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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

8RJD

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

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 (G1TPV0)
Pfam (PF01294)
UniProt (by SIFTS) (G1TKB3)		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 L13apolymer20323533.31UniProt (A0A0N8ETI8)
UniProt (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 (F6QKI9)
Pfam (PF17135)
UniProt (by SIFTS) (G1TFE0)		Oryctolagus cuniculus (rabbit)
27AA
(R)		Ribosomal protein L19polymer19623535.31UniProt (G1TYL6)
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)		Large ribosomal subunit protein eL22polymer12814813.01UniProt (Q4R5I3)
Pfam (PF01776)
UniProt (by SIFTS) (G1TSG1)		Oryctolagus cuniculus (rabbit)60S ribosomal protein L22
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)		Large ribosomal subunit protein uL23 N-terminal domain-containing proteinpolymer15617768.21UniProt (G1SE76)
Pfam (PF03939)
Pfam (PF00276)		Oryctolagus
34HA
(Y)		Ribosomal protein L26polymer14517303.41UniProt (G1SQH0)
Pfam (PF16906)
Pfam (PF00467)		Oryctolagus
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)		Large ribosomal subunit protein eL30polymer11512807.11UniProt (G1TDL2)
Pfam (PF01248)		Oryctolagus60S ribosomal protein L30
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)		Large ribosomal subunit protein eL38polymer708238.91UniProt (G1U001)
Pfam (PF01781)		Oryctolagus60S ribosomal protein L38
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 cuniculus (rabbit)eL43
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: G1TPV0)
PDBExternal DatabaseDetails
Met 1Arg 5conflict
Pro 3Leu 7conflict
Ser 4Ala 8conflict
Asn 6-insertion
Gly 7Ala 10conflict
Ile 9Arg 12conflict
Leu 10Arg 13conflict
Lys 11Leu 14conflict
Pro 12Ala 15conflict
His 13Lys 16conflict
Phe 14Ala 17conflict
His 15Leu 18conflict
Asp 17Phe 20conflict
Trp 18Phe 21conflict
Gln 19Ser 22conflict
Arg 20Ser 23conflict
Arg 21Ser 24conflict
Ala 23Ile 26conflict
Trp 25-insertion
Phe 26Leu 28conflict
Asn 27Ala 29conflict
Gln 28Phe 30conflict
Pro 29Ser 31conflict
Ala 30Phe 32conflict
Arg 31Leu 33conflict
Ile 33-insertion
Arg 34Thr 35conflict
Arg 35Phe 36conflict
Lys 37Met 38conflict
Ala 38Gly 39conflict
Arg 39Met 40conflict
Gln 40Thr 41conflict
Ala 41Gly 42conflict
Arg 42Pro 43conflict
Ala 43Val 44conflict
Arg 44Ser 45conflict
Arg 45Trp 46conflict
Ile 46Val 47conflict
Pro 48Asn 49conflict
Arg 49Phe 50conflict
Pro 50Ser 51conflict
Ala 51Ser 52conflict
Ala 52Ser 53conflict
Gly 53Ala 54conflict
Pro 54Glu 55conflict
Ile 55Leu 56conflict
Arg 56Ser 57conflict
Ile 58Phe 59conflict
Val 59Leu 60conflict
Arg 60Gly 61conflict
Cys 61Ala 62conflict
Pro 62Glu 63conflict
Thr 63Gly 64conflict
Val 64Phe 65conflict
Tyr 66-insertion
His 67-insertion
Thr 68Gly 67conflict
Val 70-insertion
Arg 71-insertion
Ala 72-insertion
Gly 73-insertion
Gly 75-insertion
Phe 76Thr 70conflict
Glu 80-insertion
