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2O5J
Biol. Unit 1
Info
Asym.Unit (1.0 MB)
Biol.Unit 1 (525 KB)
Biol.Unit 2 (524 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE T. THERMOPHILUS RNAP POLYMERASE ELONGATION COMPLEX WITH THE NTP SUBSTRATE ANALOG
Authors
:
D. G. Vassylyev, M. N. Vassylyeva
Date
:
06 Dec 06 (Deposition) - 03 Jul 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
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, Ntp Substrate, Transferase-Dna-Rna Hybrid Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. G. Vassylyev, M. N. Vassylyeva, J. Zhang, M. Palangat, I. Artsimovitch, R. Landick
Structural Basis For Substrate Loading In Bacterial Rna Polymerase.
Nature V. 448 163 2007
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: DIPHOSPHOMETHYLPHOSPHONIC ACID ADE... (APCa)
1b: DIPHOSPHOMETHYLPHOSPHONIC ACID ADE... (APCb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
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
APC
1
Ligand/Ion
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
5: AC9 (SOFTWARE)
View:
Select:
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 4058
2
AC2
SOFTWARE
CYS D:1112 , CYS D:1194 , CYS D:1201 , CYS D:1204
BINDING SITE FOR RESIDUE ZN D 6112
3
AC5
SOFTWARE
ASP D:739 , ASP D:741 , ASP D:743 , APC D:3999 , G H:16
BINDING SITE FOR RESIDUE MG D 8001
4
AC6
SOFTWARE
ASP D:739 , APC D:3999 , HOH D:8003
BINDING SITE FOR RESIDUE MG D 8002
5
AC9
SOFTWARE
ARG C:879 , ARG D:704 , PRO D:706 , ASN D:737 , ASP D:739 , ARG D:783 , ARG D:1029 , MET D:1238 , ARG D:1239 , HIS D:1242 , MG D:8001 , MG D:8002 , HOH D:8003 , HOH D:8354 , DT G:14 , G H:16
BINDING SITE FOR RESIDUE APC D 3999
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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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: RNA_POL_BETA (C: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
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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2o5je_ (E:)
1b: SCOP_d2o5jo_ (O:)
2a: SCOP_d2o5jc_ (C:)
2b: SCOP_d2o5jm_ (M:)
3a: SCOP_d2o5jd_ (D:)
3b: SCOP_d2o5jn_ (N:)
View:
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Classes
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(
)
Folds
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(
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Superfamilies
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(
)
Families
(
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(
)
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
d2o5je_
E:
1b
d2o5jo_
O:
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)
2a
d2o5jc_
C:
2b
d2o5jm_
M:
Family
:
RNA-polymerase beta-prime
(49)
Protein domain
:
automated matches
(8)
Thermus thermophilus HB8 [TaxId: 300852]
(3)
3a
d2o5jd_
D:
3b
d2o5jn_
N:
[
close SCOP info
]
CATH Domains
(9, 22)
Info
all CATH domains
1a: CATH_2o5jA01 (A:1-49,A:172-225)
1b: CATH_2o5jB01 (B:1-49,B:172-225)
1c: CATH_2o5jK01 (K:1-49,K:172-225)
1d: CATH_2o5jL01 (L:1-49,L:172-225)
2a: CATH_2o5jC03 (C:144-323)
2b: CATH_2o5jM03 (M:144-323)
3a: CATH_2o5jE00 (E:2-96)
3b: CATH_2o5jO00 (O:2-96)
4a: CATH_2o5jC02 (C:16-143,C:324-469,C:535-593)
4b: CATH_2o5jM02 (M:16-143,M:324-469,M:535-593)
5a: CATH_2o5jC01 (C:1-6,C:668-700,C:833-997)
5b: CATH_2o5jM01 (M:1-6,M:668-700,M:833-997)
6a: CATH_2o5jC05 (C:594-658)
6b: CATH_2o5jM05 (M:594-658)
7a: CATH_2o5jC06 (C:701-832)
7b: CATH_2o5jM06 (M:701-832)
8a: CATH_2o5jA02 (A:50-171)
8b: CATH_2o5jB02 (B:50-171)
8c: CATH_2o5jK02 (K:50-171)
8d: CATH_2o5jL02 (L:50-171)
9a: CATH_2o5jC04 (C:470-534)
9b: CATH_2o5jM04 (M:470-534)
View:
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)
Homologous Superfamilies
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(
)
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
2o5jA01
A:1-49,A:172-225
1b
2o5jB01
B:1-49,B:172-225
1c
2o5jK01
K:1-49,K:172-225
1d
2o5jL01
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
2o5jC03
C:144-323
2b
2o5jM03
M:144-323
Topology
:
Eukaryotic RPB6 RNA polymerase subunit
