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3E47
Asym. Unit
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Asym.Unit (1.0 MB)
Biol.Unit 1 (1017 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE YEAST 20S PROTEASOME IN COMPLEX WITH HOMOBELACTOSIN C
Authors
:
M. Groll, O. V. Larionov, A. De Meijere
Date
:
10 Aug 08 (Deposition) - 02 Sep 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2 (1x)
Keywords
:
Proteasome, Ubiquitin, Protein Degradation, Inhibitor, Immunology, Cytoplasm, Hydrolase, Nucleus, Phosphoprotein, Protease, Threonine Protease, Ubl Conjugation, Zymogen
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Groll, O. V. Larionov, R. Huber, A. De Meijere
Inhibitor-Binding Mode Of Homobelactosin C To Proteasomes: New Insights Into Class I Mhc Ligand Generation
Proc. Natl. Acad. Sci. Usa V. 103 4576 2006
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: BENZYL N-[(BENZYLOXY)CARBONYL]-L-A... (ESYa)
1b: BENZYL N-[(BENZYLOXY)CARBONYL]-L-A... (ESYb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ESY
2
Ligand/Ion
BENZYL N-[(BENZYLOXY)CARBONYL]-L-ALANYL-N~6~-[(2R,3S,4S)-3-FORMYL-2-HYDROXY-4-METHYLHEXANOYL]-L-LYSINATE
[
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ILE J:24 , THR K:1 , ARG K:19 , LYS K:33 , MET K:45 , ALA K:46 , GLY K:47 , GLY K:98 , TYR K:112 , SER K:115 , GLY K:128 , SER K:129 , GLN K:131 , SER W:24 , PHE X:132
BINDING SITE FOR RESIDUE ESY K 2000
2
AC2
SOFTWARE
SER I:24 , PHE J:132 , ILE X:24 , THR Y:1 , ARG Y:19 , LYS Y:33 , MET Y:45 , ALA Y:46 , GLY Y:47 , GLY Y:98 , TYR Y:112 , SER Y:115 , GLY Y:128 , SER Y:129 , GLN Y:131
BINDING SITE FOR RESIDUE ESY Y 2000
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(4, 48)
Info
All PROSITE Patterns/Profiles
1: PROTEASOME_BETA_2 (J:-1-178,X:-1-178,I:-1-178,W:-1-17...)
2: PROTEASOME_ALPHA_1 (C:8-30,Q:8-30,A:8-30,O:8-30,E:8-30...)
3: PROTEASOME_BETA_1 (J:4-51,X:4-51,I:4-51,W:4-51,2:4-51...)
4: PROTEASOME_ALPHA_2 (C:23-233,Q:23-233,A:23-233,O:23-23...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PROTEASOME_BETA_2
PS51476
Proteasome beta-type subunit profile.
PSB4_YEAST
1-184
2
J:-1-178
X:-1-178
PSB3_YEAST
9-190
2
I:-1-178
W:-1-178
PSB6_YEAST
28-226
2
L:-1-178
Z:-1-178
PSB7_YEAST
41-233
2
1:-1-178
M:-1-178
2
PROTEASOME_ALPHA_1
PS00388
Proteasome alpha-type subunits signature.
PSA4_YEAST
4-26
2
C:8-30
Q:8-30
PSA2_YEAST
5-27
2
A:8-30
O:8-30
PSA6_YEAST
6-28
2
E:8-30
S:8-30
PSA3_YEAST
6-28
2
B:8-30
P:8-30
PSA7_YEAST
8-30
2
F:8-30
T:8-30
PSA1_YEAST
12-34
2
G:8-30
U:8-30
3
PROTEASOME_BETA_1
PS00854
Proteasome beta-type subunits signature.
PSB4_YEAST
5-52
2
J:4-51
X:4-51
PSB3_YEAST
13-59
2
I:4-51
W:4-51
PSB1_YEAST
23-70
2
2:4-51
N:4-51
PSB6_YEAST
32-79
2
L:4-51
Z:4-51
PSB2_YEAST
33-80
2
H:4-51
V:4-51
PSB7_YEAST
45-92
2
1:4-51
M:4-51
PSB5_YEAST
79-126
2
K:4-51
Y:4-51
4
PROTEASOME_ALPHA_2
PS51475
Proteasome alpha-type subunit profile.
