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2O5I
Asym. Unit
Info
Asym.Unit (1.1 MB)
Biol.Unit 1 (542 KB)
Biol.Unit 2 (538 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE T. THERMOPHILUS RNA POLYMERASE ELONGATION COMPLEX
Authors
:
D. G. Vassylyev, T. H. Tahirov, M. N. Vassylyeva
Date
:
06 Dec 06 (Deposition) - 03 Jul 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,G,H,I,K,L,M,N,O,X,Y,Z
Biol. Unit 1: A,B,C,D,E,G,H,I (1x)
Biol. Unit 2: K,L,M,N,O,X,Y,Z (1x)
Keywords
:
Rna Polymerase, Elongation Complex, Template Dna, Non-Template Dna, Rna Transcript, Transferase-Dna-Rna Hybrid Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. G. Vassylyev, M. N. Vassylyeva, A. Perederina, T. H. Tahirov, I. Artsimovitch
Structural Basis For Transcription Elongation By Bacterial Rna Polymerase.
Nature V. 448 157 2007
[
close entry info
]
Hetero Components
(2, 6)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
2
Ligand/Ion
MAGNESIUM ION
2
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS D:58 , ALA D:59 , CYS D:60 , CYS D:73 , CYS D:76
BINDING SITE FOR RESIDUE ZN D 4058
2
AC2
SOFTWARE
CYS D:1112 , CYS D:1194 , CYS D:1201 , CYS D:1204
BINDING SITE FOR RESIDUE ZN D 6112
3
AC3
SOFTWARE
SER D:1300 , CYS N:58 , ALA N:59 , CYS N:60 , CYS N:73 , CYS N:76
BINDING SITE FOR RESIDUE ZN N 5058
4
AC4
SOFTWARE
CYS N:1112 , CYS N:1194 , CYS N:1201 , CYS N:1204
BINDING SITE FOR RESIDUE ZN N 7112
5
AC5
SOFTWARE
ASP D:739 , ASP D:741 , ASP D:743 , G H:16
BINDING SITE FOR RESIDUE MG D 8001
6
AC6
SOFTWARE
ASP N:739 , ASP N:741 , ASP N:743 , G Y:16
BINDING SITE FOR RESIDUE MG N 8002
[
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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:
Label:
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, 14)
Info
All SCOP Domains
1a: SCOP_d2o5ie_ (E:)
1b: SCOP_d2o5io_ (O:)
2a: SCOP_d2o5ia1 (A:1-49,A:173-229)
2b: SCOP_d2o5ib1 (B:1-49,B:173-229)
2c: SCOP_d2o5ik1 (K:1-49,K:173-229)
2d: SCOP_d2o5il1 (L:1-49,L:173-229)
3a: SCOP_d2o5ia2 (A:50-172)
3b: SCOP_d2o5ib2 (B:50-172)
3c: SCOP_d2o5ik2 (K:50-172)
3d: SCOP_d2o5il2 (L:50-172)
4a: SCOP_d2o5ic_ (C:)
4b: SCOP_d2o5im_ (M:)
5a: SCOP_d2o5id_ (D:)
5b: SCOP_d2o5in_ (N:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
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)
1a
d2o5ie_
E:
1b
d2o5io_
O:
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)
2a
d2o5ia1
A:1-49,A:173-229
2b
d2o5ib1
B:1-49,B:173-229
2c
d2o5ik1
K:1-49,K:173-229
2d
d2o5il1
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)
3a
d2o5ia2
A:50-172
3b
d2o5ib2
B:50-172
3c
d2o5ik2
K:50-172
3d
d2o5il2
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 HB8 [TaxId: 300852]
(4)
4a
d2o5ic_
C:
4b
d2o5im_
M:
Family
:
RNA-polymerase beta-prime
(49)
Protein domain
:
RNA-polymerase beta-prime
(16)
Thermus thermophilus [TaxId: 274]
(12)
5a
d2o5id_
D:
5b
d2o5in_
N:
[
close SCOP info
]
CATH Domains
(9, 22)
Info
all CATH domains
1a: CATH_2o5iA01 (A:1-49,A:172-225)
1b: CATH_2o5iB01 (B:1-49,B:172-225)
1c: CATH_2o5iK01 (K:1-49,K:172-225)
1d: CATH_2o5iL01 (L:1-49,L:172-225)
2a: CATH_2o5iC03 (C:144-323)
2b: CATH_2o5iM03 (M:144-323)
3a: CATH_2o5iE00 (E:2-96)
3b: CATH_2o5iO00 (O:2-96)
4a: CATH_2o5iC02 (C:16-143,C:324-469,C:535-593)
4b: CATH_2o5iM02 (M:16-143,M:324-469,M:535-593)
5a: CATH_2o5iC01 (C:1-6,C:668-700,C:833-997)
