PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
1YA7
Biol. Unit 1
Info
Asym.Unit (753 KB)
Biol.Unit 1, α-C (1.4 MB)
Biol.Unit 1 (1.4 MB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
IMPLICATIONS FOR INTERACTIONS OF PROTEASOME WITH PAN AND PA700 FROM THE 1.9 A STRUCTURE OF A PROTEASOME-11S ACTIVATOR COMPLEX
Authors
:
A. Forster, E. I. Masters, F. G. Whitby, H. Robinson, C. P. Hill
Date
:
17 Dec 04 (Deposition) - 26 Jul 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U (2x)
Keywords
:
Archaeal Proteasome, Pa26, Copmlex, Open Gate, Hydrolase-Hydrolase Activator Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Forster, E. I. Masters, F. G. Whitby, H. Robinson, C. P. Hill
The 1. 9 A Structure Of A Proteasome-11S Activator Complex And Implications For Proteasome-Pan/Pa700 Interactions.
Mol. Cell V. 18 589 2005
[
close entry info
]
Hetero Components
(2, 56)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
2q: SULFATE ION (SO4q)
2r: SULFATE ION (SO4r)
2s: SULFATE ION (SO4s)
2t: SULFATE ION (SO4t)
2u: SULFATE ION (SO4u)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
14
Ligand/Ion
GLYCEROL
2
SO4
42
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(28, 28)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:110 , LYS A:114 , SER B:63 , ILE B:64 , GLU B:65 , GLN B:68 , HOH B:3061 , ARG H:71 , HOH H:3091
BINDING SITE FOR RESIDUE SO4 B 3001
02
AC2
SOFTWARE
GLU B:110 , LYS B:114 , ILE C:64 , GLU C:65 , GLN C:68 , HOH C:3063 , ARG I:71
BINDING SITE FOR RESIDUE SO4 C 3002
03
AC3
SOFTWARE
GLU C:110 , LYS C:114 , SER D:63 , ILE D:64 , GLU D:65 , GLN D:68 , ARG J:71
BINDING SITE FOR RESIDUE SO4 D 3003
04
AC4
SOFTWARE
GLU D:110 , LYS D:114 , SER E:63 , GLU E:65 , GLN E:68 , ARG K:71
BINDING SITE FOR RESIDUE SO4 E 3004
05
AC5
SOFTWARE
GLU E:110 , LYS E:114 , SER F:63 , ILE F:64 , GLU F:65 , GLN F:68 , ARG L:71
BINDING SITE FOR RESIDUE SO4 F 3005
06
AC6
SOFTWARE
GLU F:110 , LYS F:114 , SER G:63 , ILE G:64 , GLU G:65 , GLN G:68 , ARG M:71
BINDING SITE FOR RESIDUE SO4 G 3006
07
AC7
SOFTWARE
SER A:63 , GLU A:65 , GLN A:68 , GLU G:110 , LYS G:114 , HOH G:3062 , ARG N:71
BINDING SITE FOR RESIDUE SO4 G 3007
08
AC8
SOFTWARE
THR H:1 , GLY H:47 , GLY H:128 , SER H:129 , HOH H:3045 , HOH H:3067
BINDING SITE FOR RESIDUE SO4 H 3008
09
AC9
SOFTWARE
THR N:1 , GLY N:47 , GLY N:128 , SER N:129 , HOH N:3073 , HOH N:3080
BINDING SITE FOR RESIDUE SO4 N 3009
10
BC1
SOFTWARE
THR M:1 , GLY M:47 , GLY M:128 , SER M:129
BINDING SITE FOR RESIDUE SO4 M 3010
11
BC2
SOFTWARE
THR I:1 , GLY I:47 , GLY I:128 , SER I:129
BINDING SITE FOR RESIDUE SO4 I 3011
12
BC3
SOFTWARE
