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1WCM
Biol. Unit 1
Info
Asym.Unit (651 KB)
Biol.Unit 1 (631 KB)
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(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:
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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
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Hetero Components
(0, 0)
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)
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Sorry, no Info available
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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
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
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)
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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:
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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
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(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:)
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Folds
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Superfamilies
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Families
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)
(
)
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:
[
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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)
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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
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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