PSA4_YEAST
19-233
2
C:23-233
Q:23-233
PSA2_YEAST
20-247
2
A:23-233
O:23-233
PSA6_YEAST
21-234
2
E:23-233
S:23-233
PSA3_YEAST
21-239
2
B:23-233
P:23-233
PSA5_YEAST
23-240
2
D:23-233
R:23-233
PSA7_YEAST
23-240
2
F:23-233
T:23-233
PSA1_YEAST
27-245
2
G:23-233
U:23-233
[
close PROSITE info
]
Exons
(15, 30)
Info
All Exons
Exon 1.1 (L:-9-194 (gaps) | Z:-9-194 (gaps))
Exon 2.1 (J:-1-193 (gaps) | X:-1-193 (gaps))
Exon 3.1 (I:-8-194 (gaps) | W:-8-194 (gaps))
Exon 4.1 (1:-8-211 (gaps) | M:-8-211 (gaps))
Exon 5.1 (G:6-240 (gaps) | U:6-240 (gaps))
Exon 6.1 (B:4-239 (gaps) | P:4-239 (gaps))
Exon 7.1 (D:9-244 (gaps) | R:9-244 (gaps))
Exon 8.1 (2:1-3 | N:1-3)
Exon 8.2 (2:3-18J (gaps) | N:3-18J (gaps))
Exon 9.1 (A:4-236 (gaps) | O:4-236 (gaps))
Exon 10.1 (E:4-233 (gaps) | S:4-233 (gaps))
Exon 11.1 (C:7-243 (gaps) | Q:7-243 (gaps))
Exon 12.1 (H:1-223 (gaps) | V:1-223 (gaps))
Exon 13.1 (F:5-241 (gaps) | T:5-241 (gaps))
Exon 14.1 (K:1-211 (gaps) | Y:1-211 (gaps))
View:
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All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/-
03: Boundary -/2.1
04: Boundary 2.1/-
05: Boundary -/3.1
06: Boundary 3.1/-
07: Boundary -/4.1
08: Boundary 4.1/-
09: Boundary -/5.1
10: Boundary 5.1/-
11: Boundary -/6.1
12: Boundary 6.1/-
13: Boundary -/7.1
14: Boundary 7.1/-
15: Boundary -/8.1
16: Boundary 8.1/8.2
17: Boundary 8.2/-
18: Boundary -/9.1
19: Boundary 9.1/-
20: Boundary -/10.1
21: Boundary 10.1/-
22: Boundary -/11.1
23: Boundary 11.1/-
24: Boundary -/12.1
25: Boundary 12.1/-
26: Boundary -/13.1
27: Boundary 13.1/-
28: Boundary -/14.1
29: Boundary 14.1/-
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
YBL041W
1
YBL041W.1
II:141250-141975
726
PSB6_YEAST
1-241
241
2
L:-9-194 (gaps)
Z:-9-194 (gaps)
225
225
2.1
YER012W
1
YER012W.1
V:177834-178430
597
PSB4_YEAST
1-198
198
2
J:-1-193 (gaps)
X:-1-193 (gaps)
200
200
3.1
YER094C
1
YER094C.1
V:349342-348725
618
PSB3_YEAST
1-205
205
2
I:-8-194 (gaps)
W:-8-194 (gaps)
208
208
4.1
YFR050C
1
YFR050C.1
VI:249853-249053
801
PSB7_YEAST
1-266
266
2
1:-8-211 (gaps)
M:-8-211 (gaps)
238
238
5.1
YGL011C
1
YGL011C.1
VII:475252-474494
759
PSA1_YEAST
1-252
252
2
G:6-240 (gaps)
U:6-240 (gaps)
247
247
6.1
YGR135W
1
YGR135W.1
VII:761397-762173
777
PSA3_YEAST
1-258
258
2
B:4-239 (gaps)
P:4-239 (gaps)
250
250
7.1
YGR253C
1
YGR253C.1
VII:999145-998363
783
PSA5_YEAST
1-260
260
2
D:9-244 (gaps)
R:9-244 (gaps)
249
249
8.1
YJL001W
1
YJL001W.1
X:435156-435220
65
PSB1_YEAST
1-22
22
2
2:1-3
N:1-3
3
3
8.2
YJL001W
2
YJL001W.2
X:435337-435919
583
PSB1_YEAST
22-215
194
2
2:3-18J (gaps)
N:3-18J (gaps)
198
198
9.1
YML092C
1
YML092C.1
XIII:86739-85987
753
PSA2_YEAST
1-250
250
2
A:4-236 (gaps)
O:4-236 (gaps)
255
255
10.1
YMR314W
1
YMR314W.1
XIII:901708-902412
705
PSA6_YEAST
1-234
234
2
E:4-233 (gaps)
S:4-233 (gaps)
239
239
11.1
YOL038W
1
YOL038W.1
XV:255336-256100
765
PSA4_YEAST
1-254
254
2
C:7-243 (gaps)
Q:7-243 (gaps)
246
246
12.1
YOR157C
1
YOR157C.1
XV:631752-630967
786
PSB2_YEAST
1-261
261
2
H:1-223 (gaps)
V:1-223 (gaps)
225
225
13.1
YOR362C
1
YOR362C.1
XV:1018744-1017878
867
PSA7_YEAST
1-288
288
2
F:5-241 (gaps)
T:5-241 (gaps)
248
248
14.1
YPR103W
1
YPR103W.1
XVI:732347-733210
864
PSB5_YEAST
1-287
287
2
K:1-211 (gaps)
Y:1-211 (gaps)
