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2BE5
Asym. Unit
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
)
[
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Hetero Components
(3, 10)
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
4
Ligand/Ion
MAGNESIUM ION
2
TGT
2
Ligand/Ion
TAGETITOXIN
3
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
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Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU C:685 , ARG C:879 , ASP D:739 , ARG D:1029 , HOH D:2099 , TGT D:9001
BINDING SITE FOR RESIDUE MG C 9004
02
AC2
SOFTWARE
CYS D:58 , CYS D:60 , CYS D:73 , CYS D:76
BINDING SITE FOR RESIDUE ZN D 9058
03
AC3
SOFTWARE
CYS D:1112 , CYS D:1194 , CYS D:1201 , CYS D:1204
BINDING SITE FOR RESIDUE ZN D 9112
04
AC4
SOFTWARE
ASP D:739 , ASP D:741 , ASP D:743
BINDING SITE FOR RESIDUE MG D 9003
05
AC5
SOFTWARE
ARG C:557 , SER C:878 , ARG C:879 , MG C:9004 , HOH C:9409 , ASN D:737 , ASP D:739 , ARG D:783 , ARG D:1029 , ASN D:1031 , GLN D:1034 , HOH D:2099 , HOH D:2481 , HOH D:2666 , HOH D:9123 , HOH D:9375 , HOH D:9576 , HOH D:9602
BINDING SITE FOR RESIDUE TGT D 9001
06
AC6
SOFTWARE
CYS N:58 , CYS N:60 , CYS N:73 , CYS N:76
BINDING SITE FOR RESIDUE ZN N 9059
07
AC7
SOFTWARE
CYS N:1112 , ARG N:1189 , CYS N:1194 , CYS N:1201 , CYS N:1204
BINDING SITE FOR RESIDUE ZN N 9113
08
AC8
SOFTWARE
ASP N:739 , ASP N:741 , ASP N:743
BINDING SITE FOR RESIDUE MG N 9005
09
AC9
SOFTWARE
GLU M:685 , ARG M:879 , ASP N:739 , TGT N:9002
BINDING SITE FOR RESIDUE MG N 9006
10
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 not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: RNA_POL_BETA (C:836-848,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
2
C:836-848
M:836-848
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Exons
(0, 0)
Info
All Exons
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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.
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
(
)
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)
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
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