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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

8RJC

Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 1

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(1)		Protein transport protein Sec61 subunit alpha isoform 1polymer47652279.41UniProt (P38377)
Pfam (PF10559)
Pfam (PF00344)		Canis lupus familiaris (dog)Sec61 alpha-1
2B
(2)		Protein transport protein Sec61 subunit betapolymer969987.51UniProt (P60467)
Pfam (PF03911)		Canis lupus familiaris (dog)
3C
(3)		Protein transport protein Sec61 subunit gammapolymer687752.31UniProt (P60058)
Pfam (PF00584)		Canis lupus familiaris (dog)
4D
(4)		Stress-associated endoplasmic reticulum proteinpolymer667384.81UniProt (A0A8C0RGL8)
Pfam (PF06624)
UniProt (by SIFTS) (A0A8I3PRN4)		Canis lupus familiaris (dog)
5E
(5)		Translocon-associated protein subunit alphapolymer28632002.81UniProt (P16967)
Pfam (PF03896)		Canis lupus familiaris (dog)TRAP-alpha,PGP35,Signal sequence receptor subunit alpha,SSR-alpha
6F
(6)		Translocon-associated protein subunit betapolymer18320121.01UniProt (P23438)
Pfam (PF05753)		Canis lupus familiaris (dog)TRAP-beta,Glycoprotein 25H,gp25H,Signal sequence receptor subunit beta,SSR-beta
7G
(7)		Translocon-associated protein subunit gammapolymer18521090.51UniProt (A0A8C0T6I4)
Pfam (PF07074)		Canis lupus familiaris (dog)Signal sequence receptor subunit gamma
8H
(8)		Translocon-associated protein subunit deltapolymer17318959.51UniProt (A0A8I3PXW2)
Pfam (PF05404)		Canis lupus familiaris (dog)Signal sequence receptor subunit delta
9I
(9)		Calnexinpolymer59367687.21UniProt (P24643)
Pfam (PF00262)		Canis lupus familiaris (dog)pp90
10J
(A)		Ribosomal protein L8polymer25728088.91UniProt (G1TT27)
Pfam (PF00181)
Pfam (PF03947)		Oryctolagus cuniculus (rabbit)
11K
(B)		Nascent chainpolymer22923488.71UniProt (by SIFTS) (P02699)Bos taurus
12L
(C)		Large ribosomal subunit protein uL4polymer42547727.61UniProt (A0A5F9C3C5)
Pfam (PF00573)
Pfam (PF14374)
UniProt (by SIFTS) (G1SVW5)		Oryctolagus cuniculus (rabbit)60S ribosomal protein L4
13M
(D)		Ribosomal_L18_c domain-containing proteinpolymer29734481.81UniProt (G1SYJ6)
UniProt (by SIFTS) (P19949)		Oryctolagus cuniculus (rabbit)60S ribosomal protein L5
14N
(E)		60S ribosomal protein L6polymer29133028.31UniProt (G1SKF7)
Pfam (PF03868)
Pfam (PF01159)		Oryctolagus cuniculus (rabbit)
15O
(F)		Ribosomal Protein uL30polymer24729201.81UniProt (G1TUB1)
Pfam (PF08079)
Pfam (PF00327)
UniProt (by SIFTS) (G1SV32)		Oryctolagus cuniculus (rabbit)
16P
(G)		60S ribosomal protein L7apolymer31936221.51UniProt (G1STW0)
Pfam (PF01248)		Oryctolagus cuniculus (rabbit)
17Q
(H)		60S ribosomal protein L9polymer19221871.41UniProt (G1SWI6)
Pfam (PF00347)		Oryctolagus cuniculus (rabbit)
18R
(I)		60S ribosomal protein L10polymer21424643.11UniProt (B7NZQ2)
Pfam (PF00252)		Oryctolagus cuniculus (rabbit)Ribosomal protein L10
19S
(J)		60S ribosomal protein L11polymer17820288.51UniProt (G1TUB8)
Pfam (PF00281)
