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.
PLEASE WAIT...
Getting 'Exon' information from database.
2WWA
Asym. Unit
Info
Asym.Unit (257 KB)
Biol.Unit 1 (248 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYO-EM STRUCTURE OF IDLE YEAST SSH1 COMPLEX BOUND TO THE YEAST 80S RIBOSOME
Authors
:
T. Becker, E. Mandon, S. Bhushan, A. Jarasch, J. P. Armache, S. Funes, F. J. Gumbart, T. Mielke, O. Berninghausen, K. Schulten, E. Westhof, R. G R. Beckmann
Date
:
22 Oct 09 (Deposition) - 08 Dec 09 (Release) - 19 Apr 17 (Revision)
Method
:
ELECTRON MICROSCOPY
Resolution
:
8.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O (1x)
Keywords
:
Ribosomal Protein, Ribonucleoprotein, Transmembrane, Phosphoprotein, Signal Sequence, Membrane, Ribosome, Transport, Rna-Binding, Rrna- Binding, Translocation, Protein Conducting Channel, Protein Exit Tunnel, Endoplasmic Reticulum, Cotranslational Protein Translocation, Isopeptide Bond, Protein Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Becker, S. Bhushan, A. Jarasch, J. P. Armache, S. Funes, F. Jossinet J. Gumbart, T. Mielke, O. Berninghausen, K. Schulten, E. Westhof, R. Gilmore, E. Mandon, R. Beckmann
Structure Of Monomeric Yeast And Mammalian Sec61 Complexes Interacting With The Translating Ribosome.
Science V. 326 1369 2009
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(10, 10)
Info
All PROSITE Patterns/Profiles
01: RIBOSOMAL_L19E (J:7-26,J:7-26)
02: SECE_SEC61G (B:28-56)
03: RIBOSOMAL_L39E (O:30-37)
04: RIBOSOMAL_L29 (N:40-54,N:40-54)
05: RIBOSOMAL_L31E (M:49-63)
06: RIBOSOMAL_L24 (L:53-70)
07: SECY_1 (A:78-97)
08: RIBOSOMAL_L1E (H:114-140)
09: RIBOSOMAL_L23 (K:120-135)
10: RIBOSOMAL_L22 (I:126-150)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIBOSOMAL_L19E
PS00526
Ribosomal protein L19e signature.
RL19A_YEAST
7-26
1
J:7-26
RL19B_YEAST
7-26
1
J:7-26
2
SECE_SEC61G
PS01067
Protein secE/sec61-gamma signature.
SC61G_YEAST
28-56
1
B:28-56
3
RIBOSOMAL_L39E
PS00051
Ribosomal protein L39e signature.
RL39_YEAST
30-46
1
O:30-37
4
RIBOSOMAL_L29
PS00579
Ribosomal protein L29 signature.
RL35A_YEAST
40-54
1
N:40-54
RL35B_YEAST
40-54
1
N:40-54
5
RIBOSOMAL_L31E
PS01144
Ribosomal protein L31e signature.
RL31A_YEAST
49-63
1
M:49-63
6
RIBOSOMAL_L24
PS01108
Ribosomal protein L24 signature.
RL26A_YEAST
53-70
1
L:53-70
7
SECY_1
PS00755
Protein secY signature 1.
SSH1_YEAST
78-97
1
A:78-97
8
RIBOSOMAL_L1E
PS00939
Ribosomal protein L1e signature.
RL4B_YEAST
114-140
1
H:114-140
9
RIBOSOMAL_L23
PS00050
Ribosomal protein L23 signature.
RL25_YEAST
120-135
1
K:120-135
10
RIBOSOMAL_L22
PS00464
Ribosomal protein L22 signature.
