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Getting 'Biological Unit' information from database.
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3GTO
Asym. Unit
Info
Asym.Unit (603 KB)
Biol.Unit 1 (589 KB)
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(1)
Title
:
BACKTRACKED RNA POLYMERASE II COMPLEX WITH 15MER RNA
Authors
:
D. Wang, D. A. Bushnell, X. Huang, K. D. Westover, M. Levitt, R. D. Kornbe
Date
:
27 Mar 09 (Deposition) - 09 Jun 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
4.00
Chains
:
Asym. Unit : A,B,C,E,F,H,I,J,K,L,N,R,T
Biol. Unit 1: A,B,C,E,F,H,I,J,K,L,N,R,T (1x)
Keywords
:
Transcription, Transferase, Dna-Rna Hybrid, Backtrack, Dna-Directed Rna Polymerase, Dna Binding, Isopeptide Bond, Magnesium, Metal Binding, Nucleotidyltransferase, Nucleus, Phosphoprotein, Zinc- Finger, Dna Damage, Dna Repair, Transferase-Dna-Rna Hybrid Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Wang, D. A. Bushnell, X. Huang, K. D. Westover, M. Levitt, R. D. Kornberg
Structural Basis Of Transcription: Backtracked Rna Polymerase Ii At 3. 4 Angstrom Resolution.
Science V. 324 1203 2009
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Hetero Components
(2, 9)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
1
Ligand/Ion
MAGNESIUM ION
2
ZN
8
Ligand/Ion
ZINC ION
[
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:110 , CYS A:148
BINDING SITE FOR RESIDUE ZN A 1734
2
AC2
SOFTWARE
CYS A:67 , CYS A:70 , CYS A:77 , HIS A:80
BINDING SITE FOR RESIDUE ZN A 1735
3
AC3
SOFTWARE
CYS B:1163 , CYS B:1166 , CYS B:1182 , CYS B:1185
BINDING SITE FOR RESIDUE ZN B 1307
4
AC4
SOFTWARE
CYS C:86 , CYS C:88 , CYS C:92 , CYS C:95
BINDING SITE FOR RESIDUE ZN C 319
5
AC5
SOFTWARE
CYS I:10 , CYS I:29 , THR I:31 , CYS I:32
BINDING SITE FOR RESIDUE ZN I 203
6
AC6
SOFTWARE
CYS I:75 , CYS I:78 , CYS I:103 , CYS I:106
BINDING SITE FOR RESIDUE ZN I 204
7
AC7
SOFTWARE
CYS J:7 , CYS J:10 , CYS J:45 , CYS J:46
BINDING SITE FOR RESIDUE ZN J 101
8
AC8
SOFTWARE
CYS L:31 , CYS L:34 , CYS L:48 , CYS L:51
BINDING SITE FOR RESIDUE ZN L 105
9
AC9
SOFTWARE
ASP A:481 , ASP A:483 , ASP A:485 , A R:10 , U R:11
BINDING SITE FOR RESIDUE MG A 1736
[
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_RPB3_YEAST_001 (A30D, chain C, )
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
---
---
C
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 (J:2-11)
2: RNA_POL_M_15KD (I:6-32)
3: RNA_POL_D_30KD (C:31-71)
4: RNA_POL_L_13KD (K:35-66)
5: ZF_TFIIS_2 (I:71-111)
6: ZF_TFIIS_1 (I:75-110)
7: RNA_POL_K_14KD (F:86-100)
8: RNA_POL_H_23KD (E:147-160)
9: RNA_POL_BETA (B: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
J:2-11
2
RNA_POL_M_15KD
PS01030
RNA polymerases M / 15 Kd subunits signature.
RPB9_YEAST
6-32
1
I:6-32
3
RNA_POL_D_30KD
PS00446
RNA polymerases D / 30 to 40 Kd subunits signature.
RPB3_YEAST
31-71
1
C:31-71
4
RNA_POL_L_13KD
PS01154
RNA polymerases L / 13 to 16 Kd subunits signature.
RPB11_YEAST
35-66
1
K:35-66
5
ZF_TFIIS_2
PS51133
Zinc finger TFIIS-type profile.
RPB9_YEAST
71-111
1
I:71-111
6
ZF_TFIIS_1
PS00466
Zinc finger TFIIS-type signature.
RPB9_YEAST
75-110
1
I:75-110
7
RNA_POL_K_14KD
PS01111
RNA polymerases K / 14 to 18 Kd subunits signature.