Pfam (PF00673)		Oryctolagus cuniculus (rabbit)
20T
(K)		28S rRNApolymer35431148115.41Oryctolagus cuniculus
21U
(L)		60S ribosomal protein L13polymer21124331.71UniProt (G1TKB3)
Pfam (PF01294)		Oryctolagus cuniculus (rabbit)
22V
(M)		60S ribosomal protein L14polymer21823870.51UniProt (G1SZ12)
Pfam (PF01929)		Oryctolagus cuniculus (rabbit)
23W
(N)		Ribosomal protein L15polymer20424207.31UniProt (G1T0C1)
Pfam (PF00827)		Oryctolagus cuniculus (rabbit)
24X
(O)		60S ribosomal protein L13polymer20323533.31UniProt (by SIFTS) (G1TVS8)Oryctolagus cuniculus (rabbit)
25Y
(P)		uL22polymer18421444.21UniProt (G1TVT6)
Pfam (PF00237)
UniProt (by SIFTS) (G1SCJ6)		Oryctolagus cuniculus (rabbit)
26Z
(Q)		Ribosomal protein L18polymer18721568.51UniProt (G1TFE0)
Pfam (PF17135)		Oryctolagus cuniculus (rabbit)
27AA
(R)		Ribosomal protein L19polymer19623535.31UniProt (G1TJR3)
Pfam (PF01280)		Oryctolagus cuniculus (rabbit)
28BA
(S)		60S ribosomal protein L18apolymer17620827.61UniProt (A0A287APR1)
Pfam (PF01775)
UniProt (by SIFTS) (G1TTY7)		Oryctolagus cuniculus (rabbit)
29CA
(T)		60S ribosomal protein L21polymer16018610.01UniProt (G1SHQ2)
Pfam (PF01157)		Oryctolagus cuniculus (rabbit)eL21
30DA
(U)		Ribosomal protein L22polymer12814813.01UniProt (G1TSG1)
Pfam (PF01776)		Oryctolagus cuniculus (rabbit)
31EA
(V)		Ribosomal protein L23polymer14014892.51UniProt (G1T6D1)
Pfam (PF00238)		Oryctolagus cuniculus (rabbit)
32FA
(W)		Ribosomal protein L24polymer15717825.11UniProt (G1SE28)
Pfam (PF01246)		Oryctolagus cuniculus (rabbit)eL24
33GA
(X)		Ribosomal_L23eN domain-containing proteinpolymer15617768.21UniProt (G1SE76)
Pfam (PF03939)
Pfam (PF00276)		Oryctolagus cuniculus (rabbit)uL23
34HA
(Y)		Ribosomal protein L26polymer14517303.41UniProt (G1SQH0)
Pfam (PF16906)
Pfam (PF00467)		Oryctolagus cuniculus (rabbit)
35IA
(Z)		60S ribosomal protein L27polymer13615835.81UniProt (G1TXF6)
Pfam (PF00467)
Pfam (PF01777)		Oryctolagus cuniculus (rabbit)
36JA
(a)		60S ribosomal protein L27apolymer14816620.61UniProt (G1SNY0)
Pfam (PF00828)		Oryctolagus cuniculus (rabbit)uL15
37KA
(b)		60S ribosomal protein L29polymer22624931.61UniProt (G1SGR6)
Pfam (PF01779)		Oryctolagus cuniculus (rabbit)eL29
38LA
(c)		60S ribosomal protein L30polymer11512807.11UniProt (G1TDL2)
Pfam (PF01248)		Oryctolagus cuniculus (rabbit)eL30
39MA
(d)		60S ribosomal protein L31polymer12514494.91UniProt (G1SHG0)
Pfam (PF01198)		Oryctolagus cuniculus (rabbit)eL31
40NA
(e)		Ribosomal protein L32polymer13515898.91UniProt (G1U437)
Pfam (PF01655)
UniProt (by SIFTS) (G1TUN8)		Oryctolagus cuniculus (rabbit)eL32
41OA
(f)		60S ribosomal protein L35apolymer11012580.81UniProt (G1SF08)
Pfam (PF01247)		Oryctolagus cuniculus (rabbit)eL33
42PA
(g)		60S ribosomal protein L34polymer11613196.91UniProt (G1U945)
Pfam (PF01199)
UniProt (by SIFTS) (G1TXG5)		Oryctolagus cuniculus (rabbit)eL34
43QA
(h)		60S ribosomal protein L35polymer12314566.61UniProt (G1SIT5)
Pfam (PF00831)		Oryctolagus cuniculus (rabbit)uL29
44RA
(i)		60S ribosomal protein L36polymer10512263.81UniProt (G1TTQ5)
