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2BE5
Biol. Unit 2
Info
Asym.Unit (1.2 MB)
Biol.Unit 1 (637 KB)
Biol.Unit 2 (629 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE T. THERMOPHILUS RNA POLYMERASE HOLOENZYME IN COMPLEX WITH INHIBITOR TAGETITOXIN
Authors
:
D. G. Vassylyev, V. Svetlov, M. N. Vassylyeva, A. Perederina, N. Igarashi, N. Matsugaki, S. Wakatsuki, I. Artsimovitch, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
22 Oct 05 (Deposition) - 08 Nov 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: K,L,M,N,O,P (1x)
Keywords
:
Rna Polymerase Holoenzyme, Tagetitoxin, Antibiotic, Transcription Regulation, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. G. Vassylyev, V. Svetlov, M. N. Vassylyeva, A. Perederina, N. Igarashi, N. Matsugaki, S. Wakatsuki, I. Artsimovitch
Structural Basis For Transcription Inhibition By Tagetitoxin
Nat. Struct. Mol. Biol. V. 12 1086 2005
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
2a: TAGETITOXIN (TGTa)
2b: TAGETITOXIN (TGTb)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
TGT
1
Ligand/Ion
TAGETITOXIN
3
ZN
-1
Ligand/Ion
ZINC ION
[
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]
Sites
(5, 5)
Info
All Sites
1: AC6 (SOFTWARE)
2: AC7 (SOFTWARE)
3: AC8 (SOFTWARE)
4: AC9 (SOFTWARE)
5: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC6
SOFTWARE
CYS N:58 , CYS N:60 , CYS N:73 , CYS N:76
BINDING SITE FOR RESIDUE ZN N 9059
2
AC7
SOFTWARE
CYS N:1112 , ARG N:1189 , CYS N:1194 , CYS N:1201 , CYS N:1204
BINDING SITE FOR RESIDUE ZN N 9113
3
AC8
SOFTWARE
ASP N:739 , ASP N:741 , ASP N:743
BINDING SITE FOR RESIDUE MG N 9005
4
AC9
SOFTWARE
GLU M:685 , ARG M:879 , ASP N:739 , TGT N:9002
BINDING SITE FOR RESIDUE MG N 9006
5
BC1
SOFTWARE
ARG M:557 , SER M:878 , ARG M:879 , ASN N:737 , ARG N:783 , ARG N:1029 , ASN N:1031 , GLN N:1034 , HOH N:2331 , HOH N:2485 , MG N:9006 , HOH N:9136 , HOH N:9180 , HOH N:9199 , HOH N:9224 , HOH N:9413 , HOH N:9933
BINDING SITE FOR RESIDUE TGT N 9002
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: RNA_POL_BETA (M:836-848)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RNA_POL_BETA
PS01166
RNA polymerases beta chain signature.
RPOB_THET8
836-848
1
-
M:836-848
[
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Exons
(0, 0)
Info
All Exons
View:
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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
(8, 20)
Info
All SCOP Domains
1a: SCOP_d2be5f1 (F:258-318)
1b: SCOP_d2be5p1 (P:258-318)
2a: SCOP_d2be5f2 (F:319-423)
2b: SCOP_d2be5p2 (P:319-423)
3a: SCOP_d2be5e_ (E:)
3b: SCOP_d2be5o_ (O:)
4a: SCOP_d2be5f3 (F:74-257)
4b: SCOP_d2be5p3 (P:74-257)
5a: SCOP_d2be5a1 (A:1-49,A:173-229)
5b: SCOP_d2be5b1 (B:1-49,B:173-229)
5c: SCOP_d2be5k1 (K:1-49,K:173-229)
5d: SCOP_d2be5l1 (L:1-49,L:173-229)
6a: SCOP_d2be5a2 (A:50-172)
6b: SCOP_d2be5b2 (B:50-172)
6c: SCOP_d2be5k2 (K:50-172)
6d: SCOP_d2be5l2 (L:50-172)
7a: SCOP_d2be5c_ (C:)
7b: SCOP_d2be5m_ (M:)
8a: SCOP_d2be5d_ (D:)
8b: SCOP_d2be5n_ (N:)
View:
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Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
Sigma3 and sigma4 domains of RNA polymerase sigma factors
(41)
Family
:
Sigma3 domain
(12)
Protein domain
:
Sigma70
(9)
Thermus thermophilus [TaxId: 274]
(9)
1a
d2be5f1
F:258-318
1b
d2be5p1
P:258-318
Family
:
Sigma4 domain
(23)
Protein domain
:
Sigma70 (SigA, RpoD)
(15)
Thermus thermophilus [TaxId: 274]
(9)
2a
d2be5f2
F:319-423
2b
d2be5p2
P:319-423
Fold
:
RPB6/omega subunit-like
(56)
Superfamily
:
RPB6/omega subunit-like
(56)
Family
:
RNA polymerase omega subunit
(19)
Protein domain
:
RNA polymerase omega subunit
(19)
Thermus thermophilus [TaxId: 274]
(10)
3a
d2be5e_
E:
3b
d2be5o_
O:
Fold
:
Sigma2 domain of RNA polymerase sigma factors
(19)
Superfamily
:
Sigma2 domain of RNA polymerase sigma factors
(19)
Family
:
Sigma2 domain of RNA polymerase sigma factors
(17)
Protein domain
:
Sigma70
(10)
Thermus thermophilus [TaxId: 274]
(9)
4a
d2be5f3
F:74-257
4b
d2be5p3
P:74-257
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
DCoH-like
(107)
Superfamily
:
RBP11-like subunits of RNA polymerase
(76)
Family
:
RNA polymerase alpha subunit dimerisation domain
(43)
Protein domain
:
RNA polymerase alpha
(18)
Thermus thermophilus [TaxId: 274]
(13)
5a
d2be5a1
