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3DXJ
Asym. Unit
Info
Asym.Unit (1.1 MB)
Biol.Unit 1 (575 KB)
Biol.Unit 2 (577 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS RNA POLYMERASE HOLOENZYME IN COMPLEX WITH THE ANTIBIOTIC MYXOPYRONIN
Authors
:
K. Das, E. Arnold
Date
:
24 Jul 08 (Deposition) - 14 Oct 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
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; Rnap; Drug Complex; Inhibitor; Corallopyronin; Ripostatin; Transcription; Holoenzyme; Crystallography; Twinning; Hemihedral, Dna-Directed Rna Polymerase, Nucleotidyltransferase, Transcription, Transferase, Dna-Binding, Sigma Factor, Transcription Regulation, Transcription, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Mukhopadhyay, K. Das, S. Ismail, D. Koppstein, M. Jang, B. Hudson, S. Sarafianos, S. Tuske, J. Patel, R. Jansen, H. Irschik, E. Arnold, R. H. Ebright
The Rna Polymerase "Switch Region" Is A Target For Inhibitors.
Cell(Cambridge, Mass. ) V. 135 295 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 14)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
2b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
2c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
3a: METHYL [(1E,5R)-5-{(3S)-3-[(2E,4E)... (NE6a)
3b: METHYL [(1E,5R)-5-{(3S)-3-[(2E,4E)... (NE6b)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
3
Ligand/Ion
MAGNESIUM ION
2
MPD
3
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
NE6
2
Ligand/Ion
METHYL [(1E,5R)-5-{(3S)-3-[(2E,4E)-2,5-DIMETHYLOCTA-2,4-DIENOYL]-2,4-DIOXO-3,4-DIHYDRO-2H-PYRAN-6-YL}HEXYLIDENE]CARBAMATE
4
PO4
2
Ligand/Ion
PHOSPHATE ION
5
ZN
4
Ligand/Ion
ZINC ION
[
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Sites
(13, 13)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS D:58 , CYS D:60 , LYS D:62 , CYS D:73 , CYS D:76
BINDING SITE FOR RESIDUE ZN D 1525
02
AC2
SOFTWARE
CYS D:1112 , CYS D:1194 , GLN D:1195 , THR D:1196 , CYS D:1201 , CYS D:1204
BINDING SITE FOR RESIDUE ZN D 1526
03
AC3
SOFTWARE
ASP D:739 , ASP D:741 , ASP D:743 , HOH D:1530
BINDING SITE FOR RESIDUE MG D 1527
04
AC4
SOFTWARE
GLU B:154 , ASP B:168 , LYS D:840 , TYR D:841 , HOH D:1531
BINDING SITE FOR RESIDUE MG B 701
05
AC5
SOFTWARE
CYS N:58 , ALA N:59 , CYS N:60 , GLY N:61 , LYS N:62 , CYS N:73 , CYS N:76
BINDING SITE FOR RESIDUE ZN N 1525
06
AC6
SOFTWARE
CYS N:1112 , CYS N:1194 , CYS N:1201 , CYS N:1204
BINDING SITE FOR RESIDUE ZN N 1526
07
AC7
SOFTWARE
ASP N:739 , ASP N:741 , ASP N:743 , HOH N:1529
BINDING SITE FOR RESIDUE MG N 1527
08
AC8
SOFTWARE
LYS A:83 , GLU A:84 , LEU A:85 , ARG A:175 , ASP A:202
BINDING SITE FOR RESIDUE PO4 A 316
09
AC9
SOFTWARE
GLU C:1034 , PHE D:614 , ARG D:1096 , ASP D:1100 , SER D:1439 , PHE D:1440 , LYS D:1463
BINDING SITE FOR RESIDUE PO4 D 1528
10
BC1
SOFTWARE
PHE C:1032 , TRP C:1038 , GLU C:1041 , SER C:1084 , PHE D:614 , LEU D:619 , GLY D:620 , HIS D:1103 , ALA D:1438 , SER D:1439 , THR D:1443 , LYS D:1463 , ILE D:1467 , HOH D:1539
BINDING SITE FOR RESIDUE NE6 D 1529
11
BC2
SOFTWARE
TRP M:1038 , GLU M:1041 , SER M:1084 , PHE N:614 , LEU N:619 , GLY N:620 , LYS N:621 , HIS N:1103 , ILE N:1223 , LYS N:1463 , ILE N:1467
BINDING SITE FOR RESIDUE NE6 N 1528
12
BC3
SOFTWARE
GLY C:951 , LEU C:952 , GLN C:969 , TYR D:1015
BINDING SITE FOR RESIDUE MPD C 1120
13
BC4
SOFTWARE
LEU M:952 , GLU M:965 , ASP N:952
BINDING SITE FOR RESIDUE MPD M 1120
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
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
View:
Select:
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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
(5, 12)
Info
All SCOP Domains
1a: SCOP_d3dxjf2 (F:258-318)
1b: SCOP_d3dxjp2 (P:258-318)
1c: SCOP_d3dxjp3 (P:319-422)
1d: SCOP_d3dxjf3 (F:319-422)
2a: SCOP_d3dxje_ (E:)
2b: SCOP_d3dxjo_ (O:)
3a: SCOP_d3dxjf1 (F:74-257)
3b: SCOP_d3dxjp1 (P:74-257)
4a: SCOP_d3dxjc_ (C:)
4b: SCOP_d3dxjm_ (M:)
5a: SCOP_d3dxjd_ (D:)
5b: SCOP_d3dxjn_ (N:)
View:
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Classes
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)
(
)
