UniProt (G1TG89)
Pfam (PF00410)
In PDB		Oryctolagus cuniculus (rabbit)
56X60S ribosomal protein L23apolymer15617740.21Oryctolagus cuniculus (rabbit)
57XX40S ribosomal protein S23polymer14315844.71UniProt (G1SZ47)
Pfam (PF00164)
In PDB		Oryctolagus cuniculus (rabbit)RPS23
58YRibosomal protein L26polymer14517303.41UniProt (G1SQH0)
Pfam (PF16906)
Pfam (PF00467)
In PDB		Oryctolagus cuniculus (rabbit)
59YY40S ribosomal protein S24polymer13315463.31UniProt (A0A5F9D2E6)
Pfam (PF01282)
In PDB		Oryctolagus cuniculus (rabbit)
60Z60S ribosomal protein L27polymer13615835.81UniProt (G1TXF6)
Pfam (PF00467)
Pfam (PF01777)
In PDB		Oryctolagus cuniculus (rabbit)
61ZZ40S ribosomal protein S25polymer12413645.01UniProt (G1TDB3)
Pfam (PF03297)
In PDB		Oryctolagus cuniculus (rabbit)
62a60S ribosomal protein L27apolymer14816620.61UniProt (G1SNY0)
Pfam (PF00828)
In PDB		Oryctolagus cuniculus (rabbit)uL15
63b60S ribosomal protein L29polymer24526708.71UniProt (G1SGR6)
Pfam (PF01779)
In PDB		Oryctolagus cuniculus (rabbit)
64c60S ribosomal protein L30polymer11512807.11UniProt (G1TDL2)
Pfam (PF01248)
In PDB		Oryctolagus cuniculus (rabbit)eL30
65d60S ribosomal protein L31polymer12514494.91UniProt (G1SHG0)
Pfam (PF01198)
In PDB		Oryctolagus cuniculus (rabbit)eL31
66e60S ribosomal protein L32polymer15718350.01UniProt (G1TUN8)
Pfam (PF01655)
In PDB		Oryctolagus cuniculus (rabbit)eL32
67f60S ribosomal protein L35apolymer11012580.81UniProt (G1SF08)
Pfam (PF01247)
In PDB		Oryctolagus cuniculus (rabbit)eL33
68g60S ribosomal protein L34polymer11713326.11UniProt (G1TXG5)
Pfam (PF01199)
In PDB		Oryctolagus cuniculus (rabbit)
69h60S ribosomal protein L35polymer12314566.61UniProt (G1SIT5)
Pfam (PF00831)
In PDB		Oryctolagus cuniculus (rabbit)uL29
70i60S ribosomal protein L36polymer10512263.81UniProt (G1TTQ5)
Pfam (PF01158)
In PDB		Oryctolagus cuniculus (rabbit)
71jRibosomal protein L37polymer9711111.01UniProt (U3KPD5)
Pfam (PF01907)
In PDB		Oryctolagus cuniculus (rabbit)
72k60S ribosomal protein L38polymer708238.91UniProt (G1U001)
Pfam (PF01781)
In PDB		Oryctolagus cuniculus (rabbit)eL38
73l60S ribosomal protein L39-likepolymer516455.81UniProt (G1TTN1)
Pfam (PF00832)
In PDB		Oryctolagus cuniculus (rabbit)eL39
74mUbiquitin-60S ribosomal protein L40polymer12814771.41Oryctolagus cuniculus (rabbit)
75n60s ribosomal protein l41polymer253473.51UniProt (A0A087WNH4)
Pfam (PF05162)
In PDB		Oryctolagus cuniculus (rabbit)eL41
76o60S ribosomal protein L36a-likepolymer10612477.01UniProt (G1U344)
Pfam (PF00935)
UniProt (by SIFTS) (G1T040)
In PDB		Oryctolagus cuniculus (rabbit)RPL36A
77p60S ribosomal protein L37apolymer9210299.41UniProt (G1SY53)
Pfam (PF01780)
In PDB		Oryctolagus cuniculus (rabbit)eL43
78r60S ribosomal protein L28polymer13715783.61UniProt (G1U7L1)
Pfam (PF01778)
In PDB		Oryctolagus cuniculus (rabbit)eL28
79s60S ribosomal protein L10Epolymer31834394.51Oryctolagus cuniculus (rabbit)
80s1Dap1bpolymer10912128.11UniProt (Q9I9N0)
Pfam (PF15228)
In PDB		Danio rerio (zebrafish)Death-associated protein 1b
81tEukaryotic translation initiation factor 5A-1polymer15416954.31UniProt (P10160)
Pfam (PF21485)
Pfam (PF01287)
In PDB		Oryctolagus cuniculus (rabbit)eIF-5A-1,eIF-5A1,Eukaryotic initiation factor 5A isoform 1,eIF-5A,eIF-4D
82vElongation factor 2polymer85895605.41Oryctolagus cuniculus (rabbit)
83wSERPINE1 mRNA binding protein 1polymer40744880.41UniProt (G1SW77)
Pfam (PF16174)
Pfam (PF04774)
In PDB		Oryctolagus cuniculus (rabbit)
845, v, 8, I, P...MAGNESIUM IONnon-polymer24.3201Chemie (MG)
85j, m, o, p, Aa...ZINC IONnon-polymer65.47Chemie (ZN)
Sequence modifications
AA: 1 - 295 (UniProt: G1TLT8)
PDBExternal DatabaseDetails
Thr 114Ala 114conflict
D: 2 - 297 (UniProt: G1SYJ6)
PDBExternal DatabaseDetails
Met 1-initiating methionine
EE: 1 - 263 (UniProt: G1TK17)
PDBExternal DatabaseDetails
Gly 25Ser 25conflict
Arg 51Lys 51conflict
Thr 78Ala 78conflict
Val 156Met 156conflict
II: 1 - 208 (UniProt: G1TJW1)
PDBExternal DatabaseDetails
Arg 47Gly 47conflict
L: 1 - 211 (UniProt: G1TKB3)
PDBExternal DatabaseDetails
Arg 74His 74conflict
Arg 190His 190conflict
R: 1 - 196 (UniProt: G1TYL6)
PDBExternal DatabaseDetails
Arg 38His 38conflict
Arg 151His 151conflict
TT: 1 - 145 (UniProt: G1TN62)
PDBExternal DatabaseDetails
Gly 119Trp 119conflict
k: 1 - 70 (UniProt: G1U001)
PDBExternal DatabaseDetails
Lys 24Asn 24conflict
t: 2 - 155 (UniProt: P10160)
PDBExternal DatabaseDetails
Ser 36Gly 35conflict
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains83
Total formula weight3573767.7
Non-Polymers*Number of molecules208
Total formula weight5343.2
All*Total formula weight3579110.9
*Water molecules are not included.

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PDB entries from 2024-09-04

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