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2PMZ
Biol. Unit 1
Info
Asym.Unit (986 KB)
Biol.Unit 1 (495 KB)
Biol.Unit 2 (495 KB)
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(1)
Title
:
ARCHAEAL RNA POLYMERASE FROM SULFOLOBUS SOLFATARICUS
Authors
:
K. S. Murakami
Date
:
23 Apr 07 (Deposition) - 12 Feb 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,K,L,N,P,Q,R,S,T,U,V,W,X,Y,Z
Biol. Unit 1: A,B,C,D,E,F,H,K,L,N,P (1x)
Biol. Unit 2: G,Q,R,S,T,U,V,W,X,Y,Z (1x)
Keywords
:
4Fe-4S Cluster Binding Motif, Translation, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Hirata, B. J. Klein, K. S. Murakami
The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Nature V. 451 851 2008
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: FE3-S4 CLUSTER (F3Sa)
1b: FE3-S4 CLUSTER (F3Sb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
3g: ZINC ION (ZNg)
3h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:58 , PRO A:59 , ASN A:63 , CYS A:68 , HIS A:71
BINDING SITE FOR RESIDUE ZN A 1002
2
AC2
SOFTWARE
ASP A:456 , ASP A:458 , ASP A:460
BINDING SITE FOR RESIDUE MG A 1003
3
AC3
SOFTWARE
CYS B:1061 , CYS B:1064 , CYS B:1079 , ILE B:1081
BINDING SITE FOR RESIDUE ZN B 2001
4
AC4
SOFTWARE
CYS N:7 , THR N:9 , CYS N:10 , CYS N:44 , CYS N:45
BINDING SITE FOR RESIDUE ZN N 1001
5
AC5
SOFTWARE
CYS P:9 , THR P:12 , CYS P:26 , PRO P:27 , CYS P:29
BINDING SITE FOR RESIDUE ZN P 1001
6
BC2
SOFTWARE
CYS D:183 , VAL D:187 , CYS D:203 , LEU D:205 , CYS D:206 , GLU D:207 , GLU D:208 , CYS D:209 , ILE D:219
BINDING SITE FOR RESIDUE F3S D 1001
[
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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
[
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PROSITE Patterns/Profiles
(5, 5)
Info
All PROSITE Patterns/Profiles
1: RNA_POL_N_8KD (N:2-11)
2: RNA_POL_H_23KD (H:14-27)
3: RNA_POL_L_13KD (L:17-48)
4: RNA_POL_D_30KD (D:26-66)
5: RNA_POL_K_14KD (K:28-42)
;
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.
RPON_SULSO
2-11
1
N:2-11
-
2
RNA_POL_H_23KD
PS01110
RNA polymerases H / 23 Kd subunits signature.
RPOH_SULSO
14-27
1
H:14-27
-
3
RNA_POL_L_13KD
PS01154
RNA polymerases L / 13 to 16 Kd subunits signature.
RPOL_SULSO
17-48
1
L:17-48
-
4
RNA_POL_D_30KD
PS00446
RNA polymerases D / 30 to 40 Kd subunits signature.
RPOD_SULSO
26-66
1
D:26-66
-
5
RNA_POL_K_14KD
PS01111
RNA polymerases K / 14 to 18 Kd subunits signature.
RPOK_SULSO
28-42
1
K:28-42
-
[
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]
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_2pmzE01 (E:1-81)
1b: CATH_2pmzT01 (T:1-81)
2a: CATH_2pmzH00 (H:9-82)
2b: CATH_2pmzV00 (V:9-82)
3a: CATH_2pmzN00 (N:1-64)
3b: CATH_2pmzY00 (Y:1-64)
4a: CATH_2pmzE02 (E:82-180)
4b: CATH_2pmzT02 (T:82-180)
View:
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Classes
(
)
(
)
Architectures
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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)
Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricusp2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2.
(1)
1a
2pmzE01
E:1-81
1b
2pmzT01
T:1-81
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Eukaryotic RPB6 RNA polymerase subunit
(77)
Homologous Superfamily
:
[code=3.90.940.20, no name defined]
(58)
Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricusp2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2.
(1)
2a
2pmzH00
H:9-82
2b
2pmzV00
V:9-82
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
Homeodomain-like
(288)
Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricusp2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2.
(1)
3a
2pmzN00
N:1-64
3b
2pmzY00
Y:1-64
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricusp2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2. Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2.
