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2PPB
Asym. Unit
Info
Asym.Unit (1.0 MB)
Biol.Unit 1 (533 KB)
Biol.Unit 2 (531 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE T. THERMOPHILUS RNAP POLYMERASE ELONGATION COMPLEX WITH THE NTP SUBSTRATE ANALOG AND ANTIBIOTIC STREPTOLYDIGIN
Authors
:
D. G. Vassylyev, M. N. Vassylyeva, I. Artsimovitch, R. Landick
Date
:
28 Apr 07 (Deposition) - 17 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, Antibiotic Streptolydigin, Transferase-Dna-Rna 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
(4, 12)
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: STREPTOLYDIGIN (STDa)
3b: STREPTOLYDIGIN (STDb)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
APC
2
Ligand/Ion
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
STD
2
Ligand/Ion
STREPTOLYDIGIN
4
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG C:422 , ARG C:428 , ALA C:447 , ILE C:449 , ALA D:1082 , ALA D:1085 , LEU D:1086 , ARG D:1087 , ASP D:1090 , PRO D:1257 , HOH D:9308 , DG I:5
BINDING SITE FOR RESIDUE STD D 7001
02
AC2
SOFTWARE
ARG M:422 , PHE M:425 , ALA M:447 , ILE M:449 , ALA N:1082 , ALA N:1085 , LEU N:1086 , ARG N:1087 , ASP N:1090 , PRO N:1257 , HOH N:9065 , DG Z:5
BINDING SITE FOR RESIDUE STD N 8001
03
AC3
SOFTWARE
CYS D:58 , CYS D:60 , CYS D:73 , CYS D:76
BINDING SITE FOR RESIDUE ZN D 7058
04
AC4
SOFTWARE
CYS D:1112 , CYS D:1194 , CYS D:1201 , CYS D:1204
BINDING SITE FOR RESIDUE ZN D 8112
05
AC5
SOFTWARE
CYS N:58 , CYS N:60 , CYS N:73 , CYS N:76
BINDING SITE FOR RESIDUE ZN N 7158
06
AC6
SOFTWARE
CYS N:1112 , CYS N:1194 , CYS N:1201 , CYS N:1204
BINDING SITE FOR RESIDUE ZN N 8212
07
AC7
SOFTWARE
ASP D:739 , ASP D:741 , ASP D:743 , G H:16
BINDING SITE FOR RESIDUE MG D 9001
08
AC8
SOFTWARE
ASP D:739 , APC D:5999 , HOH D:9004
BINDING SITE FOR RESIDUE MG D 9002
09
AC9
SOFTWARE
ASP N:739 , ASP N:741 , ASP N:743 , G Y:16
BINDING SITE FOR RESIDUE MG N 9003
10
BC1
SOFTWARE
APC M:6999 , HOH M:7001 , ASP N:739
BINDING SITE FOR RESIDUE MG N 9004
11
BC2
SOFTWARE
ARG C:557 , ARG C:879 , ARG D:704 , PRO D:706 , ASN D:737 , ARG D:1029 , MG D:9002 , HOH D:9003 , HOH D:9004 , HOH D:9231 , HOH D:9347 , HOH D:9498 , DT G:14 , G H:16
BINDING SITE FOR RESIDUE APC D 5999
12
BC3
SOFTWARE
ARG M:557 , ARG M:879 , HOH M:7000 , HOH M:7319 , ARG N:704 , PRO N:706 , ASN N:737 , ARG N:1029 , MG N:9004 , DT X:14 , G Y:16
BINDING SITE FOR RESIDUE APC M 6999
[
close Site info
]
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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2ppbe_ (E:)
1b: SCOP_d2ppbo_ (O:)
2a: SCOP_d2ppbc_ (C:)
2b: SCOP_d2ppbm_ (M:)
3a: SCOP_d2ppbd_ (D:)
3b: SCOP_d2ppbn_ (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
d2ppbe_
E:
1b
d2ppbo_
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
d2ppbc_
C:
2b
d2ppbm_
M:
Family
:
RNA-polymerase beta-prime
(49)
Protein domain
:
automated matches
(8)