THR J:1 , GLY J:47 , GLY J:128 , SER J:129 , HOH J:3092
BINDING SITE FOR RESIDUE SO4 J 3012
13
BC4
SOFTWARE
THR K:1 , GLY K:47 , GLY K:128 , SER K:129 , HOH K:3039 , HOH K:3063 , HOH K:3075
BINDING SITE FOR RESIDUE SO4 K 3013
14
BC5
SOFTWARE
THR L:1 , GLY L:47 , GLY L:128 , SER L:129 , HOH L:3038 , HOH L:3082 , HOH L:3094
BINDING SITE FOR RESIDUE SO4 L 3014
15
BC6
SOFTWARE
TYR A:103 , ARG A:115 , ARG H:70 , HOH H:3025 , HOH H:3061 , HOH H:3109
BINDING SITE FOR RESIDUE SO4 H 3015
16
BC7
SOFTWARE
TYR B:103 , ARG B:115 , ARG I:70 , HOH I:3025 , HOH I:3033 , HOH I:3078
BINDING SITE FOR RESIDUE SO4 I 3016
17
BC8
SOFTWARE
TYR C:103 , ARG C:115 , GLN J:69 , ARG J:70 , HOH J:3038 , HOH J:3041 , HOH J:3078
BINDING SITE FOR RESIDUE SO4 J 3017
18
BC9
SOFTWARE
TYR D:103 , ARG D:115 , ARG K:70 , HOH K:3028 , HOH K:3052 , HOH K:3079
BINDING SITE FOR RESIDUE SO4 K 3018
19
CC1
SOFTWARE
TYR E:103 , ARG E:115 , ARG L:70 , HOH L:3062 , HOH L:3105
BINDING SITE FOR RESIDUE SO4 L 3019
20
CC2
SOFTWARE
TYR F:103 , ARG F:115 , ARG M:70 , HOH M:3049 , HOH M:3105 , HOH M:3116
BINDING SITE FOR RESIDUE SO4 M 3020
21
CC3
SOFTWARE
TYR G:103 , ARG G:115 , ARG N:70 , HOH N:3034 , HOH N:3049 , HOH N:3060
BINDING SITE FOR RESIDUE SO4 N 3021
22
CC4
SOFTWARE
GLN L:53 , ARG L:57 , LYS L:60
BINDING SITE FOR RESIDUE GOL L 2001
23
CC5
SOFTWARE
GLN M:53 , ARG M:57 , LYS M:60 , HOH M:3042 , HOH M:3106
BINDING SITE FOR RESIDUE GOL M 2002
24
CC6
SOFTWARE
ARG N:57 , LYS N:60 , HOH N:3101
BINDING SITE FOR RESIDUE GOL N 2003
25
CC7
SOFTWARE
ARG H:57 , LYS H:60 , HOH H:3086 , HOH I:3073
BINDING SITE FOR RESIDUE GOL H 2004
26
CC8
SOFTWARE
GLN I:53 , VAL I:56 , ARG I:57 , LYS I:60 , HOH I:3072
BINDING SITE FOR RESIDUE GOL I 2005
27
CC9
SOFTWARE
GLN J:53 , VAL J:56 , ARG J:57 , LYS J:60 , HOH J:3063
BINDING SITE FOR RESIDUE GOL J 2006
28
DC1
SOFTWARE
GLN K:53 , VAL K:56 , ARG K:57 , LYS K:60 , HOH K:3065 , HOH K:3066
BINDING SITE FOR RESIDUE GOL K 2007
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 42)
Info
All PROSITE Patterns/Profiles
1: PROTEASOME_ALPHA_1 (A:8-30,B:8-30,C:8-30,D:8-30,E:8-30...)
2: PROTEASOME_BETA_1 (H:4-51,I:4-51,J:4-51,K:4-51,L:4-51...)
3: PROTEASOME_ALPHA_2 (A:23-233,B:23-233,C:23-233,D:23-23...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PROTEASOME_ALPHA_1
PS00388
Proteasome alpha-type subunits signature.
PSA_THEAC
8-30
14
A:8-30
B:8-30
C:8-30
D:8-30
E:8-30
F:8-30
G:8-30
2
PROTEASOME_BETA_1
PS00854
Proteasome beta-type subunits signature.
PSB_THEAC
12-59
14
H:4-51
I:4-51
J:4-51
K:4-51
L:4-51
M:4-51
N:4-51
3
PROTEASOME_ALPHA_2
PS51475
Proteasome alpha-type subunit profile.
