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1S0V
Biol. Unit 1
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
(1, 1)
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
1
Ligand/Ion
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2
MG
-1
Ligand/Ion
MAGNESIUM ION
[
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]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC5 (SOFTWARE)
3: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
APC A:2000 , HOH A:3172 , HOH A:3217
BINDING SITE FOR RESIDUE MG A 3001
2
AC5
SOFTWARE
TYR A:639 , APC A:2000 , HOH A:3015 , U F:8
BINDING SITE FOR RESIDUE MG F 3005
3
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
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: RNA_POL_PHAGE_1 (A:533-544)
2: RNA_POL_PHAGE_2 (A:625-639)
;
View:
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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
1
A:533-544
-
-
-
2
RNA_POL_PHAGE_2
PS00489
Bacteriophage-type RNA polymerase family active site signature 2.
RPOL_BPT7
625-639
1
A:625-639
-
-
-
[
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Exons
(0, 0)
Info
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1s0va_ (A:)
1b: SCOP_d1s0vb_ (B:)
1c: SCOP_d1s0vc_ (C:)
1d: SCOP_d1s0vd_ (D:)
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)
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)
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)
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)
(
)
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:
[
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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)
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)
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(
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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
[
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]
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
(
)
(
)
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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