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1K5X
Theor. Model
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Theoretical Model (110 KB)
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Title
:
STRUCTURE OF THE TRANSLATING 80S RIBOSOME FROM YEAST, OBTAINED BY DOCKING ATOMIC MODELS FOR RNA AND PROTEIN COMPONENTS INTO A 15A CRYO-EM MAP. THIS FILE 1K5X CONTAINS THE 40S RIBOSOMAL SUBUNIT, THE P-SITE BOUND TRNA AND THE MRNA CODON. THE FILE 1K5Y CONTAINS THE 60S RIBOSOMAL SUBUNIT.
Authors
:
C. M. T. Spahn, R. Beckmann, N. Eswar, P. Penczek, A. Sali, G. Blobel, J. Frank
Date
:
12 Oct 01 (Deposition) - 09 Nov 01 (Release) - 01 Apr 03 (Revision)
Method
:
THEORETICAL MODEL
Resolution
:
NOT APPLICABLE
Chains
:
Theor. Model : A,B,C,D,E,G,H,I,J,K,L,M,N,O,Q,S,T,U
Keywords
:
Cryo-Em, 40S Sacharomyces Cerevisiae Ribosome, Homology Models
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. M. Spahn, R. Beckmann, N. Eswar, P. A. Penczek, A. Sali, G. Blobel, J. Frank
Structure Of The 80S Ribosome From Saccharomyces Cerevisiae--Trna-Ribosome And Subunit-Subunit Interactions.
Cell V. 107 373 2001
(for further references see the
PDB file header
)
[
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Hetero Components
(7, 10)
Info
All Hetero Components
1a: 5-METHYLCYTIDINE-5'-MONOPHOSPHATE (5MCa)
1b: 5-METHYLCYTIDINE-5'-MONOPHOSPHATE (5MCb)
2a: 5-METHYLURIDINE 5'-MONOPHOSPHATE (5MUa)
3a: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Ua)
3b: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Ub)
4a: N2-DIMETHYLGUANOSINE-5'-MONOPHOSPH... (M2Ga)
5a: O2'-METHYLYCYTIDINE-5'-MONOPHOSPHA... (OMCa)
6a: PSEUDOURIDINE-5'-MONOPHOSPHATE (PSUa)
6b: PSEUDOURIDINE-5'-MONOPHOSPHATE (PSUb)
7a: 4-(3-[5-O-PHOSPHONORIBOFURANOSYL]-... (YYGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
5MC
2
Mod. Nucleotide
5-METHYLCYTIDINE-5'-MONOPHOSPHATE
2
5MU
1
Mod. Nucleotide
5-METHYLURIDINE 5'-MONOPHOSPHATE
3
H2U
2
Mod. Nucleotide
5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
4
M2G
1
Mod. Nucleotide
N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
5
OMC
1
Mod. Nucleotide
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
6
PSU
2
Mod. Nucleotide
PSEUDOURIDINE-5'-MONOPHOSPHATE
7
YYG
1
Mod. Nucleotide
4-(3-[5-O-PHOSPHONORIBOFURANOSYL]-4,6-DIMETHYL-8-OXO-4,8-DIHYDRO-3H-1,3,4,5,7A-PENTAAZA-S-INDACEN-YLAMINO-BUTYRIC ACID METHYL ESTER
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Sites
(0, 0)
Info
All Sites
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(20, 20)
Info
All PROSITE Patterns/Profiles
01: RIBOSOMAL_S2_1 (B:13-24)
02: RIBOSOMAL_S13_2 (M:17-145,M:17-145)
03: KH_TYPE_2 (C:20-91)
04: RIBOSOMAL_S14 (N:21-43)
05: RIBOSOMAL_S10 (J:45-60)
06: RIBOSOMAL_S12 (L:62-69,L:62-69)
07: RIBOSOMAL_S9 (I:70-88,I:70-88)
08: S5_DSRBD (E:75-138)
09: RIBOSOMAL_S7 (G:90-116)
10: RIBOSOMAL_S5 (E:92-124)
11: RIBOSOMAL_S19 (S:98-122)
12: RIBOSOMAL_S15 (O:97-127)
13: RIBOSOMAL_S8 (H:99-116,H:99-116)
14: RIBOSOMAL_S11 (K:101-123)
15: RIBOSOMAL_S4 (D:105-129)
16: S4 (D:107-181)
17: RIBOSOMAL_S2_2 (B:117-141)
18: RIBOSOMAL_S17 (Q:119-131,Q:119-131)
19: RIBOSOMAL_S13_1 (M:123-136,M:123-136)
20: RIBOSOMAL_S3 (C:146-182)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIBOSOMAL_S2_1
PS00962
Ribosomal protein S2 signature 1.
