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3EQL
Biol. Unit 1
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Asym.Unit (1.1 MB)
Biol.Unit 1 (588 KB)
Biol.Unit 2 (586 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE T. THERMOPHILUS RNA POLYMERASE HOLOENZYME IN COMPLEX WITH ANTIBIOTIC MYXOPYRONIN
Authors
:
D. G. Vassylyev, M. N. Vassylyeva, I. Artsimovitch
Date
:
30 Sep 08 (Deposition) - 28 Oct 08 (Release) - 20 Jan 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
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, Myxopyronin, Antibiotic, Transcription Regulation, Dna-Directed Rna Polymerase, Nucleotidyltransferase, Transcription, Transferase, Dna- Binding, Sigma Factor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. A. Belogurov, M. N. Vassylyeva, A. Sevostyanova, J. R. Appleman, A. X. Xiang, R. Lira, S. E. Webber, S. Klyuyev, E. Nudler, I. Artsimovitch, D. G. Vassylyev
Transcription Inactivation Through Local Refolding Of The Rna Polymerase Structure.
Nature V. 457 332 2009
(for further references see the
PDB file header
)
[
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]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
2a: MYXOPYRONIN B (MXPa)
2b: MYXOPYRONIN B (MXPb)
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
MXP
1
Ligand/Ion
MYXOPYRONIN B
3
ZN
-1
Ligand/Ion
ZINC ION
[
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]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS D:58 , CYS D:60 , CYS D:73 , CYS D:76 , HOH D:1539
BINDING SITE FOR RESIDUE ZN D1525
2
AC2
SOFTWARE
CYS D:1112 , CYS D:1194 , CYS D:1201 , CYS D:1204
BINDING SITE FOR RESIDUE ZN D1526
3
AC3
SOFTWARE
GLU C:1034 , TRP C:1038 , GLU C:1041 , SER C:1084 , LEU C:1088 , LYS D:610 , GLN D:611 , LEU D:619 , GLY D:620 , LYS D:1463 , VAL D:1466 , ILE D:1467
BINDING SITE FOR RESIDUE MXP D1527
4
AC4
SOFTWARE
ASP D:739 , ASP D:741 , ASP D:743
BINDING SITE FOR RESIDUE MG D1528
[
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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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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: SIGMA70_2 (F:384-408)
2: RNA_POL_BETA (C:836-848)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SIGMA70_2
PS00716
Sigma-70 factors family signature 2.
SIGA_THET2
382-408
1
F:384-408
-
2
RNA_POL_BETA
PS01166
RNA polymerases beta chain signature.
RPOB_THET8
836-848
1
C: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.
(no "Exon" information available for biological units yet)
SCOP Domains
(8, 20)
Info
All SCOP Domains
1a: SCOP_d3eqlf2 (F:258-318)
1b: SCOP_d3eqlp2 (P:258-318)
2a: SCOP_d3eqlf3 (F:319-423)
2b: SCOP_d3eqlp3 (P:319-423)
3a: SCOP_d3eqle_ (E:)
3b: SCOP_d3eqlo_ (O:)
4a: SCOP_d3eqlf1 (F:74-257)
4b: SCOP_d3eqlp1 (P:74-257)
5a: SCOP_d3eqla1 (A:1-49,A:173-229)
5b: SCOP_d3eqlb1 (B:1-49,B:173-229)
5c: SCOP_d3eqlk1 (K:1-49,K:173-229)
5d: SCOP_d3eqll1 (L:1-49,L:173-229)
6a: SCOP_d3eqla2 (A:50-172)
6b: SCOP_d3eqlb2 (B:50-172)
6c: SCOP_d3eqlk2 (K:50-172)
6d: SCOP_d3eqll2 (L:50-172)
7a: SCOP_d3eqlc_ (C:)
7b: SCOP_d3eqlm_ (M:)
8a: SCOP_d3eqld_ (D:)
8b: SCOP_d3eqln_ (N:)
View:
Select:
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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
d3eqlf2
F:258-318
1b
d3eqlp2
P:258-318
Family
:
Sigma4 domain
(23)
Protein domain
:
Sigma70 (SigA, RpoD)
(15)
Thermus thermophilus [TaxId: 274]
(9)
2a
d3eqlf3
F:319-423
2b
d3eqlp3
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
d3eqle_
E:
3b
d3eqlo_
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
d3eqlf1
F:74-257
4b
d3eqlp1
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
d3eqla1
A:1-49,A:173-229
5b
d3eqlb1
B:1-49,B:173-229
5c
d3eqlk1
K:1-49,K:173-229
5d
d3eqll1
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
d3eqla2
A:50-172
6b
d3eqlb2
B:50-172
6c
d3eqlk2
K:50-172
6d
d3eqll2
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
d3eqlc_
C:
7b
d3eqlm_
M:
Family
:
RNA-polymerase beta-prime
(49)
Protein domain
:
RNA-polymerase beta-prime
(16)
Thermus thermophilus [TaxId: 274]
(12)
8a
d3eqld_
D:
8b
d3eqln_
N:
[
close SCOP info
]
CATH Domains
(10, 24)
Info
all CATH domains
01a: CATH_3eqlA01 (A:1-49,A:172-225)
01b: CATH_3eqlB01 (B:1-49,B:172-225)
01c: CATH_3eqlK01 (K:1-49,K:172-225)
01d: CATH_3eqlL01 (L:1-49,L:172-225)
02a: CATH_3eqlC03 (C:144-323)
02b: CATH_3eqlM03 (M:144-323)
03a: CATH_3eqlE00 (E:2-96)
03b: CATH_3eqlO00 (O:2-96)
04a: CATH_3eqlC02 (C:16-143,C:324-469,C:535-593)
04b: CATH_3eqlM02 (M:16-143,M:324-469,M:535-593)
05a: CATH_3eqlF02 (F:260-313)
05b: CATH_3eqlP02 (P:260-313)
06a: CATH_3eqlC01 (C:1-6,C:668-700,C:833-997)
06b: CATH_3eqlM01 (M:1-6,M:668-700,M:833-997)
07a: CATH_3eqlC05 (C:594-658)
07b: CATH_3eqlM05 (M:594-658)
08a: CATH_3eqlC06 (C:701-832)
08b: CATH_3eqlM06 (M:701-832)
09a: CATH_3eqlA02 (A:50-171)
09b: CATH_3eqlB02 (B:50-171)
09c: CATH_3eqlK02 (K:50-171)
09d: CATH_3eqlL02 (L:50-171)
10a: CATH_3eqlC04 (C:470-534)
10b: CATH_3eqlM04 (M:470-534)
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
3eqlA01
A:1-49,A:172-225
01b
3eqlB01
B:1-49,B:172-225
01c
3eqlK01
K:1-49,K:172-225
01d
3eqlL01
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
3eqlC03
C:144-323
02b
3eqlM03
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
3eqlE00
E:2-96
03b
3eqlO00
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
3eqlC02
C:16-143,C:324-469,C:535-593
04b
3eqlM02
M:16-143,M:324-469,M:535-593
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
3eqlF02
F:260-313
05b
3eqlP02
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
3eqlC01
C:1-6,C:668-700,C:833-997
06b
3eqlM01
M:1-6,M:668-700,M:833-997
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
3eqlC05
C:594-658
07b
3eqlM05
M:594-658
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
3eqlC06
C:701-832
08b
3eqlM06
M:701-832
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
3eqlA02
A:50-171
09b
3eqlB02
B:50-171
09c
3eqlK02
K:50-171
09d
3eqlL02
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
3eqlC04
C:470-534
10b
3eqlM04
M:470-534
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (1.1 MB)
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