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2CW0
Biol. Unit 1
Info
Asym.Unit (1.1 MB)
Biol.Unit 1 (549 KB)
Biol.Unit 2 (551 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS RNA POLYMERASE HOLOENZYME AT 3.3 ANGSTROMS RESOLUTION
Authors
:
S. Tuske, S. G. Sarafianos, X. Wang, B. Hudson, E. Sineva, J. Mukhopadhy J. J. Birktoft, O. Leroy, S. Ismail, A. D. Clark Jr. , C. Dharia, A. Napo O. Laptenko, J. Lee, S. Borukhov, R. H. Ebright, E. Arnold
Date
:
15 Jun 05 (Deposition) - 20 Sep 05 (Release) - 05 Sep 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.30
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, Transcription, Bent-Bridge Helix, Transferase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
S. Tuske, S. G. Sarafianos, X. Wang, B. Hudson, E. Sineva, J. Mukhopadhyay, J. J. Birktoft, O. Leroy, S. Ismail, A. D. Clark Jr. , C. Dharia, A. Napoli, O. Laptenko, J. Lee, S. Borukhov, R. H. Ebright, E. Arnold
Inhibition Of Bacterial Rna Polymerase By Streptolydigin: Stabilization Of A Straight-Bridge-Helix Active-Center Conformation
Cell(Cambridge, Mass. ) V. 122 541 2005
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Hetero Components
(0, 0)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC5 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS D:58 , CYS D:60 , CYS D:73 , CYS D:76
BINDING SITE FOR RESIDUE ZN D 1525
2
AC2
SOFTWARE
CYS D:1112 , CYS D:1194 , CYS D:1201 , CYS D:1204
BINDING SITE FOR RESIDUE ZN D 1526
3
AC5
SOFTWARE
ASP D:739 , ASP D:741
BINDING SITE FOR RESIDUE MG D 1527
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: RNA_POL_BETA (C:836-848)
;
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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
C:836-848
-
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Exons
(0, 0)
Info
All Exons
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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_d2cw0f1 (F:258-318)
1b: SCOP_d2cw0p1 (P:258-318)
2a: SCOP_d2cw0f2 (F:319-423)
2b: SCOP_d2cw0p2 (P:319-423)
3a: SCOP_d2cw0e1 (E:2-96)
3b: SCOP_d2cw0o1 (O:2-96)
4a: SCOP_d2cw0f3 (F:74-257)
4b: SCOP_d2cw0p3 (P:74-257)
5a: SCOP_d2cw0a1 (A:1-49,A:173-229)
5b: SCOP_d2cw0b1 (B:1-49,B:173-229)
5c: SCOP_d2cw0k1 (K:1-49,K:173-229)
5d: SCOP_d2cw0l1 (L:1-49,L:173-229)
6a: SCOP_d2cw0a2 (A:50-172)
6b: SCOP_d2cw0b2 (B:50-172)
6c: SCOP_d2cw0k2 (K:50-172)
6d: SCOP_d2cw0l2 (L:50-172)
7a: SCOP_d2cw0c1 (C:1-1119)
7b: SCOP_d2cw0m1 (M:1-1119)
8a: SCOP_d2cw0d1 (D:2-1505)
8b: SCOP_d2cw0n1 (N:2-1505)
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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
:
Sigma3 domain
(12)
Protein domain
:
Sigma70
(9)
Thermus thermophilus [TaxId: 274]
(9)
1a
d2cw0f1
F:258-318
1b
d2cw0p1
P:258-318
Family
:
Sigma4 domain
(23)
Protein domain
:
Sigma70 (SigA, RpoD)
(15)
Thermus thermophilus [TaxId: 274]
(9)
2a
d2cw0f2
F:319-423
2b
d2cw0p2
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
d2cw0e1
E:2-96
3b
d2cw0o1
O:2-96
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
d2cw0f3
F:74-257
4b
d2cw0p3
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
d2cw0a1
A:1-49,A:173-229
5b
d2cw0b1
B:1-49,B:173-229
5c
d2cw0k1
K:1-49,K:173-229
5d
d2cw0l1
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
d2cw0a2
A:50-172
6b
d2cw0b2
B:50-172
6c
d2cw0k2
K:50-172
6d
d2cw0l2
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
:
RNA-polymerase beta
(9)