RSSA1_YEAST
14-25
1
B:13-24
2
RIBOSOMAL_S13_2
PS50159
Ribosomal protein S13 family profile.
RS18A_YEAST
17-146
1
M:17-145
RS18B_YEAST
17-146
1
M:17-145
3
KH_TYPE_2
PS50823
Type-2 KH domain profile.
RS3_YEAST
21-92
1
C:20-91
4
RIBOSOMAL_S14
PS00527
Ribosomal protein S14 signature.
RS29B_YEAST
22-44
1
N:21-43
5
RIBOSOMAL_S10
PS00361
Ribosomal protein S10 signature.
RS20_YEAST
45-60
1
J:45-60
6
RIBOSOMAL_S12
PS00055
Ribosomal protein S12 signature.
RS23A_YEAST
62-69
1
L:62-69
RS23B_YEAST
62-69
1
L:62-69
7
RIBOSOMAL_S9
PS00360
Ribosomal protein S9 signature.
RS16A_YEAST
71-89
1
I:70-88
RS16B_YEAST
71-89
1
I:70-88
8
S5_DSRBD
PS50881
S5 double stranded RNA-binding domain profile.
RS2_YEAST
76-139
1
E:75-138
9
RIBOSOMAL_S7
PS00052
Ribosomal protein S7 signature.
RS5_YEAST
91-117
1
G:90-116
10
RIBOSOMAL_S5
PS00585
Ribosomal protein S5 signature.
RS2_YEAST
93-125
1
E:92-124
11
RIBOSOMAL_S19
PS00323
Ribosomal protein S19 signature.
RS15_YEAST
98-122
1
S:98-122
12
RIBOSOMAL_S15
PS00362
Ribosomal protein S15 signature.
RS13_YEAST
98-128
1
O:97-127
13
RIBOSOMAL_S8
PS00053
Ribosomal protein S8 signature.
RS22A_YEAST
100-117
1
H:99-116
RS22B_YEAST
100-117
1
H:99-116
14
RIBOSOMAL_S11
PS00054
Ribosomal protein S11 signature.
RS14A_YEAST
102-124
1
K:101-123
15
RIBOSOMAL_S4
PS00632
Ribosomal protein S4 signature.
RS9A_YEAST
105-129
1
D:105-129
16
S4
PS50889
S4 RNA-binding domain profile.
RS9A_YEAST
107-181
1
D:107-181
17
RIBOSOMAL_S2_2
PS00963
Ribosomal protein S2 signature 2.
RSSA1_YEAST
118-142
1
B:117-141
18
RIBOSOMAL_S17
PS00056
Ribosomal protein S17 signature.
RS11A_YEAST
120-132
1
Q:119-131
RS11B_YEAST
120-132
1
Q:119-131
19
RIBOSOMAL_S13_1
PS00646
Ribosomal protein S13 signature.
RS18A_YEAST
123-136
1
M:123-136
RS18B_YEAST
123-136
1
M:123-136
20
RIBOSOMAL_S3
PS00548
Ribosomal protein S3 signature.