(77)
Homologous Superfamily
:
[code=3.90.940.10, no name defined]
(71)
[unclassified]
(17)
3a
2o5jE00
E:2-96
3b
2o5jO00
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
2o5jC02
C:16-143,C:324-469,C:535-593
4b
2o5jM02
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
2o5jC01
C:1-6,C:668-700,C:833-997
5b
2o5jM01
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
2o5jC05
C:594-658
6b
2o5jM05
M:594-658
Homologous Superfamily
:
[code=2.40.50.150, no name defined]
(48)
[unclassified]
(17)
7a
2o5jC06
C:701-832
7b
2o5jM06
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
2o5jA02
A:50-171
8b
2o5jB02
B:50-171
8c
2o5jK02
K:50-171
8d
2o5jL02
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
2o5jC04
C:470-534
9b
2o5jM04
M:470-534
[
close CATH info
]
Pfam Domains
(14, 34)
Info
all PFAM domains
01a: PFAM_RNA_pol_Rpb2_6_2o5jM01 (M:541-1026)
01b: PFAM_RNA_pol_Rpb2_6_2o5jM02 (M:541-1026)
02a: PFAM_RNA_pol_L_2o5jL01 (L:25-223)
02b: PFAM_RNA_pol_L_2o5jL02 (L:25-223)
02c: PFAM_RNA_pol_L_2o5jL03 (L:25-223)
02d: PFAM_RNA_pol_L_2o5jL04 (L:25-223)
03a: PFAM_RNA_pol_A_bac_2o5jL05 (L:52-180)
03b: PFAM_RNA_pol_A_bac_2o5jL06 (L:52-180)
03c: PFAM_RNA_pol_A_bac_2o5jL07 (L:52-180)
03d: PFAM_RNA_pol_A_bac_2o5jL08 (L:52-180)
04a: PFAM_RNA_pol_Rpb1_1_2o5jN01 (N:417-618)
04b: PFAM_RNA_pol_Rpb1_1_2o5jN02 (N:417-618)
04c: PFAM_RNA_pol_Rpb1_1_2o5jN03 (N:417-618)
04d: PFAM_RNA_pol_Rpb1_1_2o5jN04 (N:417-618)
05a: PFAM_RNA_pol_Rpb1_2_2o5jN05 (N:620-765)
05b: PFAM_RNA_pol_Rpb1_2_2o5jN06 (N:620-765)
06a: PFAM_RNA_pol_Rpb1_3_2o5jN07 (N:768-954)
06b: PFAM_RNA_pol_Rpb1_3_2o5jN08 (N:768-954)
07a: PFAM_RNA_pol_Rpb1_4_2o5jN09 (N:983-1066)
07b: PFAM_RNA_pol_Rpb1_4_2o5jN10 (N:983-1066)
08a: PFAM_RNA_pol_Rpb1_5_2o5jN11 (N:1064-1437)
08b: PFAM_RNA_pol_Rpb1_5_2o5jN12 (N:1064-1437)
09a: PFAM_RNA_pol_Rpb2_1_2o5jM03 (M:17-389)
09b: PFAM_RNA_pol_Rpb2_1_2o5jM04 (M:17-389)
10a: PFAM_RNA_pol_Rpb2_2_2o5jM05 (M:142-334)
10b: PFAM_RNA_pol_Rpb2_2_2o5jM06 (M:142-334)
11a: PFAM_RNA_pol_Rpb2_3_2o5jM07 (M:393-462)
11b: PFAM_RNA_pol_Rpb2_3_2o5jM08 (M:393-462)
12a: PFAM_RNA_pol_Rpb2_45_2o5jM09 (M:471-535)
12b: PFAM_RNA_pol_Rpb2_45_2o5jM10 (M:471-535)
13a: PFAM_RNA_pol_Rpb2_7_2o5jM11 (M:1028-1104)
13b: PFAM_RNA_pol_Rpb2_7_2o5jM12 (M:1028-1104)
14a: PFAM_RNA_pol_Rpb6_2o5jO01 (O:7-57)
14b: PFAM_RNA_pol_Rpb6_2o5jO02 (O:7-57)
View:
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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_6-2o5jM01
M:541-1026
01b
RNA_pol_Rpb2_6-2o5jM02
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-2o5jL01
L:25-223
02b
RNA_pol_L-2o5jL02
L:25-223
02c
RNA_pol_L-2o5jL03
L:25-223
02d
RNA_pol_L-2o5jL04
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-2o5jL05
L:52-180
03b
RNA_pol_A_bac-2o5jL06
L:52-180
03c
RNA_pol_A_bac-2o5jL07
L:52-180
03d
RNA_pol_A_bac-2o5jL08
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_1-2o5jN01
N:417-618
04b
RNA_pol_Rpb1_1-2o5jN02
N:417-618
04c
RNA_pol_Rpb1_1-2o5jN03
N:417-618
04d
RNA_pol_Rpb1_1-2o5jN04
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_2-2o5jN05
N:620-765
05b
RNA_pol_Rpb1_2-2o5jN06
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_3-2o5jN07
N:768-954
06b
RNA_pol_Rpb1_3-2o5jN08
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_4-2o5jN09
N:983-1066
07b
RNA_pol_Rpb1_4-2o5jN10
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_5-2o5jN11
N:1064-1437
08b
RNA_pol_Rpb1_5-2o5jN12
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_1-2o5jM03
M:17-389
09b
RNA_pol_Rpb2_1-2o5jM04
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_2-2o5jM05
M:142-334
10b
RNA_pol_Rpb2_2-2o5jM06
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_3-2o5jM07
M:393-462
11b
RNA_pol_Rpb2_3-2o5jM08
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_45-2o5jM09
M:471-535
12b
RNA_pol_Rpb2_45-2o5jM10
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_7-2o5jM11
M:1028-1104
13b
RNA_pol_Rpb2_7-2o5jM12
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_Rpb6-2o5jO01
O:7-57
14b
RNA_pol_Rpb6-2o5jO02
O:7-57
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