RL17A_YEAST
126-150
1
I:126-150
[
close PROSITE info
]
Exons
(10, 10)
Info
All Exons
Exon 1.1 (J:1-1)
Exon 1.2 (J:1-53)
Exon 2.1 (M:9-19)
Exon 2.2 (M:20-92)
Exon 3.1 (N:1-1)
Exon 3.2 (N:2-69)
Exon 4.1 (H:1-269)
Exon 5.1 (I:1-103)
Exon 5.2 (I:104-153)
Exon 6.2 (K:57-139)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/-
04: Boundary -/2.1
05: Boundary 2.1/2.2
06: Boundary 2.2/-
07: Boundary -/3.1
08: Boundary 3.1/3.2
09: Boundary 3.2/-
10: Boundary -/4.1
11: Boundary 4.1/-
12: Boundary -/5.1
13: Boundary 5.1/5.2
14: Boundary 5.2/-
15: Boundary 6.1/6.2
16: Boundary 6.2/-
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
YBR084C-A
1
YBR084C-A.1
II:415255-415254
2
RL19B_YEAST
1-1
1
1
J:1-1
1
1.2
YBR084C-A
2
YBR084C-A.2
II:414747-414180
568
RL19B_YEAST
1-189
189
1
J:1-53
53
2.1
YDL075W
1
YDL075W.1
IV:322226-322282
57
RL31A_YEAST
1-19
19
1
M:9-19
11
2.2
YDL075W
2
YDL075W.2
IV:322704-322988
285
RL31A_YEAST
20-113
94
1
M:20-92
73
3.1
YDL191W
1
YDL191W.1
IV:117665-117667
3
RL35B_YEAST
1-1
1
1
N:1-1
1
3.2
YDL191W
2
YDL191W.2
IV:118159-118518
360
RL35B_YEAST
2-120
119
1
N:2-69
68
4.1
YDR012W
1
YDR012W.1
IV:471851-472939
1089
RL4B_YEAST
1-362
362
1
H:1-269
269
5.1
YKL180W
1
YKL180W.1
XI:109274-109582
309
RL17A_YEAST
1-103
103
1
I:1-103
103
5.2
YKL180W
2
YKL180W.2
XI:109889-110134
246
RL17A_YEAST
104-184
81
1
I:104-153
50
6.1
YOL127W
1
YOL127W.1
XV:80348-80360
13
RL25_YEAST
1-5
5
0
-
-
6.2
YOL127W
2
YOL127W.2
XV:80775-81190
416
RL25_YEAST
5-142
138
1
K:57-139
83
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(10, 10)
Info
all PFAM domains
01a: PFAM_KOW_2wwaL01 (L:52-91)
02a: PFAM_Ribosomal_L23_2wwaK01 (K:60-139)
03a: PFAM_Plug_translocon_2wwaA01 (A:41-77)
04a: PFAM_Ribosomal_L22_2wwaI01 (I:17-152)
05a: PFAM_Ribosomal_L31e_2wwaM01 (M:9-88)
06a: PFAM_Ribosomal_L39_2wwaO01 (O:9-37)
07a: PFAM_Ribosomal_L4_2wwaH01 (H:20-261)
08a: PFAM_Sec61_beta_2wwaC01 (C:58-78)
09a: PFAM_SecE_2wwaB01 (B:24-80)
10a: PFAM_SecY_2wwaA02 (A:78-473)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
KOW
(56)
Family
:
KOW
(52)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
01a
KOW-2wwaL01
L:52-91
Clan
:
RRM
(206)
Family
:
Ribosomal_L23
(47)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
02a
Ribosomal_L23-2wwaK01
K:60-139
Clan
:
no clan defined [family: Plug_translocon]
(6)
Family
:
Plug_translocon
(6)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
03a
Plug_translocon-2wwaA01
A:41-77
Clan
:
no clan defined [family: Ribosomal_L22]
(46)
Family
:
Ribosomal_L22
(46)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
04a
Ribosomal_L22-2wwaI01
I:17-152
Clan
:
no clan defined [family: Ribosomal_L31e]
(41)
Family
:
Ribosomal_L31e
(41)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
05a
Ribosomal_L31e-2wwaM01
M:9-88
Clan
:
no clan defined [family: Ribosomal_L39]
(41)
Family
:
Ribosomal_L39
(41)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
06a
Ribosomal_L39-2wwaO01
O:9-37
Clan
:
no clan defined [family: Ribosomal_L4]
(46)
Family
:
Ribosomal_L4
(46)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
07a
Ribosomal_L4-2wwaH01
H:20-261
Clan
:
no clan defined [family: Sec61_beta]
(5)
Family
:
Sec61_beta
(5)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
08a
Sec61_beta-2wwaC01
C:58-78
Clan
:
no clan defined [family: SecE]
(3)
Family
:
SecE
(3)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
09a
SecE-2wwaB01
B:24-80
Clan
:
no clan defined [family: SecY]
(6)
Family
:
SecY
(6)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
10a
SecY-2wwaA02
A:78-473
[
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
Asymmetric Unit 1
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 (257 KB)
Header - Asym.Unit
Biol.Unit 1 (248 KB)
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
2WWA
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help