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
:
automated matches
(4)
Protein domain
:
automated matches
(4)
Thermus thermophilus HB8 [TaxId: 300852]
(3)
1a
d3dxjf2
F:258-318
1b
d3dxjp2
P:258-318
1c
d3dxjp3
P:319-422
1d
d3dxjf3
F:319-422
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 HB8 [TaxId: 300852]
(6)
2a
d3dxje_
E:
2b
d3dxjo_
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
:
automated matches
(2)
Thermus thermophilus HB8 [TaxId: 300852]
(1)
3a
d3dxjf1
F:74-257
3b
d3dxjp1
P:74-257
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 HB8 [TaxId: 300852]
(4)
4a
d3dxjc_
C:
4b
d3dxjm_
M:
Family
:
RNA-polymerase beta-prime
(49)
Protein domain
:
automated matches
(8)
Thermus thermophilus HB8 [TaxId: 300852]
(3)
5a
d3dxjd_
D:
5b
d3dxjn_
N:
[
close SCOP info
]
CATH Domains
(10, 24)
Info
all CATH domains
01a: CATH_3dxjA01 (A:1-49,A:172-225)
01b: CATH_3dxjB01 (B:1-49,B:172-225)
01c: CATH_3dxjK01 (K:1-49,K:172-225)
01d: CATH_3dxjL01 (L:1-49,L:172-225)
02a: CATH_3dxjC03 (C:144-323)
02b: CATH_3dxjM03 (M:144-323)
03a: CATH_3dxjE00 (E:2-96)
03b: CATH_3dxjO00 (O:2-96)
04a: CATH_3dxjC02 (C:16-143,C:324-469,C:535-593)
04b: CATH_3dxjM02 (M:16-143,M:324-469,M:535-593)
05a: CATH_3dxjF02 (F:260-313)
05b: CATH_3dxjP02 (P:260-313)
06a: CATH_3dxjC01 (C:1-6,C:668-700,C:833-997)
06b: CATH_3dxjM01 (M:1-6,M:668-700,M:833-997)
07a: CATH_3dxjC05 (C:594-658)
07b: CATH_3dxjM05 (M:594-658)
08a: CATH_3dxjC06 (C:701-832)
08b: CATH_3dxjM06 (M:701-832)
09a: CATH_3dxjA02 (A:50-171)
09b: CATH_3dxjB02 (B:50-171)
09c: CATH_3dxjK02 (K:50-171)
09d: CATH_3dxjL02 (L:50-171)
10a: CATH_3dxjC04 (C:470-534)
10b: CATH_3dxjM04 (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 hb8. Organism_taxid: 300852. Thermus thermophilushb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852.
(1)
01a
3dxjA01
A:1-49,A:172-225
01b
3dxjB01
B:1-49,B:172-225
01c
3dxjK01
K:1-49,K:172-225
01d
3dxjL01
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 hb8. Organism_taxid: 300852. Thermus thermophilushb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852.
(1)
02a
3dxjC03
C:144-323
02b
3dxjM03
M:144-323
Topology
:
Eukaryotic RPB6 RNA polymerase subunit
(77)
Homologous Superfamily
:
[code=3.90.940.10, no name defined]
(71)
Thermus thermophilus hb8. Organism_taxid: 300852. Thermus thermophilushb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852.
(1)
03a
3dxjE00
E:2-96
03b
3dxjO00
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 hb8. Organism_taxid: 300852. Thermus thermophilushb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852.
(1)
04a
3dxjC02
C:16-143,C:324-469,C:535-593
04b
3dxjM02
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 hb8. Organism_taxid: 300852. Thermus thermophilushb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852.
(1)
05a
3dxjF02
F:260-313
05b
3dxjP02
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 hb8. Organism_taxid: 300852. Thermus thermophilushb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852.
(1)
06a
3dxjC01
C:1-6,C:668-700,C:833-997
06b
3dxjM01
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 hb8. Organism_taxid: 300852. Thermus thermophilushb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852.
(1)
07a
3dxjC05
C:594-658
07b
3dxjM05
M:594-658
Homologous Superfamily
:
[code=2.40.50.150, no name defined]
(48)
Thermus thermophilus hb8. Organism_taxid: 300852. Thermus thermophilushb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852.
(1)
08a
3dxjC06
C:701-832
08b
3dxjM06
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 hb8. Organism_taxid: 300852. Thermus thermophilushb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852.
(1)
09a
3dxjA02
A:50-171
09b
3dxjB02
B:50-171
09c
3dxjK02
K:50-171
09d
3dxjL02
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 hb8. Organism_taxid: 300852. Thermus thermophilushb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852. Thermus thermophilus hb8. Organism_taxid: 300852.
(1)
10a
3dxjC04
C:470-534
10b
3dxjM04
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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