Pfam (PF01158)		Oryctolagus cuniculus (rabbit)
45SA
(j)		Ribosomal protein L37polymer9711111.01UniProt (U3KPD5)
Pfam (PF01907)		Oryctolagus cuniculus (rabbit)
46TA
(k)		60S ribosomal protein L38polymer708238.91UniProt (G1U001)
Pfam (PF01781)		Oryctolagus cuniculus (rabbit)eL38
47UA
(l)		60S ribosomal protein L39-likepolymer516455.81UniProt (G1TTN1)
Pfam (PF00832)		Oryctolagus cuniculus (rabbit)eL39
48VA
(m)		eL40polymer10211699.81UniProt (by SIFTS) (P0DXC2)Oryctolagus cuniculus
49WA
(n)		60S ribosomal protein L41polymer253473.51UniProt (A0A087WNH4)
Pfam (PF05162)		Oryctolagus cuniculus (rabbit)
50XA
(o)		60S ribosomal protein L36a-likepolymer10612477.01UniProt (G1U344)
Pfam (PF00935)
UniProt (by SIFTS) (G1T040)		Oryctolagus cuniculus (rabbit)eL42
51YA
(p)		60S ribosomal protein L37apolymer9210299.41UniProt (G1SY53)
Pfam (PF01780)		Oryctolagus
52ZA
(q)		P-site tRNApolymer7624436.61Sus scrofa
53AB
(r)		60S ribosomal protein L28polymer13715783.61UniProt (G1U7L1)
Pfam (PF01778)		Oryctolagus cuniculus (rabbit)eL28
54BB
(u)		5S rRNApolymer12038691.91GenBank (4CXE_4)Oryctolagus cuniculus (rabbit)
55CB
(v)		5.8S rRNApolymer15650143.61GenBank (4CXE_3)Oryctolagus cuniculus (rabbit)
56DB
(w)		Ribosomal protein L3polymer40346108.01UniProt (G1TL06)
Pfam (PF00297)		Oryctolagus cuniculus (rabbit)uL3
57AC, AD, AE, AF, AG...
(K, g, j, I, u...)		MAGNESIUM IONnon-polymer24.3218Chemie (MG)
58BJ, DJ, EJ, FJ, GJ
(g, j, m, o, p)		ZINC IONnon-polymer65.45Chemie (ZN)
Sequence modifications
F: 1 - 247 (UniProt: G1TUB1)
PDBExternal DatabaseDetails
Arg 61Gly 61conflict
Arg 93Gly 93conflict
Met 131Val 131conflict
Ile 153Val 153conflict
G: 1 - 319 (UniProt: G1STW0)
PDBExternal DatabaseDetails
Gly 244Cys 244conflict
L: 1 - 211 (UniProt: G1TKB3)
PDBExternal DatabaseDetails
Arg 74His 74conflict
Arg 190His 190conflict
Q: 2 - 188 (UniProt: G1TFE0)
PDBExternal DatabaseDetails
Asp 4Asn 4conflict
Arg 14Trp 14conflict
Met 53Leu 53conflict
Arg 58Trp 58conflict
Arg 75Gln 75conflict
Ala 80Pro 80conflict
Val 86Ile 86conflict
Arg 104His 104conflict
Arg 110Cys 110conflict
Val 137Gly 137conflict
Gly 157Arg 157conflict
Arg 181Trp 181conflict
R: 1 - 196 (UniProt: G1TJR3)
PDBExternal DatabaseDetails
Arg 38Cys 38conflict
Arg 64Gln 64conflict
Thr 94Lys 94conflict
U: 1 - 128 (UniProt: G1TSG1)
PDBExternal DatabaseDetails
Leu 18Val 18conflict
Gly 32Arg 32conflict
Ala 36Glu 36conflict
Phe 39Ser 39conflict
Gly 54Arg 54conflict
Val 60Ala 60conflict
Ser 62Thr 62conflict
Leu 63Ile 63conflict
Arg 97His 97conflict
Thr 106Ser 106conflict
Glu 126Asp 126conflict
k: 1 - 70 (UniProt: G1U001)
PDBExternal DatabaseDetails
Lys 24Asn 24conflict
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains56
Total formula weight2361068.5
Non-Polymers*Number of molecules223
Total formula weight5625.5
All*Total formula weight2366694.1
*Water molecules are not included.

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PDB entries from 2025-06-11

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