Thermus thermophilus [TaxId: 274]
(5)
7a
d2cw0c1
C:1-1119
7b
d2cw0m1
M:1-1119
Family
:
RNA-polymerase beta-prime
(49)
Protein domain
:
RNA-polymerase beta-prime
(16)
Thermus thermophilus [TaxId: 274]
(12)
8a
d2cw0d1
D:2-1505
8b
d2cw0n1
N:2-1505
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CATH Domains
(10, 24)
Info
all CATH domains
01a: CATH_2cw0A01 (A:1-49,A:172-225)
01b: CATH_2cw0B01 (B:1-49,B:172-225)
01c: CATH_2cw0K01 (K:1-49,K:172-225)
01d: CATH_2cw0L01 (L:1-49,L:172-225)
02a: CATH_2cw0C03 (C:144-323)
02b: CATH_2cw0M03 (M:144-323)
03a: CATH_2cw0E00 (E:2-96)
03b: CATH_2cw0O00 (O:2-96)
04a: CATH_2cw0C02 (C:9-143,C:324-470,C:536-592)
04b: CATH_2cw0M02 (M:9-143,M:324-470,M:536-592)
05a: CATH_2cw0F02 (F:260-313)
05b: CATH_2cw0P02 (P:260-313)
06a: CATH_2cw0C01 (C:2-8,C:668-698,C:832-1004)
06b: CATH_2cw0M01 (M:2-8,M:668-698,M:832-1004)
07a: CATH_2cw0C05 (C:593-667)
07b: CATH_2cw0M05 (M:593-667)
08a: CATH_2cw0C06 (C:699-831)
08b: CATH_2cw0M06 (M:699-831)
09a: CATH_2cw0A02 (A:50-171)
09b: CATH_2cw0B02 (B:50-171)
09c: CATH_2cw0K02 (K:50-171)
09d: CATH_2cw0L02 (L:50-171)
10a: CATH_2cw0C04 (C:471-535)
10b: CATH_2cw0M04 (M:471-535)
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)
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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 hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus. Organism_taxid: 274.
(1)
01a
2cw0A01
A:1-49,A:172-225
01b
2cw0B01
B:1-49,B:172-225
01c
2cw0K01
K:1-49,K:172-225
01d
2cw0L01
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 hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus. Organism_taxid: 274.
(1)
02a
2cw0C03
C:144-323
02b
2cw0M03
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 hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus. Organism_taxid: 274.
(1)
03a
2cw0E00
E:2-96
03b
2cw0O00
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 hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus. Organism_taxid: 274.
(1)
04a
2cw0C02
C:9-143,C:324-470,C:536-592
04b
2cw0M02
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 hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus. Organism_taxid: 274.
(1)
05a
2cw0F02
F:260-313
05b
2cw0P02
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 hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus. Organism_taxid: 274.
(1)
06a
2cw0C01
C:2-8,C:668-698,C:832-1004
06b
2cw0M01
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 hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus. Organism_taxid: 274.
(1)
07a
2cw0C05
C:593-667
07b
2cw0M05
M:593-667
Homologous Superfamily
:
[code=2.40.50.150, no name defined]
(48)
Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus. Organism_taxid: 274.
(1)
08a
2cw0C06
C:699-831
08b
2cw0M06
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 hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus. Organism_taxid: 274.
(1)
09a
2cw0A02
A:50-171
09b
2cw0B02
B:50-171
09c
2cw0K02
K:50-171
09d
2cw0L02
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 hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8. Thermus thermophilus. Organism_taxid: 274.
(1)
10a
2cw0C04
C:471-535
10b
2cw0M04
M:471-535
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Pfam Domains
(0, 0)
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Asym.Unit (1.1 MB)
Header - Asym.Unit
Biol.Unit 1 (549 KB)
Header - Biol.Unit 1
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