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2B63
Asym. Unit
Info
Asym.Unit (667 KB)
Biol.Unit 1 (646 KB)
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(1)
Title
:
COMPLETE RNA POLYMERASE II-RNA INHIBITOR COMPLEX
Authors
:
H. Kettenberger, A. Eisenfuehr, F. Brueckner, M. Theis, M. Famulok, P. Cramer
Date
:
30 Sep 05 (Deposition) - 06 Dec 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,R
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,R (1x)
Keywords
:
Rna Polymerase Ii, Rna, Aptamer, Protein-Rna Complex, Inhibitor, Transferase/Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Kettenberger, A. Eisenfuehr, F. Brueckner, M. Theis, M. Famulok, P. Cramer
Structure Of An Rna Polymerase Ii-Rna Inhibitor Complex Elucidates Transcription Regulation By Noncoding Rnas
Nat. Struct. Mol. Biol. V. 13 44 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 13)
Info
All Hetero Components
1a: 5-BROMO-URIDINE-5'-MONOPHOSPHATE (5BUa)
1b: 5-BROMO-URIDINE-5'-MONOPHOSPHATE (5BUb)
1c: 5-BROMO-URIDINE-5'-MONOPHOSPHATE (5BUc)
1d: 5-BROMO-URIDINE-5'-MONOPHOSPHATE (5BUd)
2a: MAGNESIUM ION (MGa)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
3g: ZINC ION (ZNg)
3h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
5BU
4
Mod. Nucleotide
5-BROMO-URIDINE-5'-MONOPHOSPHATE
2
MG
1
Ligand/Ion
MAGNESIUM ION
3
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
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
MET A:108 , CYS A:110 , CYS A:148 , CYS A:167
BINDING SITE FOR RESIDUE ZN A 2456
2
AC2
SOFTWARE
CYS A:67 , CYS A:70 , CYS A:77 , HIS A:80
BINDING SITE FOR RESIDUE ZN A 2457
3
AC3
SOFTWARE
ASP A:481 , ASP A:483 , ASP A:485
BINDING SITE FOR RESIDUE MG A 2458
4
AC4
SOFTWARE
CYS B:1163 , CYS B:1166 , CYS B:1182 , CYS B:1185
BINDING SITE FOR RESIDUE ZN B 2225
5
AC5
SOFTWARE
CYS C:86 , CYS C:88 , HIS C:91 , CYS C:92 , CYS C:95
BINDING SITE FOR RESIDUE ZN C 1269
6
AC6
SOFTWARE
CYS I:7 , CYS I:10 , CYS I:29 , CYS I:32
BINDING SITE FOR RESIDUE ZN I 1121
7
AC7
SOFTWARE
CYS I:75 , CYS I:78 , CYS I:103 , CYS I:106 , HIS I:108
BINDING SITE FOR RESIDUE ZN I 1122
8
AC8
SOFTWARE
CYS J:7 , CYS J:10 , CYS J:45 , CYS J:46
BINDING SITE FOR RESIDUE ZN J 1066
9
AC9
SOFTWARE
CYS L:31 , CYS L:34 , CYS L:48 , CYS L:51
BINDING SITE FOR RESIDUE ZN L 1071
[
close Site info
]
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)
[
close SNP/Variant info
]
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
[
close PROSITE info
]
Exons
(9, 9)
Info
All Exons
Exon 1.1 (E:2-215)
Exon 2.1 (A:2-1455 (gaps))
Exon 3.1 (G:1-171)
Exon 4.1 (L:25-70)
Exon 5.1 (C:3-268)
Exon 6.1 (D:4-221 (gaps))
Exon 7.1 (B:20-1224 (gaps))
Exon 8.1 (J:1-65)
Exon 9.2 (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
14: Boundary 7.1/-
15: Boundary -/8.1
16: Boundary 8.1/-
17: Boundary 9.1/9.2
18: Boundary 9.2/-
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:2-1455 (gaps)
1454
3.1
YDR404C
1
YDR404C.1
IV:1277162-1276647
516
RPB7_YEAST
1-171
171
1
G:1-171
171
4.1
YHR143W-A
1
YHR143W-A.1
VIII:387236-387448
213
RPAB4_YEAST
1-70
70
1
L:25-70
46
5.1
YIL021W
1
YIL021W.1
IX:312903-313859
957
RPB3_YEAST
1-318
318
1
C:3-268
266
6.1
YJL140W
1
YJL140W.1
X:150957-151622
666
RPB4_YEAST
1-221
221
1
D:4-221 (gaps)
218
7.1
YOR151C
1
YOR151C.1
XV:616672-612998
3675
RPB2_YEAST
1-1224
1224
1
B:20-1224 (gaps)
1205
8.1
YOR210W
1
YOR210W.1
XV:738321-738533
213
RPAB5_YEAST
1-70
70
1
J:1-65
65
9.1
YPR187W
1
YPR187W.1