Thermus thermophilus HB8 [TaxId: 300852]
(3)
3a
d2ppbd_
D:
3b
d2ppbn_
N:
[
close SCOP info
]
CATH Domains
(9, 22)
Info
all CATH domains
1a: CATH_2ppbA01 (A:1-49,A:172-225)
1b: CATH_2ppbB01 (B:1-49,B:172-225)
1c: CATH_2ppbK01 (K:1-49,K:172-225)
1d: CATH_2ppbL01 (L:1-49,L:172-225)
2a: CATH_2ppbC03 (C:144-323)
2b: CATH_2ppbM03 (M:144-323)
3a: CATH_2ppbE00 (E:2-96)
3b: CATH_2ppbO00 (O:2-96)
4a: CATH_2ppbC02 (C:16-143,C:324-469,C:535-593)
4b: CATH_2ppbM02 (M:16-143,M:324-469,M:535-593)
5a: CATH_2ppbC01 (C:1-6,C:668-700,C:833-997)
5b: CATH_2ppbM01 (M:1-6,M:668-700,M:833-997)
6a: CATH_2ppbC05 (C:594-658)
6b: CATH_2ppbM05 (M:594-658)
7a: CATH_2ppbC06 (C:701-832)
7b: CATH_2ppbM06 (M:701-832)
8a: CATH_2ppbA02 (A:50-171)
8b: CATH_2ppbB02 (B:50-171)
8c: CATH_2ppbK02 (K:50-171)
8d: CATH_2ppbL02 (L:50-171)
9a: CATH_2ppbC04 (C:470-534)
9b: CATH_2ppbM04 (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
2ppbA01
A:1-49,A:172-225
1b
2ppbB01
B:1-49,B:172-225
1c
2ppbK01
K:1-49,K:172-225
1d
2ppbL01
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
2ppbC03
C:144-323
2b
2ppbM03
M:144-323
Topology
:
Eukaryotic RPB6 RNA polymerase subunit
(77)
Homologous Superfamily
:
[code=3.90.940.10, no name defined]
(71)
[unclassified]
(17)
3a
2ppbE00
E:2-96
3b
2ppbO00
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
2ppbC02
C:16-143,C:324-469,C:535-593
4b
2ppbM02
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
2ppbC01
C:1-6,C:668-700,C:833-997
5b
2ppbM01
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
2ppbC05
C:594-658
6b
2ppbM05
M:594-658
Homologous Superfamily
:
[code=2.40.50.150, no name defined]
(48)
[unclassified]
(17)
7a
2ppbC06
C:701-832
7b
2ppbM06
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
2ppbA02
A:50-171
8b
2ppbB02
B:50-171
8c
2ppbK02
K:50-171
8d
2ppbL02
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
2ppbC04
C:470-534
9b
2ppbM04
M:470-534
[
close CATH info
]
Pfam Domains
(14, 34)
Info
all PFAM domains
01a: PFAM_RNA_pol_Rpb2_6_2ppbM01 (M:541-1026)
01b: PFAM_RNA_pol_Rpb2_6_2ppbM02 (M:541-1026)
02a: PFAM_RNA_pol_L_2ppbL01 (L:25-223)
02b: PFAM_RNA_pol_L_2ppbL02 (L:25-223)
02c: PFAM_RNA_pol_L_2ppbL03 (L:25-223)
02d: PFAM_RNA_pol_L_2ppbL04 (L:25-223)
03a: PFAM_RNA_pol_A_bac_2ppbL05 (L:52-180)
03b: PFAM_RNA_pol_A_bac_2ppbL06 (L:52-180)
03c: PFAM_RNA_pol_A_bac_2ppbL07 (L:52-180)
03d: PFAM_RNA_pol_A_bac_2ppbL08 (L:52-180)
04a: PFAM_RNA_pol_Rpb1_1_2ppbN01 (N:417-618)
04b: PFAM_RNA_pol_Rpb1_1_2ppbN02 (N:417-618)
04c: PFAM_RNA_pol_Rpb1_1_2ppbN03 (N:417-618)
04d: PFAM_RNA_pol_Rpb1_1_2ppbN04 (N:417-618)
05a: PFAM_RNA_pol_Rpb1_2_2ppbN05 (N:620-765)
05b: PFAM_RNA_pol_Rpb1_2_2ppbN06 (N:620-765)
06a: PFAM_RNA_pol_Rpb1_3_2ppbN07 (N:768-954)
06b: PFAM_RNA_pol_Rpb1_3_2ppbN08 (N:768-954)
07a: PFAM_RNA_pol_Rpb1_4_2ppbN09 (N:983-1066)
07b: PFAM_RNA_pol_Rpb1_4_2ppbN10 (N:983-1066)
08a: PFAM_RNA_pol_Rpb1_5_2ppbN11 (N:1064-1437)
08b: PFAM_RNA_pol_Rpb1_5_2ppbN12 (N:1064-1437)