Leu 81-insertion
Val 83Tyr 75conflict
Ala 84Ser 76conflict
Gly 85Phe 77conflict
Ile 86Ser 78conflict
His 87Arg 79conflict
Lys 88Cys 80conflict
Lys 89Thr 81conflict
Val 90Leu 82conflict
Arg 92-insertion
Thr 93-insertion
Ile 94Cys 84conflict
Gly 95Arg 85conflict
Ile 96Asp 86conflict
Pro 100Leu 90conflict
Arg 101Phe 91conflict
Asn 104Arg 94conflict
Lys 105Gly 95conflict
Ser 109Met 99conflict
Leu 110Pro 100conflict
Gln 111Ile 101conflict
Ala 112Val 102conflict
Asn 113Arg 103conflict
Val 114Ala 104conflict
Gln 115Thr 105conflict
Arg 116Phe 106conflict
-Trp 108deletion
-Met 109deletion
Lys 118Pro 110conflict
Glu 119Ala 111conflict
Tyr 120Thr 112conflict
Lys 123Ser 115conflict
Leu 124Ser 116conflict
Val 125Arg 117conflict
Phe 127Lys 119conflict
Lys 130Pro 122conflict
Pro 131Ala 123conflict
Ser 132Arg 124conflict
Ala 133Thr 125conflict
Pro 134Phe 126conflict
Lys 135Val 127conflict
Lys 136Trp 128conflict
Gly 137Tyr 129conflict
Asp 138Arg 130conflict
Ser 139Thr 131conflict
Ser 140Val 132conflict
Ala 141Gly 133conflict
Glu 142Gln 134conflict
Glu 143Arg 135conflict
Leu 144Thr 136conflict
Lys 145Met 137conflict
Leu 146Gly 138conflict
Ala 147Arg 139conflict
Thr 148Met 140conflict
Gln 149Gly 141conflict
Thr 151Ala 143conflict
Gly 152Pro 144conflict
Pro 153Ala 145conflict
Val 154Asp 146conflict
Met 155Leu 147conflict
Pro 156Ala 148conflict
Ile 157Arg 149conflict
Asn 159Leu 151conflict
Phe 161Glu 153conflict
Lys 162Pro 154conflict
Lys 163Gly 155conflict
Glu 164Gly 156conflict
Lys 165His 157conflict
Arg 167Pro 159conflict
Val 168Leu 160conflict
Ile 169Pro 161conflict
Thr 170Val 162conflict
Glu 171Leu 163conflict
Glu 172Val 164conflict
Lys 174Val 166conflict
Asn 175Arg 167conflict
Phe 176Leu 168conflict
Lys 177Gln 169conflict
Ala 178Asp 170conflict
Phe 179His 171conflict
Ser 181Ile 173conflict
Leu 182Pro 174conflict
Arg 183Ala 175conflict
Met 184Gly 176conflict
Ala 185Arg 177conflict
Arg 186His 178conflict
Ala 187Gly 179conflict
Asn 188Cys 180conflict
Ala 189Val 181conflict
Arg 190Leu 182conflict
Phe 192Arg 184conflict
Gly 193Ala 185conflict
Ile 194Arg 186conflict
Arg 195Thr 187conflict
Ala 196Glu 188conflict
Ala 199Lys 191conflict
Lys 200Ser 192conflict
Ala 202Pro 194conflict
Ala 203Gln 195conflict
Glu 204His 196conflict
Gln 205Phe 197conflict
Val 207Thr 199conflict
Glu 208Gly 200conflict
Lys 209Cys 201conflict
Lys 210Arg 202conflict
Lys 211His 203conflict
O: 1 - 203 (UniProt: A0A0N8ETI8)
PDBExternal DatabaseDetails
Leu 174Ile 174conflict
Asp 194Glu 194conflict
Q: 2 - 188 (UniProt: F6QKI9)
PDBExternal DatabaseDetails
Arg 134Cys 134conflict
R: 1 - 196 (UniProt: G1TYL6)
PDBExternal DatabaseDetails
Arg 38His 38conflict
Arg 151His 151conflict
U: 1 - 128 (UniProt: Q4R5I3)
PDBExternal DatabaseDetails
Leu 18Val 18conflict
Ser 62Thr 62conflict
Leu 63Ile 63conflict
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.

246704

PDB entries from 2025-12-24

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