RPAB2_YEAST
86-100
1
F:86-100
8
RNA_POL_H_23KD
PS01110
RNA polymerases H / 23 Kd subunits signature.
RPAB1_YEAST
147-160
1
E:147-160
9
RNA_POL_BETA
PS01166
RNA polymerases beta chain signature.
RPB2_YEAST
977-989
1
B:977-989
[
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]
Exons
(7, 7)
Info
All Exons
Exon 1.1 (E:2-215)
Exon 2.1 (A:3-1445 (gaps))
Exon 3.1 (L:25-70)
Exon 4.1 (C:3-268)
Exon 5.1 (B:20-1224 (gaps))
Exon 6.1 (J:1-65)
Exon 7.2 (F:72-155)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/-
03: Boundary -/2.1
04: Boundary 2.1/-
05: Boundary -/3.1
06: Boundary 3.1/-
07: Boundary -/4.1
08: Boundary 4.1/-
09: Boundary -/5.1
10: Boundary 5.1/-
11: Boundary -/6.1
12: Boundary 6.1/-
13: Boundary 7.1/7.2
14: Boundary 7.2/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
YBR154C
1
YBR154C.1
II:549003-548356
648
RPAB1_YEAST
1-215
215
1
E:2-215
214
2.1
YDL140C
1
YDL140C.1
IV:210562-205361
5202
RPB1_YEAST
1-1733
1733
1
A:3-1445 (gaps)
1443
3.1
YHR143W-A
1
YHR143W-A.1
VIII:387236-387448
213
RPAB4_YEAST
1-70
70
1
L:25-70
46
4.1
YIL021W
1
YIL021W.1
IX:312903-313859
957
RPB3_YEAST
1-318
318
1
C:3-268
266
5.1
YOR151C
1
YOR151C.1
XV:616672-612998
3675
RPB2_YEAST
1-1224
1224
1
B:20-1224 (gaps)
1205
6.1
YOR210W
1
YOR210W.1
XV:738321-738533
213
RPAB5_YEAST
1-70
70
1
J:1-65
65
7.1
YPR187W
1
YPR187W.1
XVI:911253-911272
20
RPAB2_YEAST
1-7
7
0
-
-
7.2
YPR187W
2
YPR187W.2
XVI:911349-911796
448
RPAB2_YEAST
7-155
149
1
F:72-155
84
[
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]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
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CATH Domains
(9, 11)
Info
all CATH domains
1a: CATH_3gtoK00 (K:1-114)
1b: CATH_3gtoC01 (C:3-42,C:169-268)
2a: CATH_3gtoE01 (E:2-142)
3a: CATH_3gtoF00 (F:72-155)
4a: CATH_3gtoE02 (E:143-215)
5a: CATH_3gtoJ00 (J:1-65)
6a: CATH_3gtoH00 (H:2-146)
7a: CATH_3gtoC02 (C:43-168)
8a: CATH_3gtoI01 (I:2-46)
8b: CATH_3gtoI02 (I:47-120)
9a: CATH_3gtoL00 (L:25-70)
View:
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Classes
(
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(
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Architectures
(
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(
)
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)
Yeast (Saccharomyces cerevisiae)
(12)
1a
3gtoK00
K:1-114
1b
3gtoC01
C:3-42,C:169-268
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)
Yeast (Saccharomyces cerevisiae)
(13)
2a
3gtoE01
E: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)
Yeast (Saccharomyces cerevisiae)
(12)
3a
3gtoF00
F:72-155
Homologous Superfamily
:
[code=3.90.940.20, no name defined]
(58)
Yeast (Saccharomyces cerevisiae)
(13)
4a
3gtoE02
E:143-215
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
Homeodomain-like
(288)
Yeast (Saccharomyces cerevisiae)
(12)
5a
3gtoJ00
J:1-65
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
Yeast (Saccharomyces cerevisiae)
(12)
6a
3gtoH00
H:2-146
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)
Yeast (Saccharomyces cerevisiae)
(12)
7a
3gtoC02
C:43-168
Architecture
:
Single Sheet
(341)
Topology
:
N-terminal domain of TfIIb
(166)
Homologous Superfamily
:
[code=2.20.25.10, no name defined]
(79)
Yeast (Saccharomyces cerevisiae)
(12)
8a
3gtoI01
I:2-46
8b
3gtoI02
I:47-120
Topology
:
Rubrerythrin, domain 2
(145)
Homologous Superfamily
:
RNA polymerase ii, chain L
(52)
Yeast (Saccharomyces cerevisiae)
(12)
9a
3gtoL00
L:25-70
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asym.Unit (603 KB)
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