A:1-49,A:173-229
5b
d2be5b1
B:1-49,B:173-229
5c
d2be5k1
K:1-49,K:173-229
5d
d2be5l1
L:1-49,L:173-229
Fold
:
Insert subdomain of RNA polymerase alpha subunit
(43)
Superfamily
:
Insert subdomain of RNA polymerase alpha subunit
(43)
Family
:
Insert subdomain of RNA polymerase alpha subunit
(43)
Protein domain
:
RNA polymerase alpha subunit
(18)
Thermus thermophilus [TaxId: 274]
(13)
6a
d2be5a2
A:50-172
6b
d2be5b2
B:50-172
6c
d2be5k2
K:50-172
6d
d2be5l2
L:50-172
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
beta and beta-prime subunits of DNA dependent RNA-polymerase
(103)
Superfamily
:
beta and beta-prime subunits of DNA dependent RNA-polymerase
(103)
Family
:
RNA-polymerase beta
(54)
Protein domain
:
automated matches
(17)
Thermus thermophilus [TaxId: 274]
(7)
7a
d2be5c_
C:
7b
d2be5m_
M:
Family
:
RNA-polymerase beta-prime
(49)
Protein domain
:
RNA-polymerase beta-prime
(16)
Thermus thermophilus [TaxId: 274]
(12)
8a
d2be5d_
D:
8b
d2be5n_
N:
[
close SCOP info
]
CATH Domains
(10, 24)
Info
all CATH domains
01a: CATH_2be5A01 (A:1-49,A:172-225)
01b: CATH_2be5B01 (B:1-49,B:172-225)
01c: CATH_2be5K01 (K:1-49,K:172-225)
01d: CATH_2be5L01 (L:1-49,L:172-225)
02a: CATH_2be5C03 (C:144-323)
02b: CATH_2be5M03 (M:144-323)
03a: CATH_2be5E00 (E:2-96)
03b: CATH_2be5O00 (O:2-96)
04a: CATH_2be5C02 (C:9-143,C:324-470,C:536-592)
04b: CATH_2be5M02 (M:9-143,M:324-470,M:536-592)
05a: CATH_2be5F02 (F:260-313)
05b: CATH_2be5P02 (P:260-313)
06a: CATH_2be5C01 (C:2-8,C:668-698,C:832-1004)
06b: CATH_2be5M01 (M:2-8,M:668-698,M:832-1004)
07a: CATH_2be5C05 (C:593-667)
07b: CATH_2be5M05 (M:593-667)
08a: CATH_2be5C06 (C:699-831)
08b: CATH_2be5M06 (M:699-831)
09a: CATH_2be5A02 (A:50-171)
09b: CATH_2be5B02 (B:50-171)
09c: CATH_2be5K02 (K:50-171)
09d: CATH_2be5L02 (L:50-171)
10a: CATH_2be5C04 (C:471-535)
10b: CATH_2be5M04 (M:471-535)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Gyrase A; domain 2
(166)
Homologous Superfamily
:
[code=3.30.1360.10, no name defined]
(72)
Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274.
(9)
01a
2be5A01
A:1-49,A:172-225
01b
2be5B01
B:1-49,B:172-225
01c
2be5K01
K:1-49,K:172-225
01d
2be5L01
L:1-49,L:172-225
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)
Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274.
(9)
02a
2be5C03
C:144-323
02b
2be5M03
M:144-323
Topology
:
Eukaryotic RPB6 RNA polymerase subunit
(77)
Homologous Superfamily
:
[code=3.90.940.10, no name defined]
(71)
Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274.
(9)
03a
2be5E00
E:2-96
03b
2be5O00
O:2-96
Topology
:
Rna Polymerase Beta Subunit; Chain: C,domain 2
(18)
Homologous Superfamily
:
[code=3.90.1100.10, no name defined]
(18)
Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274.
(9)
04a
2be5C02
C:9-143,C:324-470,C:536-592
04b
2be5M02
M:9-143,M:324-470,M:536-592
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
'winged helix' repressor DNA binding domain
(507)
Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274.
(9)
05a
2be5F02
F:260-313
05b
2be5P02
P:260-313
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
(18)
Homologous Superfamily
:
[code=2.40.270.10, no name defined]
(18)
Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274.
(9)
06a
2be5C01
C:2-8,C:668-698,C:832-1004
06b
2be5M01
M:2-8,M:668-698,M:832-1004
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
[code=2.40.50.100, no name defined]
(113)
Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274.
(9)
07a
2be5C05
C:593-667
07b
2be5M05
M:593-667
Homologous Superfamily
:
[code=2.40.50.150, no name defined]
(48)
Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274.
(9)
08a
2be5C06
C:699-831
08b
2be5M06
M:699-831
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)
Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274.
(9)
09a
2be5A02
A:50-171
09b
2be5B02
B:50-171
09c
2be5K02
K:50-171
09d
2be5L02
L:50-171
Architecture
:
Roll
(1513)
Topology
:
Rna Polymerase Beta Subunit; Chain: C, domain 4
(18)
Homologous Superfamily
:
[code=2.30.150.10, no name defined]
(18)
Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus. Organism_taxid: 274.
(9)
10a
2be5C04
C:471-535
10b
2be5M04
M:471-535
[
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]
Pfam Domains
(0, 0)
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