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1S0V
Asym. Unit
Info
Asym.Unit (639 KB)
Biol.Unit 1 (163 KB)
Biol.Unit 2 (163 KB)
Biol.Unit 3 (162 KB)
Biol.Unit 4 (161 KB)
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(1)
Title
:
STRUCTURAL BASIS FOR SUBSTRATE SELECTION BY T7 RNA POLYMERASE
Authors
:
D. Temiakov, V. Patlan, M. Anikin, W. T. Mcallister, S. Yokoyama, D. G. Vassylyev, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
05 Jan 04 (Deposition) - 24 Feb 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,E,F,G (1x)
Biol. Unit 2: B,H,I,J (1x)
Biol. Unit 3: C,K,L,M (1x)
Biol. Unit 4: D,N,O,P (1x)
Keywords
:
T7 Rna Polymerase, Dna, Rna, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transferase/Dna/Rna Complex, Transferase/Dna-Rna Hybrid Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Temiakov, V. Patlan, M. Anikin, W. T. Mcallister, S. Yokoyama, D. G. Vassylyev
Structural Basis For Substrate Selection By T7 Rna Polymerase.
Cell(Cambridge, Mass. ) V. 116 381 2004
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(2, 12)
Info
All Hetero Components
1a: DIPHOSPHOMETHYLPHOSPHONIC ACID ADE... (APCa)
1b: DIPHOSPHOMETHYLPHOSPHONIC ACID ADE... (APCb)
1c: DIPHOSPHOMETHYLPHOSPHONIC ACID ADE... (APCc)
1d: DIPHOSPHOMETHYLPHOSPHONIC ACID ADE... (APCd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
APC
4
Ligand/Ion
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2
MG
8
Ligand/Ion
MAGNESIUM ION
[
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]
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
APC A:2000 , HOH A:3172 , HOH A:3217
BINDING SITE FOR RESIDUE MG A 3001
02
AC2
SOFTWARE
ASP B:471 , APC B:2001
BINDING SITE FOR RESIDUE MG B 3002
03
AC3
SOFTWARE
APC C:2002 , HOH C:3136
BINDING SITE FOR RESIDUE MG C 3003
04
AC4
SOFTWARE
ASP D:471 , APC D:2003
BINDING SITE FOR RESIDUE MG D 3004
05
AC5
SOFTWARE
TYR A:639 , APC A:2000 , HOH A:3015 , U F:8
BINDING SITE FOR RESIDUE MG F 3005
06
AC6
SOFTWARE
TYR B:639 , APC B:2001 , HOH B:3164
BINDING SITE FOR RESIDUE MG B 3006
07
AC7
SOFTWARE
TYR C:639 , APC C:2002
BINDING SITE FOR RESIDUE MG C 3007
08
AC8
SOFTWARE
TYR D:639 , APC D:2003 , U O:8
BINDING SITE FOR RESIDUE MG D 3008
09
AC9
SOFTWARE
LYS A:472 , TYR A:571 , ARG A:627 , LYS A:631 , ARG A:632 , MET A:635 , THR A:636 , MG A:3001 , HOH A:3005 , HOH A:3015 , HOH A:3048 , HOH A:3217 , HOH A:3238 , DT E:10 , U F:8 , MG F:3005
BINDING SITE FOR RESIDUE APC A 2000
10
BC1
SOFTWARE
LYS B:472 , ARG B:627 , LYS B:631 , ARG B:632 , MET B:635 , MG B:3002 , MG B:3006 , HOH B:3164 , HOH B:3218 , DT H:10 , DA H:11 , U I:8
BINDING SITE FOR RESIDUE APC B 2001
11
BC2
SOFTWARE
TYR C:571 , ARG C:627 , LYS C:631 , ARG C:632 , MET C:635 , THR C:636 , MG C:3003 , MG C:3007 , HOH C:3136 , HOH C:3152 , HOH C:3154 , HOH C:3207 , HOH C:3208 , DA K:11 , U L:8
BINDING SITE FOR RESIDUE APC C 2002
12
BC3
SOFTWARE
LYS D:472 , TYR D:571 , ARG D:627 , LYS D:631 , ARG D:632 , MET D:635 , THR D:636 , MG D:3004 , MG D:3008 , HOH D:3045 , DT N:10 , U O:8
BINDING SITE FOR RESIDUE APC D 2003
[
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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
(2, 8)
Info
All PROSITE Patterns/Profiles
1: RNA_POL_PHAGE_1 (A:533-544,B:533-544,C:533-544,D:53...)
2: RNA_POL_PHAGE_2 (A:625-639,B:625-639,C:625-639,D:62...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RNA_POL_PHAGE_1
PS00900
Bacteriophage-type RNA polymerase family active site signature 1.