PSA_THEAC
23-233
14
A:23-233
B:23-233
C:23-233
D:23-233
E:23-233
F:23-233
G:23-233
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 21)
Info
All SCOP Domains
1a: SCOP_d1ya7p_ (P:)
1b: SCOP_d1ya7s_ (S:)
1c: SCOP_d1ya7t_ (T:)
1d: SCOP_d1ya7u_ (U:)
1e: SCOP_d1ya7q_ (Q:)
1f: SCOP_d1ya7r_ (R:)
2a: SCOP_d1ya7o1 (O:4-231)
3a: SCOP_d1ya7a_ (A:)
3b: SCOP_d1ya7b_ (B:)
3c: SCOP_d1ya7c_ (C:)
3d: SCOP_d1ya7d_ (D:)
3e: SCOP_d1ya7e_ (E:)
3f: SCOP_d1ya7f_ (F:)
3g: SCOP_d1ya7g_ (G:)
3h: SCOP_d1ya7h_ (H:)
3i: SCOP_d1ya7i_ (I:)
3j: SCOP_d1ya7j_ (J:)
3k: SCOP_d1ya7k_ (K:)
3l: SCOP_d1ya7l_ (L:)
3m: SCOP_d1ya7m_ (M:)
3n: SCOP_d1ya7n_ (N:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Four-helical up-and-down bundle
(308)
Superfamily
:
Proteasome activator
(7)
Family
:
Proteasome activator
(7)
Protein domain
:
automated matches
(5)
Trypanosome (Trypanosoma brucei) [TaxId: 5691]
(5)
1a
d1ya7p_
P:
1b
d1ya7s_
S:
1c
d1ya7t_
T:
1d
d1ya7u_
U:
1e
d1ya7q_
Q:
1f
d1ya7r_
R:
Protein domain
:
Proteasome activator protein PA26
(1)
Trypanosome (Trypanosoma brucei) [TaxId: 5691]
(1)
2a
d1ya7o1
O:4-231
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)
Thermoplasma acidophilum [TaxId: 2303]
(7)
3a
d1ya7a_
A:
3b
d1ya7b_
B:
3c
d1ya7c_
C:
3d
d1ya7d_
D:
3e
d1ya7e_
E:
3f
d1ya7f_
F:
3g
d1ya7g_
G:
3h
d1ya7h_
H:
3i
d1ya7i_
I:
3j
d1ya7j_
J:
3k
d1ya7k_
K:
3l
d1ya7l_
L:
3m
d1ya7m_
M:
3n
d1ya7n_
N:
[
close SCOP info
]
CATH Domains
(2, 21)
Info
all CATH domains
1a: CATH_1ya7A00 (A:7-233)
1b: CATH_1ya7D00 (D:7-233)
1c: CATH_1ya7E00 (E:7-233)
1d: CATH_1ya7F00 (F:7-233)
1e: CATH_1ya7G00 (G:7-233)
1f: CATH_1ya7H00 (H:1-203)
1g: CATH_1ya7I00 (I:1-203)
1h: CATH_1ya7J00 (J:1-203)
1i: CATH_1ya7K00 (K:1-203)
1j: CATH_1ya7L00 (L:1-203)
1k: CATH_1ya7M00 (M:1-203)
1l: CATH_1ya7N00 (N:1-203)
1m: CATH_1ya7B00 (B:7-233)
1n: CATH_1ya7C00 (C:7-233)
2a: CATH_1ya7O01 (O:4-221)
2b: CATH_1ya7R01 (R:4-221)
2c: CATH_1ya7S01 (S:4-221)
2d: CATH_1ya7T01 (T:4-221)
2e: CATH_1ya7U01 (U:4-221)
2f: CATH_1ya7P01 (P:4-221)
2g: CATH_1ya7Q01 (Q:4-221)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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)
Thermoplasma acidophilum. Organism_taxid: 2303.