XVI:911253-911272
20
RPAB2_YEAST
1-7
7
0
-
-
9.2
YPR187W
2
YPR187W.2
XVI:911349-911796
448
RPAB2_YEAST
7-155
149
1
F:72-155
84
[
close EXON info
]
SCOP Domains
(13, 15)
Info
All SCOP Domains
01a: SCOP_d2b63j1 (J:1-65)
02a: SCOP_d2b63f1 (F:72-155)
03a: SCOP_d2b63h1 (H:2-146)
04a: SCOP_d2b63k1 (K:1-114)
05a: SCOP_d2b63c1 (C:3-37,C:173-268)
06a: SCOP_d2b63c2 (C:42-172)
07a: SCOP_d2b63e2 (E:144-215)
08a: SCOP_d2b63e1 (E:2-143)
09a: SCOP_d2b63d1 (D:15-75)
09b: SCOP_d2b63g1 (G:1-79)
10a: SCOP_d2b63b1 (B:20-1224)
11a: SCOP_d2b63a1 (A:2-1450)
12a: SCOP_d2b63l1 (L:25-70)
13a: SCOP_d2b63i1 (I:2-49)
13b: SCOP_d2b63i2 (I:50-120)
View:
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Classes
(
)
(
)
Folds
(
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(
)
(
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Families
(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
RNA polymerase subunit RPB10
(37)
Family
:
RNA polymerase subunit RPB10
(37)
Protein domain
:
RNA polymerase subunit RPB10
(30)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(28)
01a
d2b63j1
J:1-65
Fold
:
RPB6/omega subunit-like
(56)
Superfamily
:
RPB6/omega subunit-like
(56)
Family
:
RPB6
(37)
Protein domain
:
RPB6
(32)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(30)
02a
d2b63f1
F:72-155
Class
:
All beta proteins
(24004)
Fold
:
OB-fold
(1179)
Superfamily
:
Nucleic acid-binding proteins
(590)
Family
:
RNA polymerase subunit RBP8
(37)
Protein domain
:
RNA polymerase subunit RBP8
(37)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(35)
03a
d2b63h1
H:2-146
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
DCoH-like
(107)
Superfamily
:
RBP11-like subunits of RNA polymerase
(76)
Family
:
RBP11/RpoL
(31)
Protein domain
:
RPB11
(24)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(23)
04a
d2b63k1
K:1-114
Family
:
RNA polymerase alpha subunit dimerisation domain
(43)
Protein domain
:
RPB3
(25)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(24)
05a
d2b63c1
C:3-37,C:173-268
Fold
:
Insert subdomain of RNA polymerase alpha subunit
(43)
Superfamily
:
Insert subdomain of RNA polymerase alpha subunit
(43)
Family
:
Insert subdomain of RNA polymerase alpha subunit
(43)
Protein domain
:
RPB3
(25)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(24)
06a
d2b63c2
C:42-172
Fold
:
RPB5-like RNA polymerase subunit
(34)
Superfamily
:
RPB5-like RNA polymerase subunit
(34)
Family
:
RPB5
(29)
Protein domain
:
Eukaryotic RPB5 C-terminal domain
(27)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(26)
07a
d2b63e2
E:144-215
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Restriction endonuclease-like
(209)
Superfamily
:
Eukaryotic RPB5 N-terminal domain
(32)
Family
:
Eukaryotic RPB5 N-terminal domain
(32)
Protein domain
:
Eukaryotic RPB5 N-terminal domain
(27)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(26)
08a
d2b63e1
E:2-143
Class
:
Low resolution protein structures
(283)
Fold
:
RNA polymerase
(26)
Superfamily
:
RNA polymerase
(26)
Family
:
RNA polymerase
(26)
Protein domain
:
Complete 12-subunit RNA polymerase II complex
(23)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(23)
09a
d2b63d1
D:15-75
09b
d2b63g1
G:1-79
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
:
RBP2
(28)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(27)
10a
d2b63b1
B:20-1224
Family
:
RNA-polymerase beta-prime
(49)
Protein domain
:
RBP1
(25)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(24)