RPOL_BPT7
533-544
4
A:533-544
B:533-544
C:533-544
D:533-544
2
RNA_POL_PHAGE_2
PS00489
Bacteriophage-type RNA polymerase family active site signature 2.
RPOL_BPT7
625-639
4
A:625-639
B:625-639
C:625-639
D:625-639
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1s0va_ (A:)
1b: SCOP_d1s0vb_ (B:)
1c: SCOP_d1s0vc_ (C:)
1d: SCOP_d1s0vd_ (D:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
T7 RNA polymerase
(12)
Protein domain
:
T7 RNA polymerase
(11)
Bacteriophage T7 [TaxId: 10760]
(11)
1a
d1s0va_
A:
1b
d1s0vb_
B:
1c
d1s0vc_
C:
1d
d1s0vd_
D:
[
close SCOP info
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CATH Domains
(5, 20)
Info
all CATH domains
1a: CATH_1s0vA03 (A:421-449,A:528-553,A:785-872)
1b: CATH_1s0vB03 (B:421-449,B:528-553,B:785-872)
1c: CATH_1s0vC03 (C:421-449,C:528-553,C:785-872)
1d: CATH_1s0vD03 (D:421-449,D:528-553,D:785-872)
2a: CATH_1s0vA05 (A:554-784)
2b: CATH_1s0vB05 (B:554-784)
2c: CATH_1s0vC05 (C:554-784)
2d: CATH_1s0vD05 (D:554-784)
3a: CATH_1s0vA02 (A:326-411)
3b: CATH_1s0vB02 (B:326-411)
3c: CATH_1s0vC02 (C:326-411)
3d: CATH_1s0vD02 (D:326-411)
4a: CATH_1s0vA04 (A:450-527)
4b: CATH_1s0vB04 (B:450-527)
4c: CATH_1s0vC04 (C:450-527)
4d: CATH_1s0vD04 (D:450-527)
5a: CATH_1s0vA01 (A:8-325)
5b: CATH_1s0vB01 (B:8-325)
5c: CATH_1s0vC01 (C:8-325)
5d: CATH_1s0vD01 (D:8-325)
View:
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(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.370, no name defined]
(99)
[unclassified]
(84)
1a
1s0vA03
A:421-449,A:528-553,A:785-872
1b
1s0vB03
B:421-449,B:528-553,B:785-872
1c
1s0vC03
C:421-449,C:528-553,C:785-872
1d
1s0vD03
D:421-449,D:528-553,D:785-872
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
[unclassified]
(230)
2a
1s0vA05
A:554-784
2b
1s0vB05
B:554-784
2c
1s0vC05
C:554-784
2d
1s0vD05
D:554-784
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.260, no name defined]
(11)
[unclassified]
(7)
3a
1s0vA02
A:326-411
3b
1s0vB02
B:326-411
3c
1s0vC02
C:326-411
3d
1s0vD02
D:326-411
Homologous Superfamily
:
[code=1.10.287.280, no name defined]
(11)
[unclassified]
(7)
4a
1s0vA04
A:450-527
4b
1s0vB04
B:450-527
4c
1s0vC04
C:450-527
4d
1s0vD04
D:450-527
Topology
:
T7 RNA polymerase; domain 1
(11)
Homologous Superfamily
:
T7 RNA polymerase, domain 1
(11)
[unclassified]
(7)
5a
1s0vA01
A:8-325
5b
1s0vB01
B:8-325
5c
1s0vC01
C:8-325
5d
1s0vD01
D:8-325
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_RNA_pol_1s0vD01 (D:449-882)
1b: PFAM_RNA_pol_1s0vD02 (D:449-882)
1c: PFAM_RNA_pol_1s0vD03 (D:449-882)
1d: PFAM_RNA_pol_1s0vD04 (D:449-882)
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Clans
(
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(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: RNA_pol]
(7)
Family
:
RNA_pol
(7)
Enterobacteria phage T7 (Bacteriophage T7)
(7)
1a
RNA_pol-1s0vD01
D:449-882
1b
RNA_pol-1s0vD02
D:449-882
1c
RNA_pol-1s0vD03
D:449-882
1d
RNA_pol-1s0vD04
D:449-882
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Asym.Unit (639 KB)
Header - Asym.Unit
Biol.Unit 1 (163 KB)
Header - Biol.Unit 1
Biol.Unit 2 (163 KB)
Header - Biol.Unit 2
Biol.Unit 3 (162 KB)
Header - Biol.Unit 3
Biol.Unit 4 (161 KB)
Header - Biol.Unit 4
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