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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1WCM
Asym. Unit
Info
Asym.Unit (651 KB)
Biol.Unit 1 (631 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
COMPLETE 12-SUBUNIT RNA POLYMERASE II AT 3.8 ANG
Authors
:
K. -J. Armache, S. Mitterweger, A. Meinhart, P. Cramer
Date
:
17 Nov 04 (Deposition) - 14 Dec 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L (1x)
Keywords
:
Dna-Binding, Dna-Directed Rna Polymerase, Dna-Dependent Rna Polymerase, Cellular Rna Polymerase, Multisubunit Co, Metal- Binding, Nuclear Protein, Repeat, Transcription, Phosphorylation, Transferase, Zinc, Zinc-Finger
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. -J. Armache, S. Mitterweger, A. Meinhart, P. Cramer
Structures Of Complete Rna Polymerase Ii And Its Subcomplex, Rpb4/7
J. Biol. Chem. V. 280 7131 2005
[
close entry info
]
Hetero Components
(2, 9)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
2g: ZINC ION (ZNg)
2h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
1
Ligand/Ion
MAGNESIUM ION
2
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
MET A:108 , CYS A:110 , CYS A:148 , CYS A:167
BINDING SITE FOR RESIDUE ZN A2456
2
AC2
SOFTWARE
CYS A:67 , CYS A:70 , CYS A:77 , HIS A:80
BINDING SITE FOR RESIDUE ZN A2457
3
AC3
SOFTWARE
ASP A:481 , ASP A:483 , ASP A:485
BINDING SITE FOR RESIDUE MG A2458
4
AC4
SOFTWARE
CYS B:1163 , CYS B:1166 , CYS B:1182 , CYS B:1185
BINDING SITE FOR RESIDUE ZN B2225
5
AC5
SOFTWARE
CYS C:86 , CYS C:88 , HIS C:91 , CYS C:92 , CYS C:95
BINDING SITE FOR RESIDUE ZN C1269
6
AC6
SOFTWARE
CYS I:7 , CYS I:10 , CYS I:29 , CYS I:32
BINDING SITE FOR RESIDUE ZN I1121
7
AC7
SOFTWARE
CYS I:75 , CYS I:78 , CYS I:103 , CYS I:106
BINDING SITE FOR RESIDUE ZN I1122
8
AC8
SOFTWARE
CYS J:7 , CYS J:10 , CYS J:45 , CYS J:46
BINDING SITE FOR RESIDUE ZN J1066
9
AC9
SOFTWARE
CYS L:31 , CYS L:34 , CYS L:48 , CYS L:51
BINDING SITE FOR RESIDUE ZN L1071
[
close Site info
]
SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_RPB3_YEAST_001 (A30D, chain C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_RPB3_YEAST_001
*
A
30
D
RPB3_YEAST
---
---
C
A
30
D
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(9, 9)
Info
All PROSITE Patterns/Profiles
1: RNA_POL_N_8KD (J:2-11)
2: RNA_POL_M_15KD (I:6-32)
3: RNA_POL_D_30KD (C:31-71)
4: RNA_POL_L_13KD (K:35-66)
5: ZF_TFIIS_2 (I:71-111)
6: ZF_TFIIS_1 (I:75-110)
7: RNA_POL_K_14KD (F:86-100)
8: RNA_POL_H_23KD (E:147-160)
9: RNA_POL_BETA (B:977-989)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RNA_POL_N_8KD
PS01112
RNA polymerases N / 8 Kd subunits signature.
RPAB5_YEAST
2-11
1
J:2-11
2
RNA_POL_M_15KD
PS01030
RNA polymerases M / 15 Kd subunits signature.
RPB9_YEAST
6-32
1
I:6-32
3
RNA_POL_D_30KD
PS00446
RNA polymerases D / 30 to 40 Kd subunits signature.
RPB3_YEAST
31-71
1
C:31-71
4
RNA_POL_L_13KD
PS01154
RNA polymerases L / 13 to 16 Kd subunits signature.