(1)
4a
2pmzE02
E:82-180
4b
2pmzT02
T:82-180
[
close CATH info
]
Pfam Domains
(18, 40)
Info
all PFAM domains
01a: PFAM_RNA_pol_Rpb4_2pmzU01 (U:11-89)
01b: PFAM_RNA_pol_Rpb4_2pmzU02 (U:11-89)
02a: PFAM_RNA_pol_Rpb2_6_2pmzR01 (R:649-1022)
02b: PFAM_RNA_pol_Rpb2_6_2pmzR02 (R:649-1022)
03a: PFAM_S1_2pmzT01 (T:79-153)
03b: PFAM_S1_2pmzT02 (T:79-153)
04a: PFAM_RNA_pol_L_2pmzS01 (S:13-254)
04b: PFAM_RNA_pol_L_2pmzS02 (S:13-254)
04c: PFAM_RNA_pol_L_2pmzX01 (X:13-81)
04d: PFAM_RNA_pol_L_2pmzX02 (X:13-81)
05a: PFAM_SHS2_Rpb7_N_2pmzT03 (T:8-77)
05b: PFAM_SHS2_Rpb7_N_2pmzT04 (T:8-77)
06a: PFAM_DNA_RNApol_7kD_2pmzZ01 (Z:6-38)
06b: PFAM_DNA_RNApol_7kD_2pmzZ02 (Z:6-38)
07a: PFAM_RNA_pol_A_bac_2pmzS03 (S:44-157)
07b: PFAM_RNA_pol_A_bac_2pmzS04 (S:44-157)
08a: PFAM_RNA_pol_N_2pmzY01 (Y:1-60)
08b: PFAM_RNA_pol_N_2pmzY02 (Y:1-60)
09a: PFAM_RNA_pol_Rpb1_1_2pmzQ01 (Q:4-313)
09b: PFAM_RNA_pol_Rpb1_1_2pmzQ02 (Q:4-313)
10a: PFAM_RNA_pol_Rpb1_2_2pmzQ03 (Q:315-482)
10b: PFAM_RNA_pol_Rpb1_2_2pmzQ04 (Q:315-482)
11a: PFAM_RNA_pol_Rpb1_3_2pmzQ05 (Q:485-651)
11b: PFAM_RNA_pol_Rpb1_3_2pmzQ06 (Q:485-651)
12a: PFAM_RNA_pol_Rpb1_4_2pmzQ07 (Q:676-782)
12b: PFAM_RNA_pol_Rpb1_4_2pmzQ08 (Q:676-782)
13a: PFAM_RNA_pol_Rpb1_5_2pmzQ09 (Q:789-869)
13b: PFAM_RNA_pol_Rpb1_5_2pmzQ10 (Q:789-869)
13c: PFAM_RNA_pol_Rpb1_5_2pmzG01 (G:22-344)
13d: PFAM_RNA_pol_Rpb1_5_2pmzG02 (G:22-344)
14a: PFAM_RNA_pol_Rpb2_4_2pmzR03 (R:520-584)
14b: PFAM_RNA_pol_Rpb2_4_2pmzR04 (R:520-584)
15a: PFAM_RNA_pol_Rpb2_5_2pmzR05 (R:604-644)
15b: PFAM_RNA_pol_Rpb2_5_2pmzR06 (R:604-644)
16a: PFAM_RNA_pol_Rpb2_7_2pmzR07 (R:1024-1116)
16b: PFAM_RNA_pol_Rpb2_7_2pmzR08 (R:1024-1116)
17a: PFAM_RNA_pol_Rpb5_C_2pmzV01 (V:9-82)
17b: PFAM_RNA_pol_Rpb5_C_2pmzV02 (V:9-82)
18a: PFAM_RNA_pol_Rpb6_2pmzW01 (W:20-78)
18b: PFAM_RNA_pol_Rpb6_2pmzW02 (W:20-78)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HRDC-like
(19)
Family
:
RNA_pol_Rpb4
(11)
Sulfolobus solfataricus
(1)
01a
RNA_pol_Rpb4-2pmzU01
U:11-89
01b
RNA_pol_Rpb4-2pmzU02
U:11-89
Clan
:
LEF-8-like
(36)
Family
:
RNA_pol_Rpb2_6
(36)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
02a
RNA_pol_Rpb2_6-2pmzR01
R:649-1022
02b
RNA_pol_Rpb2_6-2pmzR02
R:649-1022
Clan
:
OB
(224)
Family
:
S1
(23)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
03a
S1-2pmzT01
T:79-153
03b
S1-2pmzT02
T:79-153
Clan
:
RBP11-like
(36)
Family
:
RNA_pol_L
(36)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
04a
RNA_pol_L-2pmzS01
S:13-254
04b
RNA_pol_L-2pmzS02
S:13-254
04c
RNA_pol_L-2pmzX01
X:13-81
04d
RNA_pol_L-2pmzX02
X:13-81
Clan
:
SHS2
(26)
Family
:
SHS2_Rpb7-N
(12)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
05a
SHS2_Rpb7-N-2pmzT03
T:8-77
05b
SHS2_Rpb7-N-2pmzT04
T:8-77
Clan
:
Zn_Beta_Ribbon
(109)
Family
:
DNA_RNApol_7kD
(28)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
06a
DNA_RNApol_7kD-2pmzZ01
Z:6-38
06b
DNA_RNApol_7kD-2pmzZ02
Z:6-38
Clan
:
no clan defined [family: RNA_pol_A_bac]
(36)
Family
:
RNA_pol_A_bac
(36)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
07a
RNA_pol_A_bac-2pmzS03
S:44-157
07b
RNA_pol_A_bac-2pmzS04
S:44-157
Clan
:
no clan defined [family: RNA_pol_N]
(28)
Family
:
RNA_pol_N
(28)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
08a
RNA_pol_N-2pmzY01
Y:1-60
08b
RNA_pol_N-2pmzY02
Y:1-60
Clan
:
no clan defined [family: RNA_pol_Rpb1_1]
(37)
Family
:
RNA_pol_Rpb1_1
(37)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
09a
RNA_pol_Rpb1_1-2pmzQ01
Q:4-313
09b
RNA_pol_Rpb1_1-2pmzQ02
Q:4-313
Clan
:
no clan defined [family: RNA_pol_Rpb1_2]
(36)
Family
:
RNA_pol_Rpb1_2
(36)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
10a
RNA_pol_Rpb1_2-2pmzQ03
Q:315-482
10b
RNA_pol_Rpb1_2-2pmzQ04
Q:315-482
Clan
:
no clan defined [family: RNA_pol_Rpb1_3]
(36)
Family
:
RNA_pol_Rpb1_3
(36)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
11a
RNA_pol_Rpb1_3-2pmzQ05
Q:485-651
11b
RNA_pol_Rpb1_3-2pmzQ06
Q:485-651
Clan
:
no clan defined [family: RNA_pol_Rpb1_4]
(36)
Family
:
RNA_pol_Rpb1_4
(36)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
12a
RNA_pol_Rpb1_4-2pmzQ07
Q:676-782
12b
RNA_pol_Rpb1_4-2pmzQ08
Q:676-782
Clan
:
no clan defined [family: RNA_pol_Rpb1_5]
(36)
Family
:
RNA_pol_Rpb1_5
(36)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
13a
RNA_pol_Rpb1_5-2pmzQ09
Q:789-869
13b
RNA_pol_Rpb1_5-2pmzQ10
Q:789-869
13c
RNA_pol_Rpb1_5-2pmzG01
G:22-344
13d
RNA_pol_Rpb1_5-2pmzG02
G:22-344
Clan
:
no clan defined [family: RNA_pol_Rpb2_4]
(28)
Family
:
RNA_pol_Rpb2_4
(28)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
14a
RNA_pol_Rpb2_4-2pmzR03
R:520-584
14b
RNA_pol_Rpb2_4-2pmzR04
R:520-584
Clan
:
no clan defined [family: RNA_pol_Rpb2_5]
(28)
Family
:
RNA_pol_Rpb2_5
(28)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
15a
RNA_pol_Rpb2_5-2pmzR05
R:604-644
15b
RNA_pol_Rpb2_5-2pmzR06
R:604-644
Clan
:
no clan defined [family: RNA_pol_Rpb2_7]
(36)
Family
:
RNA_pol_Rpb2_7
(36)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
16a
RNA_pol_Rpb2_7-2pmzR07
R:1024-1116
16b
RNA_pol_Rpb2_7-2pmzR08
R:1024-1116
Clan
:
no clan defined [family: RNA_pol_Rpb5_C]
(28)
Family
:
RNA_pol_Rpb5_C
(28)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
17a
RNA_pol_Rpb5_C-2pmzV01
V:9-82
17b
RNA_pol_Rpb5_C-2pmzV02
V:9-82
Clan
:
no clan defined [family: RNA_pol_Rpb6]
(37)
Family
:
RNA_pol_Rpb6
(37)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
18a
RNA_pol_Rpb6-2pmzW01
W:20-78
18b
RNA_pol_Rpb6-2pmzW02
W:20-78
[
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select non-helix/non-sheet protein parts
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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)
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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") .
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