11a
d2b63a1
A:2-1450
Class
:
Small proteins
(3458)
Fold
:
Rubredoxin-like
(572)
Superfamily
:
RNA polymerase subunits
(39)
Family
:
RBP12 subunit of RNA polymerase II
(36)
Protein domain
:
RBP12 subunit of RNA polymerase II
(31)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(30)
12a
d2b63l1
L:25-70
Superfamily
:
Zinc beta-ribbon
(41)
Family
:
Transcriptional factor domain
(36)
Protein domain
:
RBP9 subunit of RNA polymerase II
(26)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(24)
13a
d2b63i1
I:2-49
13b
d2b63i2
I:50-120
[
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]
CATH Domains
(12, 15)
Info
all CATH domains
01a: CATH_2b63G01 (G:1-82)
02a: CATH_2b63K00 (K:1-115)
02b: CATH_2b63C01 (C:3-42,C:169-268)
03a: CATH_2b63E01 (E:2-142)
04a: CATH_2b63B04 (B:221-397)
05a: CATH_2b63F00 (F:72-155)
06a: CATH_2b63E02 (E:143-215)
07a: CATH_2b63J00 (J:1-65)
08a: CATH_2b63B07 (B:783-798,B:853-973)
09a: CATH_2b63G02 (G:83-171)
09b: CATH_2b63H00 (H:2-146)
10a: CATH_2b63C02 (C:43-168)
11a: CATH_2b63I01 (I:2-46)
11b: CATH_2b63I02 (I:47-120)
12a: CATH_2b63L00 (L:25-70)
View:
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Classes
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)
Architectures
(
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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)
[unclassified]
(5)
01a
2b63G01
G:1-82
Topology
:
Gyrase A; domain 2
(166)
Homologous Superfamily
:
[code=3.30.1360.10, no name defined]
(72)
[unclassified]
(17)
02a
2b63K00
K:1-115
02b
2b63C01
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)
[unclassified]
(14)
03a
2b63E01
E:2-142
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)
04a
2b63B04
B:221-397
Topology
:
Eukaryotic RPB6 RNA polymerase subunit
(77)
Homologous Superfamily
:
[code=3.90.940.10, no name defined]
(71)
[unclassified]
(17)
05a
2b63F00
F:72-155
Homologous Superfamily
:
[code=3.90.940.20, no name defined]
(58)
[unclassified]
(14)
06a
2b63E02
E:143-215
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
Homeodomain-like
(288)
[unclassified]
(65)
07a
2b63J00
J:1-65
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
[code=2.40.50.150, no name defined]
(48)
[unclassified]
(17)
08a
2b63B07
B:783-798,B:853-973
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
[unclassified]
(49)
09a
2b63G02
G:83-171
09b
2b63H00
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)
[unclassified]
(17)
10a
2b63C02
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)
[unclassified]
(14)
11a
2b63I01
I:2-46
11b
2b63I02
I:47-120
Topology
:
Rubrerythrin, domain 2
(145)
Homologous Superfamily
:
RNA polymerase ii, chain L
(52)
[unclassified]
(14)
12a
2b63L00
L:25-70
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Atom Selection
(currently selected atoms:
all
)
Protein
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 F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain R
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
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by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
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(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
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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)
[
close Script example commands
]
Log
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") .
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