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3HOU
Biol. Unit 2
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Asym.Unit (1.3 MB)
Biol.Unit 1 (654 KB)
Biol.Unit 2 (655 KB)
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(1)
Title
:
COMPLETE RNA POLYMERASE II ELONGATION COMPLEX I WITH A T-U MISMATCH
Authors
:
J. F. Sydow, F. Brueckner, A. C. M. Cheung, G. E. Damsma, S. Dengl, E. Lehmann, D. Vassylyev, P. Cramer
Date
:
03 Jun 09 (Deposition) - 28 Jul 09 (Release) - 28 Jul 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,Q,R,S,T,U,V,W,X,1,2,3,4,5,6
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,1,2,3 (1x)
Biol. Unit 2: M,N,O,P,Q,R,S,T,U,V,W,X,4,5,6 (1x)
Keywords
:
Rna Polymerase Ii, Metal-Binding, Transcription Bubble, Elongation Complex, Transcription, Dna-Rna Mismatch, Dna- Binding, Dna-Directed Rna Polymerase, Isopeptide Bond, Magnesium, Nucleotidyltransferase, Nucleus, Phosphoprotein, Transferase, Ubl Conjugation, Zinc, Zinc-Finger, Polymorphism, Cytoplasm, Dna Damage, Dna Repair, Mrna Processing, Transcription, Transferase/Dna/Rna Hybrid Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. F. Sydow, F. Brueckner, A. C. M. Cheung, G. E. Damsma, S. Dengl, E. Lehmann, D. Vassylyev, P. Cramer
Structural Basis Of Transcription: Mismatch-Specific Fidelity Mechanisms And Paused Rna Polymerase Ii With Frayed Rna.
Mol. Cell V. 34 710 2009
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHO... (BRUa)
1b: 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHO... (BRUb)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
2g: ZINC ION (ZNg)
2h: ZINC ION (ZNh)
2i: ZINC ION (ZNi)
2j: ZINC ION (ZNj)
2k: ZINC ION (ZNk)
2l: ZINC ION (ZNl)
2m: ZINC ION (ZNm)
2n: ZINC ION (ZNn)
2o: ZINC ION (ZNo)
2p: ZINC ION (ZNp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BRU
1
Mod. Nucleotide
5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(8, 8)
Info
All Sites
1: AC9 (SOFTWARE)
2: BC1 (SOFTWARE)
3: BC2 (SOFTWARE)
4: BC3 (SOFTWARE)
5: BC4 (SOFTWARE)
6: BC5 (SOFTWARE)
7: BC6 (SOFTWARE)
8: BC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC9
SOFTWARE
CYS M:107 , CYS M:110 , CYS M:148 , CYS M:167
BINDING SITE FOR RESIDUE ZN M 9992
2
BC1
SOFTWARE
CYS M:67 , CYS M:70 , CYS M:77 , HIS M:80
BINDING SITE FOR RESIDUE ZN M 9993
3
BC2
SOFTWARE
CYS N:1163 , CYS N:1166 , CYS N:1182 , CYS N:1185
BINDING SITE FOR RESIDUE ZN N 9994
4
BC3
SOFTWARE
CYS O:86 , CYS O:88 , CYS O:92 , CYS O:95
BINDING SITE FOR RESIDUE ZN O 9995
5
BC4
SOFTWARE
CYS U:7 , CYS U:10 , CYS U:29 , CYS U:32
BINDING SITE FOR RESIDUE ZN U 9996
6
BC5
SOFTWARE
CYS U:75 , CYS U:78 , CYS U:103 , CYS U:106 , HIS U:108
BINDING SITE FOR RESIDUE ZN U 9997
7
BC6
SOFTWARE
CYS V:7 , CYS V:10 , CYS V:45 , CYS V:46
BINDING SITE FOR RESIDUE ZN V 9998
8
BC7
SOFTWARE
CYS X:31 , CYS X:34 , CYS X:48 , CYS X:51
BINDING SITE FOR RESIDUE ZN X 9999
[
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]
SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_RPB3_YEAST_001 (A30D, chain O, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_RPB3_YEAST_001
*
A
30
D
RPB3_YEAST
---
---
O
A
30
D
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(9, 9)
Info
All PROSITE Patterns/Profiles
1: RNA_POL_N_8KD (V:2-11)
2: RNA_POL_M_15KD (U:6-32)
3: RNA_POL_D_30KD (O:31-71)
4: RNA_POL_L_13KD (W:35-66)
5: ZF_TFIIS_2 (U:71-111)
6: ZF_TFIIS_1 (U:75-110)
7: RNA_POL_K_14KD (R:86-100)
8: RNA_POL_H_23KD (Q:147-160)
9: RNA_POL_BETA (N:977-989)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RNA_POL_N_8KD
PS01112
RNA polymerases N / 8 Kd subunits signature.
RPAB5_YEAST
2-11
1
-
V:2-11
2
RNA_POL_M_15KD
PS01030
RNA polymerases M / 15 Kd subunits signature.
RPB9_YEAST
6-32
1
-
U:6-32
3
RNA_POL_D_30KD
PS00446
RNA polymerases D / 30 to 40 Kd subunits signature.