RS3_YEAST
147-183
1
C:146-182
[
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]
Exons
(19, 19)
Info
All Exons
Exon 1.2 (K:8-132)
Exon 2.1 (N:20-48)
Exon 3.4 (Q:68-143)
Exon 4.2 (O:65-129)
Exon 5.1 (E:74-222)
Exon 6.1 (B:13-29)
Exon 6.2 (B:30-197)
Exon 7.1 (J:21-117)
Exon 8.1 (G:75-224)
Exon 9.1 (H:3-44)
Exon 9.2 (H:44-129)
Exon 10.1 (M:15-16)
Exon 10.2 (M:16-145)
Exon 11.1 (I:4-7)
Exon 11.2 (I:8-142)
Exon 12.1 (C:5-192)
Exon 13.1 (S:47-126)
Exon 14.2 (D:19-196)
Exon 15.4 (L:28-145)
View:
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All Exon Boundaries
01: Boundary 1.1/1.2
02: Boundary 1.2/-
03: Boundary -/2.1
04: Boundary 2.1/-
05: Boundary 3.3/3.4
06: Boundary 3.4/-
07: Boundary 4.1/4.2
08: Boundary 4.2/-
09: Boundary -/5.1
10: Boundary 5.1/-
11: Boundary -/6.1
12: Boundary 6.1/6.2
13: Boundary 6.2/-
14: Boundary -/7.1
15: Boundary 7.1/-
16: Boundary -/8.1
17: Boundary 8.1/-
18: Boundary -/9.1
19: Boundary 9.1/9.2
20: Boundary 9.2/-
21: Boundary -/10.1
22: Boundary 10.1/10.2
23: Boundary 10.2/-
24: Boundary -/11.1
25: Boundary 11.1/11.2
26: Boundary 11.2/-
27: Boundary -/12.1
28: Boundary 12.1/-
29: Boundary -/13.1
30: Boundary 13.1/-
31: Boundary 14.1/14.2
32: Boundary 14.2/-
33: Boundary 15.3/15.4
34: Boundary 15.4/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
YCR031C
1
YCR031C.1
III:178216-178210
7
RS14A_YEAST
1-3
3
0
-
-
1.2
YCR031C
2
YCR031C.2
III:177902-177496
407
RS14A_YEAST
3-137
135
1
K:8-132
125
2.1
YDL061C
1
YDL061C.1
IV:340798-340628
171
RS29B_YEAST
1-56
56
1
N:20-48
29
3.3
YDR025W
3
YDR025W.1
IV:491513-491557
45
RS11B_YEAST
1-15
15
0
-
-
3.4
YDR025W
4
YDR025W.2
IV:491897-492322
426
RS11B_YEAST
16-156
141
1
Q:68-143
76
4.1
YDR064W
1
YDR064W.1
IV:579457-579477
21
RS13_YEAST
1-7
7
0
-
-
4.2
YDR064W
2
YDR064W.2
IV:580017-580451
435
RS13_YEAST
8-151
144
1
O:65-129
65
5.1
YGL123W
1
YGL123W.1
VII:277623-278387
765
RS2_YEAST
1-254
254
1
E:74-222
149
6.1
YGR214W
1
YGR214W.1
VII:920580-920669
90
RSSA1_YEAST
1-30
30
1
B:13-29
17
6.2
YGR214W
2
YGR214W.2
VII:921125-921793
669
RSSA1_YEAST
31-252
222
1
B:30-197
168
7.1
YHL015W
1
YHL015W.1
VIII:75409-75774
366
RS20_YEAST
1-121
121
1
J:21-117
97
8.1
YJR123W
1
YJR123W.1
X:651891-652568
678
RS5_YEAST
1-225
225
1
G:75-224
150
9.1
YLR367W
1
YLR367W.1
XII:856441-856573
133
RS22B_YEAST
1-45
45
1
H:3-44
42
9.2
YLR367W
2
YLR367W.2
XII:857057-857316
260
RS22B_YEAST
45-130
86
1
H:44-129
86
10.1
YML026C
1
YML026C.1
XIII:223828-223782
47
RS18B_YEAST
1-16
16
1
M:15-16
2
10.2
YML026C
2
YML026C.2
XIII:223380-222987
394
RS18B_YEAST
16-146
131
1
M:16-145
130
11.1
YMR143W
1
YMR143W.1
XIII:551927-551950
24
RS16B_YEAST
1-8
8
1
I:4-7
4
11.2
YMR143W
2
YMR143W.2
XIII:552495-552902
408
RS16B_YEAST
9-143
135
1
I:8-142
135
12.1
YNL178W
1
YNL178W.1
XIV:302682-303404
723
RS3_YEAST
1-240
240
1
C:5-192
188
13.1
YOL040C
1
YOL040C.1
XV:253576-253148
429
RS15_YEAST
1-142
142
1
S:47-126
80
14.1
YPL081W
1
YPL081W.1
XVI:404947-404953
7
RS9A_YEAST
1-3
3
0
-
-
14.2
YPL081W
2
YPL081W.2
XVI:405455-406041
587
RS9A_YEAST
3-197
195
1
D:19-196
178
15.3
YPR132W
3
YPR132W.1
XVI:794961-795025
65
RS23B_YEAST
1-22
22
0
-
-
15.4
YPR132W
4
YPR132W.2
XVI:795391-795763
373
RS23B_YEAST
22-145
124
1
L:28-145
118
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