RPB11_YEAST
35-66
1
K:35-66
5
ZF_TFIIS_2
PS51133
Zinc finger TFIIS-type profile.
RPB9_YEAST
71-111
1
I:71-111
6
ZF_TFIIS_1
PS00466
Zinc finger TFIIS-type signature.
RPB9_YEAST
75-110
1
I:75-110
7
RNA_POL_K_14KD
PS01111
RNA polymerases K / 14 to 18 Kd subunits signature.
RPAB2_YEAST
86-100
1
F:86-100
8
RNA_POL_H_23KD
PS01110
RNA polymerases H / 23 Kd subunits signature.
RPAB1_YEAST
147-160
1
E:147-160
9
RNA_POL_BETA
PS01166
RNA polymerases beta chain signature.
RPB2_YEAST
977-989
1
B:977-989
[
close PROSITE info
]
Exons
(9, 9)
Info
All Exons
Exon 1.1 (E:2-215)
Exon 2.1 (A:2-1455 (gaps))
Exon 3.1 (G:1-171)
Exon 4.1 (L:25-70)
Exon 5.1 (C:3-268)
Exon 6.1 (D:4-221 (gaps))
Exon 7.1 (B:20-1224 (gaps))
Exon 8.1 (J:1-65)
Exon 9.2 (F:72-155)
View:
Select:
Label:
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/-
17: Boundary 9.1/9.2
18: Boundary 9.2/-
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
YBR154C
1
YBR154C.1
II:549003-548356
648
RPAB1_YEAST
1-215
215
1
E:2-215
214
2.1
YDL140C
1
YDL140C.1
IV:210562-205361
5202
RPB1_YEAST
1-1733
1733
1
A:2-1455 (gaps)
1454
3.1
YDR404C
1
YDR404C.1
IV:1277162-1276647
516
RPB7_YEAST
1-171
171
1
G:1-171
171
4.1
YHR143W-A
1
YHR143W-A.1
VIII:387236-387448
213
RPAB4_YEAST
1-70
70
1
L:25-70
46
5.1
YIL021W
1
YIL021W.1
IX:312903-313859
957
RPB3_YEAST
1-318
318
1
C:3-268
266
6.1
YJL140W
1
YJL140W.1
X:150957-151622
666
RPB4_YEAST
1-221
221
1
D:4-221 (gaps)
218
7.1
YOR151C
1
YOR151C.1
XV:616672-612998
3675
RPB2_YEAST
1-1224
1224
1
B:20-1224 (gaps)
1205
8.1
YOR210W
1
YOR210W.1
XV:738321-738533
213
RPAB5_YEAST
1-70
70
1
J:1-65
65
9.1
YPR187W
1
YPR187W.1
XVI:911253-911272
20
RPAB2_YEAST
1-7
7
0
-
-
9.2
YPR187W
2
YPR187W.2
XVI:911349-911796
448
RPAB2_YEAST
7-155
149
1
F:72-155
84
[
close EXON info
]
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d1wcma_ (A:)
1b: SCOP_d1wcmb_ (B:)
1c: SCOP_d1wcmc_ (C:)
1d: SCOP_d1wcmd_ (D:)
1e: SCOP_d1wcme_ (E:)
1f: SCOP_d1wcmf_ (F:)
1g: SCOP_d1wcmg_ (G:)
1h: SCOP_d1wcmh_ (H:)
1i: SCOP_d1wcmi_ (I:)
1j: SCOP_d1wcmj_ (J:)
1k: SCOP_d1wcmk_ (K:)
1l: SCOP_d1wcml_ (L:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Low resolution protein structures
(283)
Fold
:
RNA polymerase
(26)
Superfamily
:
RNA polymerase
(26)
Family
:
RNA polymerase
(26)
Protein domain
:
Complete 12-subunit RNA polymerase II complex
(23)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(23)
1a
d1wcma_
A:
1b
d1wcmb_
B:
1c
d1wcmc_
C:
1d
d1wcmd_
D:
1e
d1wcme_
E:
1f
d1wcmf_
F:
1g
d1wcmg_
G:
1h
d1wcmh_
H:
1i
d1wcmi_
I:
1j
d1wcmj_
J:
1k
d1wcmk_
K:
1l
d1wcml_
L:
[
close SCOP info
]
CATH Domains
(12, 15)
Info
all CATH domains
01a: CATH_1wcmG01 (G:1-82)
02a: CATH_1wcmK00 (K:1-115)