09a: PFAM_RNA_pol_Rpb2_1_2ppbM03 (M:17-389)
09b: PFAM_RNA_pol_Rpb2_1_2ppbM04 (M:17-389)
10a: PFAM_RNA_pol_Rpb2_2_2ppbM05 (M:142-334)
10b: PFAM_RNA_pol_Rpb2_2_2ppbM06 (M:142-334)
11a: PFAM_RNA_pol_Rpb2_3_2ppbM07 (M:393-462)
11b: PFAM_RNA_pol_Rpb2_3_2ppbM08 (M:393-462)
12a: PFAM_RNA_pol_Rpb2_45_2ppbM09 (M:471-535)
12b: PFAM_RNA_pol_Rpb2_45_2ppbM10 (M:471-535)
13a: PFAM_RNA_pol_Rpb2_7_2ppbM11 (M:1028-1104)
13b: PFAM_RNA_pol_Rpb2_7_2ppbM12 (M:1028-1104)
14a: PFAM_RNA_pol_Rpb6_2ppbO01 (O:7-57)
14b: PFAM_RNA_pol_Rpb6_2ppbO02 (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_6-2ppbM01
M:541-1026
01b
RNA_pol_Rpb2_6-2ppbM02
M:541-1026
Clan
:
RBP11-like
(36)
Family
:
RNA_pol_L
(36)
Thermus thermophilus
(2)
02a
RNA_pol_L-2ppbL01
L:25-223
02b
RNA_pol_L-2ppbL02
L:25-223
02c
RNA_pol_L-2ppbL03
L:25-223
02d
RNA_pol_L-2ppbL04
L:25-223
Clan
:
no clan defined [family: RNA_pol_A_bac]
(36)
Family
:
RNA_pol_A_bac
(36)
Thermus thermophilus
(2)
03a
RNA_pol_A_bac-2ppbL05
L:52-180
03b
RNA_pol_A_bac-2ppbL06
L:52-180
03c
RNA_pol_A_bac-2ppbL07
L:52-180
03d
RNA_pol_A_bac-2ppbL08
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_1-2ppbN01
N:417-618
04b
RNA_pol_Rpb1_1-2ppbN02
N:417-618
04c
RNA_pol_Rpb1_1-2ppbN03
N:417-618
04d
RNA_pol_Rpb1_1-2ppbN04
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_2-2ppbN05
N:620-765
05b
RNA_pol_Rpb1_2-2ppbN06
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_3-2ppbN07
N:768-954
06b
RNA_pol_Rpb1_3-2ppbN08
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_4-2ppbN09
N:983-1066
07b
RNA_pol_Rpb1_4-2ppbN10
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_5-2ppbN11
N:1064-1437
08b
RNA_pol_Rpb1_5-2ppbN12
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_1-2ppbM03
M:17-389
09b
RNA_pol_Rpb2_1-2ppbM04
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_2-2ppbM05
M:142-334
10b
RNA_pol_Rpb2_2-2ppbM06
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_3-2ppbM07
M:393-462
11b
RNA_pol_Rpb2_3-2ppbM08
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_45-2ppbM09
M:471-535
12b
RNA_pol_Rpb2_45-2ppbM10
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_7-2ppbM11
M:1028-1104
13b
RNA_pol_Rpb2_7-2ppbM12
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_Rpb6-2ppbO01
O:7-57
14b
RNA_pol_Rpb6-2ppbO02
O:7-57
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
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Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain G
Chain H
Chain I
Chain K
Chain L
Chain M
Chain N
Chain O
Chain X
Chain Y
Chain Z
Asymmetric Unit 1
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(selected part)
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(selected part)
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by Chain (Biol. Unit)
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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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