214
214
[
close EXON info
]
SCOP Domains
(2, 26)
Info
All SCOP Domains
1a: SCOP_d3e47g_ (G:)
1b: SCOP_d3e47u_ (U:)
2a: SCOP_d3e471_ (1:)
2b: SCOP_d3e472_ (2:)
2c: SCOP_d3e47a_ (A:)
2d: SCOP_d3e47b_ (B:)
2e: SCOP_d3e47c_ (C:)
2f: SCOP_d3e47e_ (E:)
2g: SCOP_d3e47f_ (F:)
2h: SCOP_d3e47h_ (H:)
2i: SCOP_d3e47i_ (I:)
2j: SCOP_d3e47j_ (J:)
2k: SCOP_d3e47k_ (K:)
2l: SCOP_d3e47l_ (L:)
2m: SCOP_d3e47m_ (M:)
2n: SCOP_d3e47n_ (N:)
2o: SCOP_d3e47o_ (O:)
2p: SCOP_d3e47p_ (P:)
2q: SCOP_d3e47q_ (Q:)
2r: SCOP_d3e47s_ (S:)
2s: SCOP_d3e47t_ (T:)
2t: SCOP_d3e47v_ (V:)
2u: SCOP_d3e47w_ (W:)
2v: SCOP_d3e47x_ (X:)
2w: SCOP_d3e47y_ (Y:)
2x: SCOP_d3e47z_ (Z:)
View:
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Classes
(
)
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)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ntn hydrolase-like
(356)
Superfamily
:
N-terminal nucleophile aminohydrolases (Ntn hydrolases)
(352)
Family
:
Proteasome subunits
(222)
Protein domain
:
automated matches
(78)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(39)
1a
d3e47g_
G:
1b
d3e47u_
U:
Protein domain
:
Proteasome alpha subunit (non-catalytic)
(66)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(54)
2a
d3e471_
1:
2b
d3e472_
2:
2c
d3e47a_
A:
2d
d3e47b_
B:
2e
d3e47c_
C:
2f
d3e47e_
E:
2g
d3e47f_
F:
2h
d3e47h_
H:
2i
d3e47i_
I:
2j
d3e47j_
J:
2k
d3e47k_
K:
2l
d3e47l_
L:
2m
d3e47m_
M:
2n
d3e47n_
N:
2o
d3e47o_
O:
2p
d3e47p_
P:
2q
d3e47q_
Q:
2r
d3e47s_
S:
2s
d3e47t_
T:
2t
d3e47v_
V:
2u
d3e47w_
W:
2v
d3e47x_
X:
2w
d3e47y_
Y:
2x
d3e47z_
Z:
[
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CATH Domains
(1, 26)
Info
all CATH domains
1a: CATH_3e47L00 (L:-9-194)
1b: CATH_3e47E00 (E:4-233)
1c: CATH_3e47S00 (S:4-233)
1d: CATH_3e47K00 (K:1-211)
1e: CATH_3e47Y00 (Y:1-211)
1f: CATH_3e47C00 (C:7-243)
1g: CATH_3e47Q00 (Q:7-243)
1h: CATH_3e47G00 (G:6-240)
1i: CATH_3e47U00 (U:6-240)
1j: CATH_3e47Z00 (Z:-9-194)
1k: CATH_3e47B00 (B:4-239)
1l: CATH_3e47P00 (P:4-239)
1m: CATH_3e47F00 (F:5-241)
1n: CATH_3e47T00 (T:5-241)
1o: CATH_3e47200 (2:1-18J)
1p: CATH_3e47N00 (N:1-18J)
1q: CATH_3e47I00 (I:-8-194)
1r: CATH_3e47W00 (W:-8-194)
1s: CATH_3e47A00 (A:4-236)
1t: CATH_3e47O00 (O:4-236)
1u: CATH_3e47J00 (J:-1-193)
1v: CATH_3e47X00 (X:-1-193)
1w: CATH_3e47H00 (H:1-223)
1x: CATH_3e47V00 (V:1-223)
1y: CATH_3e47100 (1:-8-211)
1z: CATH_3e47M00 (M:-8-211)
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Homologous Superfamilies
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
(128)
Homologous Superfamily
:
Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
(124)
Baker's yeast (Saccharomyces cerevisiae)
(14)
1a
3e47L00
L:-9-194
1b
3e47E00
E:4-233
1c
3e47S00
S:4-233
1d
3e47K00
K:1-211
1e
3e47Y00
Y:1-211
1f
3e47C00
C:7-243
1g
3e47Q00
Q:7-243
1h
3e47G00
G:6-240
1i
3e47U00
U:6-240
1j
3e47Z00
Z:-9-194
1k
3e47B00
B:4-239
1l
3e47P00
P:4-239
1m
3e47F00
F:5-241
1n
3e47T00
T:5-241
1o
3e47200
2:1-18J
1p
3e47N00
N:1-18J
1q
3e47I00
I:-8-194
1r
3e47W00
W:-8-194
1s
3e47A00
A:4-236
1t
3e47O00
O:4-236
1u
3e47J00
J:-1-193
1v
3e47X00
X:-1-193
1w
3e47H00
H:1-223
1x
3e47V00
V:1-223
1y
3e47100
1:-8-211
1z
3e47M00
M:-8-211
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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