5b: CATH_2o5iM01 (M:1-6,M:668-700,M:833-997)
6a: CATH_2o5iC05 (C:594-658)
6b: CATH_2o5iM05 (M:594-658)
7a: CATH_2o5iC06 (C:701-832)
7b: CATH_2o5iM06 (M:701-832)
8a: CATH_2o5iA02 (A:50-171)
8b: CATH_2o5iB02 (B:50-171)
8c: CATH_2o5iK02 (K:50-171)
8d: CATH_2o5iL02 (L:50-171)
9a: CATH_2o5iC04 (C:470-534)
9b: CATH_2o5iM04 (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)
[unclassified]
(17)
1a
2o5iA01
A:1-49,A:172-225
1b
2o5iB01
B:1-49,B:172-225
1c
2o5iK01
K:1-49,K:172-225
1d
2o5iL01
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)
[unclassified]
(17)
2a
2o5iC03
C:144-323
2b
2o5iM03
M:144-323
Topology
:
Eukaryotic RPB6 RNA polymerase subunit
(77)
Homologous Superfamily
:
[code=3.90.940.10, no name defined]
(71)
[unclassified]
(17)
3a
2o5iE00
E:2-96
3b
2o5iO00
O:2-96
Topology
:
Rna Polymerase Beta Subunit; Chain: C,domain 2
(18)
Homologous Superfamily
:
[code=3.90.1100.10, no name defined]
(18)
[unclassified]
(3)
4a
2o5iC02
C:16-143,C:324-469,C:535-593
4b
2o5iM02
M:16-143,M:324-469,M:535-593
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)
[unclassified]
(3)
5a
2o5iC01
C:1-6,C:668-700,C:833-997
5b
2o5iM01
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)
[unclassified]
(3)
6a
2o5iC05
C:594-658
6b
2o5iM05
M:594-658
Homologous Superfamily
:
[code=2.40.50.150, no name defined]
(48)
[unclassified]
(17)
7a
2o5iC06
C:701-832
7b
2o5iM06
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)
[unclassified]
(17)
8a
2o5iA02
A:50-171
8b
2o5iB02
B:50-171
8c
2o5iK02
K:50-171
8d
2o5iL02
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)
[unclassified]
(3)
9a
2o5iC04
C:470-534
9b
2o5iM04
M:470-534
[
close CATH info
]
Pfam Domains
(14, 34)
Info
all PFAM domains
01a: PFAM_RNA_pol_Rpb2_6_2o5iM01 (M:541-1026)
01b: PFAM_RNA_pol_Rpb2_6_2o5iM02 (M:541-1026)
02a: PFAM_RNA_pol_L_2o5iL01 (L:25-223)
02b: PFAM_RNA_pol_L_2o5iL02 (L:25-223)
02c: PFAM_RNA_pol_L_2o5iL03 (L:25-223)
02d: PFAM_RNA_pol_L_2o5iL04 (L:25-223)
03a: PFAM_RNA_pol_A_bac_2o5iL05 (L:52-180)
03b: PFAM_RNA_pol_A_bac_2o5iL06 (L:52-180)
03c: PFAM_RNA_pol_A_bac_2o5iL07 (L:52-180)
03d: PFAM_RNA_pol_A_bac_2o5iL08 (L:52-180)
04a: PFAM_RNA_pol_Rpb1_1_2o5iN01 (N:417-618)
04b: PFAM_RNA_pol_Rpb1_1_2o5iN02 (N:417-618)
04c: PFAM_RNA_pol_Rpb1_1_2o5iN03 (N:417-618)
04d: PFAM_RNA_pol_Rpb1_1_2o5iN04 (N:417-618)
05a: PFAM_RNA_pol_Rpb1_2_2o5iN05 (N:620-765)
05b: PFAM_RNA_pol_Rpb1_2_2o5iN06 (N:620-765)
06a: PFAM_RNA_pol_Rpb1_3_2o5iN07 (N:768-954)
06b: PFAM_RNA_pol_Rpb1_3_2o5iN08 (N:768-954)
07a: PFAM_RNA_pol_Rpb1_4_2o5iN09 (N:983-1066)
07b: PFAM_RNA_pol_Rpb1_4_2o5iN10 (N:983-1066)
08a: PFAM_RNA_pol_Rpb1_5_2o5iN11 (N:1064-1437)
08b: PFAM_RNA_pol_Rpb1_5_2o5iN12 (N:1064-1437)
09a: PFAM_RNA_pol_Rpb2_1_2o5iM03 (M:17-389)
09b: PFAM_RNA_pol_Rpb2_1_2o5iM04 (M:17-389)
10a: PFAM_RNA_pol_Rpb2_2_2o5iM05 (M:142-334)
10b: PFAM_RNA_pol_Rpb2_2_2o5iM06 (M:142-334)
11a: PFAM_RNA_pol_Rpb2_3_2o5iM07 (M:393-462)
11b: PFAM_RNA_pol_Rpb2_3_2o5iM08 (M:393-462)
12a: PFAM_RNA_pol_Rpb2_45_2o5iM09 (M:471-535)
12b: PFAM_RNA_pol_Rpb2_45_2o5iM10 (M:471-535)
13a: PFAM_RNA_pol_Rpb2_7_2o5iM11 (M:1028-1104)
13b: PFAM_RNA_pol_Rpb2_7_2o5iM12 (M:1028-1104)
14a: PFAM_RNA_pol_Rpb6_2o5iO01 (O:7-57)
14b: PFAM_RNA_pol_Rpb6_2o5iO02 (O:7-57)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
LEF-8-like
(36)
Family
:
RNA_pol_Rpb2_6