RPB3_YEAST
31-71
1
-
O:31-71
4
RNA_POL_L_13KD
PS01154
RNA polymerases L / 13 to 16 Kd subunits signature.
RPB11_YEAST
35-66
1
-
W:35-66
5
ZF_TFIIS_2
PS51133
Zinc finger TFIIS-type profile.
RPB9_YEAST
71-111
1
-
U:71-111
6
ZF_TFIIS_1
PS00466
Zinc finger TFIIS-type signature.
RPB9_YEAST
75-110
1
-
U:75-110
7
RNA_POL_K_14KD
PS01111
RNA polymerases K / 14 to 18 Kd subunits signature.
RPAB2_YEAST
86-100
1
-
R:86-100
8
RNA_POL_H_23KD
PS01110
RNA polymerases H / 23 Kd subunits signature.
RPAB1_YEAST
147-160
1
-
Q:147-160
9
RNA_POL_BETA
PS01166
RNA polymerases beta chain signature.
RPB2_YEAST
977-989
1
-
N:977-989
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(0, 0)
Info
All SCOP Domains
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Sorry, no Info available
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CATH Domains
(10, 26)
Info
all CATH domains
01a: CATH_3houG01 (G:1-82)
01b: CATH_3houS01 (S:1-82)
02a: CATH_3houK00 (K:1-114)
02b: CATH_3houC01 (C:3-42,C:169-268)
02c: CATH_3houO01 (O:3-42,O:169-268)
02d: CATH_3houW00 (W:1-114)
03a: CATH_3houE01 (E:2-142)
03b: CATH_3houQ01 (Q:2-142)
04a: CATH_3houF00 (F:69-155)
04b: CATH_3houR00 (R:69-155)
05a: CATH_3houE02 (E:143-215)
05b: CATH_3houQ02 (Q:143-215)
06a: CATH_3houJ00 (J:1-65)
06b: CATH_3houV00 (V:1-65)
07a: CATH_3houG02 (G:83-171)
07b: CATH_3houH00 (H:2-146)
07c: CATH_3houT00 (T:2-146)
07d: CATH_3houS02 (S:83-171)
08a: CATH_3houC02 (C:43-168)
08b: CATH_3houO02 (O:43-168)
09a: CATH_3houI01 (I:2-46)
09b: CATH_3houI02 (I:47-120)
09c: CATH_3houU02 (U:47-120)
09d: CATH_3houU01 (U:2-46)
10a: CATH_3houL00 (L:25-70)
10b: CATH_3houX00 (X:25-70)
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Classes
(
)
(
)
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(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
DNA-directed RNA polymerase ii subunit; domain 1
(30)
Baker's yeast (Saccharomyces cerevisiae)
(10)
01a
3houG01
G:1-82
01b
3houS01
S:1-82
Topology
:
Gyrase A; domain 2
(166)
Homologous Superfamily
:
[code=3.30.1360.10, no name defined]
(72)
Baker's yeast (Saccharomyces cerevisiae)
(19)
02a
3houK00
K:1-114
02b
3houC01
C:3-42,C:169-268
02c
3houO01
O:3-42,O:169-268
02d
3houW00
W:1-114
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1
(53)
Homologous Superfamily
:
[code=3.40.1340.10, no name defined]
(53)
Baker's yeast (Saccharomyces cerevisiae)
(19)
03a
3houE01
E:2-142
03b
3houQ01
Q:2-142
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Eukaryotic RPB6 RNA polymerase subunit
(77)
Homologous Superfamily
:
[code=3.90.940.10, no name defined]
(71)
Baker's yeast (Saccharomyces cerevisiae)
(19)
04a
3houF00
F:69-155
04b
3houR00
R:69-155
Homologous Superfamily
:
[code=3.90.940.20, no name defined]
(58)
Baker's yeast (Saccharomyces cerevisiae)
(19)
05a
3houE02
E:143-215
05b
3houQ02
Q:143-215
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
Homeodomain-like
(288)
Baker's yeast (Saccharomyces cerevisiae)
(21)
06a
3houJ00
J:1-65
06b
3houV00
V:1-65
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
Baker's yeast (Saccharomyces cerevisiae)
(28)
07a
3houG02
G:83-171
07b
3houH00
H:2-146
07c
3houT00
T:2-146
07d
3houS02
S:83-171
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)
Baker's yeast (Saccharomyces cerevisiae)
(19)
08a
3houC02
C:43-168
08b
3houO02
O:43-168
Architecture
:
Single Sheet
(341)
Topology
:
N-terminal domain of TfIIb
(166)
Homologous Superfamily
:
[code=2.20.25.10, no name defined]
(79)
Baker's yeast (Saccharomyces cerevisiae)
(19)
09a
3houI01
I:2-46
09b
3houI02
I:47-120
09c
3houU02
U:47-120
09d
3houU01
U:2-46
Topology
:
Rubrerythrin, domain 2
(145)
Homologous Superfamily
:
RNA polymerase ii, chain L
(52)
Baker's yeast (Saccharomyces cerevisiae)
(19)
10a
3houL00
L:25-70
10b
3houX00
X:25-70
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Pfam Domains
(0, 0)
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Asym.Unit (1.3 MB)
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Biol.Unit 1 (654 KB)
Header - Biol.Unit 1
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