02b: CATH_1wcmC01 (C:3-42,C:169-268)
03a: CATH_1wcmE01 (E:2-142)
04a: CATH_1wcmB04 (B:221-397)
05a: CATH_1wcmF00 (F:72-155)
06a: CATH_1wcmE02 (E:143-215)
07a: CATH_1wcmJ00 (J:1-65)
08a: CATH_1wcmB07 (B:783-798,B:853-973)
09a: CATH_1wcmG02 (G:83-171)
09b: CATH_1wcmH00 (H:2-146)
10a: CATH_1wcmC02 (C:43-168)
11a: CATH_1wcmI01 (I:2-46)
11b: CATH_1wcmI02 (I:47-120)
12a: CATH_1wcmL00 (L:25-70)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
DNA-directed RNA polymerase ii subunit; domain 1
(30)
Yeast (Saccharomyces cerevisiae)
(3)
01a
1wcmG01
G:1-82
Topology
:
Gyrase A; domain 2
(166)
Homologous Superfamily
:
[code=3.30.1360.10, no name defined]
(72)
Yeast (Saccharomyces cerevisiae)
(12)
02a
1wcmK00
K:1-115
02b
1wcmC01
C:3-42,C:169-268
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1
(53)
Homologous Superfamily
:
[code=3.40.1340.10, no name defined]
(53)
Yeast (Saccharomyces cerevisiae)
(13)
03a
1wcmE01
E:2-142
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
(48)
Homologous Superfamily
:
[code=3.90.1110.10, no name defined]
(48)
Yeast (Saccharomyces cerevisiae)
(1)
04a
1wcmB04
B:221-397
Topology
:
Eukaryotic RPB6 RNA polymerase subunit
(77)
Homologous Superfamily
:
[code=3.90.940.10, no name defined]
(71)
Yeast (Saccharomyces cerevisiae)
(12)
05a
1wcmF00
F:72-155
Homologous Superfamily
:
[code=3.90.940.20, no name defined]
(58)
Yeast (Saccharomyces cerevisiae)
(13)
06a
1wcmE02
E:143-215
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
Homeodomain-like
(288)
Yeast (Saccharomyces cerevisiae)
(12)
07a
1wcmJ00
J:1-65
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
[code=2.40.50.150, no name defined]
(48)
Yeast (Saccharomyces cerevisiae)
(1)
08a
1wcmB07
B:783-798,B:853-973
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
Yeast (Saccharomyces cerevisiae)
(12)
09a
1wcmG02
G:83-171
09b
1wcmH00
H:2-146
Architecture
:
Beta Complex
(381)
Topology
:
RNA Polymerase Alpha Subunit; Chain A, domain 2
(118)
Homologous Superfamily
:
RNA Polymerase Alpha Subunit; Chain A, domain 2
(71)
Yeast (Saccharomyces cerevisiae)
(12)
10a
1wcmC02
C:43-168
Architecture
:
Single Sheet
(341)
Topology
:
N-terminal domain of TfIIb
(166)
Homologous Superfamily
:
[code=2.20.25.10, no name defined]
(79)
Yeast (Saccharomyces cerevisiae)
(12)
11a
1wcmI01
I:2-46
11b
1wcmI02
I:47-120
Topology
:
Rubrerythrin, domain 2
(145)
Homologous Superfamily
:
RNA polymerase ii, chain L
(52)
Yeast (Saccharomyces cerevisiae)
(12)
12a
1wcmL00
L:25-70
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (651 KB)
Header - Asym.Unit
Biol.Unit 1 (631 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
1WCM
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