(6)
1a
1ya7A00
A:7-233
1b
1ya7D00
D:7-233
1c
1ya7E00
E:7-233
1d
1ya7F00
F:7-233
1e
1ya7G00
G:7-233
1f
1ya7H00
H:1-203
1g
1ya7I00
I:1-203
1h
1ya7J00
J:1-203
1i
1ya7K00
K:1-203
1j
1ya7L00
L:1-203
1k
1ya7M00
M:1-203
1l
1ya7N00
N:1-203
1m
1ya7B00
B:7-233
1n
1ya7C00
C:7-233
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Four Helix Bundle (Hemerythrin (Met), subunit A)
(300)
Homologous Superfamily
:
[code=1.20.120.180, no name defined]
(10)
Thermoplasma acidophilum. Organism_taxid: 2303.
(5)
2a
1ya7O01
O:4-221
2b
1ya7R01
R:4-221
2c
1ya7S01
S:4-221
2d
1ya7T01
T:4-221
2e
1ya7U01
U:4-221
2f
1ya7P01
P:4-221
2g
1ya7Q01
Q:4-221
[
close CATH info
]
Pfam Domains
(2, 21)
Info
all PFAM domains
1a: PFAM_Proteasome_1ya7G01 (G:31-216)
1b: PFAM_Proteasome_1ya7G02 (G:31-216)
1c: PFAM_Proteasome_1ya7G03 (G:31-216)
1d: PFAM_Proteasome_1ya7G04 (G:31-216)
1e: PFAM_Proteasome_1ya7G05 (G:31-216)
1f: PFAM_Proteasome_1ya7G06 (G:31-216)
1g: PFAM_Proteasome_1ya7G07 (G:31-216)
1h: PFAM_Proteasome_1ya7N01 (N:1-178)
1i: PFAM_Proteasome_1ya7N02 (N:1-178)
1j: PFAM_Proteasome_1ya7N03 (N:1-178)
1k: PFAM_Proteasome_1ya7N04 (N:1-178)
1l: PFAM_Proteasome_1ya7N05 (N:1-178)
1m: PFAM_Proteasome_1ya7N06 (N:1-178)
1n: PFAM_Proteasome_1ya7N07 (N:1-178)
2a: PFAM_Proteasome_A_N_1ya7G08 (G:8-30)
2b: PFAM_Proteasome_A_N_1ya7G09 (G:8-30)
2c: PFAM_Proteasome_A_N_1ya7G10 (G:8-30)
2d: PFAM_Proteasome_A_N_1ya7G11 (G:8-30)
2e: PFAM_Proteasome_A_N_1ya7G12 (G:8-30)
2f: PFAM_Proteasome_A_N_1ya7G13 (G:8-30)
2g: PFAM_Proteasome_A_N_1ya7G14 (G:8-30)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NTN
(93)
Family
:
Proteasome
(36)
Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)
(8)
1a
Proteasome-1ya7G01
G:31-216
1b
Proteasome-1ya7G02
G:31-216
1c
Proteasome-1ya7G03
G:31-216
1d
Proteasome-1ya7G04
G:31-216
1e
Proteasome-1ya7G05
G:31-216
1f
Proteasome-1ya7G06
G:31-216
1g
Proteasome-1ya7G07
G:31-216
1h
Proteasome-1ya7N01
N:1-178
1i
Proteasome-1ya7N02
N:1-178
1j
Proteasome-1ya7N03
N:1-178
1k
Proteasome-1ya7N04
N:1-178
1l
Proteasome-1ya7N05
N:1-178
1m
Proteasome-1ya7N06
N:1-178
1n
Proteasome-1ya7N07
N:1-178
Clan
:
no clan defined [family: Proteasome_A_N]
(20)
Family
:
Proteasome_A_N
(20)
Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)
(8)
2a
Proteasome_A_N-1ya7G08
G:8-30
2b
Proteasome_A_N-1ya7G09
G:8-30
2c
Proteasome_A_N-1ya7G10
G:8-30
2d
Proteasome_A_N-1ya7G11
G:8-30
2e
Proteasome_A_N-1ya7G12
G:8-30
2f
Proteasome_A_N-1ya7G13
G:8-30
2g
Proteasome_A_N-1ya7G14
G:8-30
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
Chain Q
Chain R
Chain S
Chain T
Chain U
Asymmetric Unit 1
Asymmetric Unit 2
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (753 KB)
Header - Asym.Unit
Biol.Unit 1 (1.4 MB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1YA7
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help