(36)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(5)
01a
RNA_pol_Rpb2_6-2o5iM01
M:541-1026
01b
RNA_pol_Rpb2_6-2o5iM02
M:541-1026
Clan
:
RBP11-like
(36)
Family
:
RNA_pol_L
(36)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(3)
02a
RNA_pol_L-2o5iL01
L:25-223
02b
RNA_pol_L-2o5iL02
L:25-223
02c
RNA_pol_L-2o5iL03
L:25-223
02d
RNA_pol_L-2o5iL04
L:25-223
Clan
:
no clan defined [family: RNA_pol_A_bac]
(36)
Family
:
RNA_pol_A_bac
(36)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(3)
03a
RNA_pol_A_bac-2o5iL05
L:52-180
03b
RNA_pol_A_bac-2o5iL06
L:52-180
03c
RNA_pol_A_bac-2o5iL07
L:52-180
03d
RNA_pol_A_bac-2o5iL08
L:52-180
Clan
:
no clan defined [family: RNA_pol_Rpb1_1]
(37)
Family
:
RNA_pol_Rpb1_1
(37)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(5)
04a
RNA_pol_Rpb1_1-2o5iN01
N:417-618
04b
RNA_pol_Rpb1_1-2o5iN02
N:417-618
04c
RNA_pol_Rpb1_1-2o5iN03
N:417-618
04d
RNA_pol_Rpb1_1-2o5iN04
N:417-618
Clan
:
no clan defined [family: RNA_pol_Rpb1_2]
(36)
Family
:
RNA_pol_Rpb1_2
(36)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(5)
05a
RNA_pol_Rpb1_2-2o5iN05
N:620-765
05b
RNA_pol_Rpb1_2-2o5iN06
N:620-765
Clan
:
no clan defined [family: RNA_pol_Rpb1_3]
(36)
Family
:
RNA_pol_Rpb1_3
(36)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(5)
06a
RNA_pol_Rpb1_3-2o5iN07
N:768-954
06b
RNA_pol_Rpb1_3-2o5iN08
N:768-954
Clan
:
no clan defined [family: RNA_pol_Rpb1_4]
(36)
Family
:
RNA_pol_Rpb1_4
(36)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(5)
07a
RNA_pol_Rpb1_4-2o5iN09
N:983-1066
07b
RNA_pol_Rpb1_4-2o5iN10
N:983-1066
Clan
:
no clan defined [family: RNA_pol_Rpb1_5]
(36)
Family
:
RNA_pol_Rpb1_5
(36)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(5)
08a
RNA_pol_Rpb1_5-2o5iN11
N:1064-1437
08b
RNA_pol_Rpb1_5-2o5iN12
N:1064-1437
Clan
:
no clan defined [family: RNA_pol_Rpb2_1]
(37)
Family
:
RNA_pol_Rpb2_1
(37)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(5)
09a
RNA_pol_Rpb2_1-2o5iM03
M:17-389
09b
RNA_pol_Rpb2_1-2o5iM04
M:17-389
Clan
:
no clan defined [family: RNA_pol_Rpb2_2]
(36)
Family
:
RNA_pol_Rpb2_2
(36)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(5)
10a
RNA_pol_Rpb2_2-2o5iM05
M:142-334
10b
RNA_pol_Rpb2_2-2o5iM06
M:142-334
Clan
:
no clan defined [family: RNA_pol_Rpb2_3]
(35)
Family
:
RNA_pol_Rpb2_3
(35)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(5)
11a
RNA_pol_Rpb2_3-2o5iM07
M:393-462
11b
RNA_pol_Rpb2_3-2o5iM08
M:393-462
Clan
:
no clan defined [family: RNA_pol_Rpb2_45]
(8)
Family
:
RNA_pol_Rpb2_45
(8)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(5)
12a
RNA_pol_Rpb2_45-2o5iM09
M:471-535
12b
RNA_pol_Rpb2_45-2o5iM10
M:471-535
Clan
:
no clan defined [family: RNA_pol_Rpb2_7]
(36)
Family
:
RNA_pol_Rpb2_7
(36)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(5)
13a
RNA_pol_Rpb2_7-2o5iM11
M:1028-1104
13b
RNA_pol_Rpb2_7-2o5iM12
M:1028-1104
Clan
:
no clan defined [family: RNA_pol_Rpb6]
(37)
Family
:
RNA_pol_Rpb6
(37)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(5)
14a
RNA_pol_Rpb6-2o5iO01
O:7-57
14b
RNA_pol_Rpb6-2o5iO02
O:7-57
[
close Pfam info
]
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Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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Asym.Unit (1.1 MB)
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