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.
1YKE
Asym. Unit
Info
Asym.Unit (78 KB)
Biol.Unit 1 (38 KB)
Biol.Unit 2 (37 KB)
Biol.Unit 3 (73 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE MEDIATOR MED7/MED21 SUBCOMPLEX
Authors
:
S. Baumli, S. Hoeppner, P. Cramer
Date
:
18 Jan 05 (Deposition) - 22 Feb 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Gene Regulation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Baumli, S. Hoeppner, P. Cramer
A Conserved Mediator Hinge Revealed In The Structure Of The Med7. Med21 (Med7. Srb7) Heterodimer.
J. Biol. Chem. V. 280 18171 2005
(for further references see the
PDB file header
)
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(2, 4)
Info
All Exons
Exon 1.1 (B:3-133 (gaps) | D:3-130 (gaps))
Exon 2.1 (A:108-205 | C:108-205)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
3: Boundary -/2.1
4: Boundary 2.1/-
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
YDR308C
1
YDR308C.1
IV:1078446-1078024
423
MED21_YEAST
1-140
140
2
B:3-133 (gaps)
D:3-130 (gaps)
131
128
2.1
YOL135C
1
YOL135C.1
XV:70044-69376
669
MED7_YEAST
1-222
222
2
A:108-205
C:108-205
98
98
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1ykeb1 (B:3-133)
1b: SCOP_d1yked1 (D:3-130)
2a: SCOP_d1ykea1 (A:108-205)
2b: SCOP_d1ykec1 (C:108-205)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Mediator hinge subcomplex-like
(4)
Superfamily
:
Mediator hinge subcomplex-like
(4)
Family
:
CSE2-like
(2)
Protein domain
:
RNA polymerase II holoenzyme component SRB7 (MED21)
(2)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(2)
1a
d1ykeb1
B:3-133
1b
d1yked1
D:3-130
Family
:
MED7 hinge region
(2)
Protein domain
:
RNA polymerase II mediator complex protein MED7
(1)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
2a
d1ykea1
A:108-205
2b
d1ykec1
C:108-205
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Med21_1ykeD01 (D:3-130)
1b: PFAM_Med21_1ykeD02 (D:3-130)
2a: PFAM_Med7_1ykeC01 (C:108-204)
2b: PFAM_Med7_1ykeC02 (C:108-204)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Med21]
(2)
Family
:
Med21
(2)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
1a
Med21-1ykeD01
D:3-130
1b
Med21-1ykeD02
D:3-130
Clan
:
no clan defined [family: Med7]
(2)
Family
:
Med7
(2)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
2a
Med7-1ykeC01
C:108-204
2b
Med7-1ykeC02
C:108-204
[
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
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 (78 KB)
Header - Asym.Unit
Biol.Unit 1 (38 KB)
Header - Biol.Unit 1
Biol.Unit 2 (37 KB)
Header - Biol.Unit 2
Biol.Unit 3 (73 KB)
Header - Biol.Unit 3
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
1YKE
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
