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1TWF
Biol. Unit 2
Info
Asym.Unit (587 KB)
Biol.Unit 1 (576 KB)
Biol.Unit 2, α-C (1.1 MB)
Biol.Unit 2 (1.1 MB)
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(1)
Title
:
RNA POLYMERASE II COMPLEXED WITH UTP AT 2.3 A RESOLUTION
Authors
:
K. D. Westover, D. A. Bushnell, R. D. Kornberg
Date
:
30 Jun 04 (Deposition) - 16 Nov 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,E,F,H,I,J,K,L
Biol. Unit 1: A,B,C,E,F,H,I,J,K,L (1x)
Biol. Unit 2: A,B,C,E,F,H,I,J,K,L (2x)
Keywords
:
Transcription, Mrna, Multiprotein Complex, Molecular Machine, Zinc Motifs
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
K. D. Westover, D. A. Bushnell, R. D. Kornberg
Structural Basis Of Transcription: Nucleotide Selection By Rotation In The Rna Polymerase Ii Active Center.
Cell(Cambridge, Mass. ) V. 119 481 2004
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: MANGANESE (II) ION (MNa)
1b: MANGANESE (II) ION (MNb)
2a: URIDINE 5'-TRIPHOSPHATE (UTPa)
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
MN
-1
Ligand/Ion
MANGANESE (II) ION
2
UTP
2
Ligand/Ion
URIDINE 5'-TRIPHOSPHATE
3
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS J:7 , CYS J:10 , CYS J:45 , CYS J:46
BINDING SITE FOR RESIDUE ZN J 3001
02
AC2
SOFTWARE
CYS C:86 , CYS C:88 , CYS C:92 , CYS C:95
BINDING SITE FOR RESIDUE ZN C 3002
03
AC3
SOFTWARE
CYS I:7 , CYS I:10 , CYS I:29 , CYS I:32
BINDING SITE FOR RESIDUE ZN I 3003
04
AC4
SOFTWARE
CYS I:75 , CYS I:78 , CYS I:103 , CYS I:106
BINDING SITE FOR RESIDUE ZN I 3004
05
AC5
SOFTWARE
CYS L:31 , CYS L:34 , CYS L:48 , CYS L:51
BINDING SITE FOR RESIDUE ZN L 3005
06
AC6
SOFTWARE
CYS A:107 , CYS A:110 , CYS A:148 , CYS A:167
BINDING SITE FOR RESIDUE ZN A 3006
07
AC7
SOFTWARE
CYS B:1163 , CYS B:1166 , CYS B:1182 , CYS B:1185
BINDING SITE FOR RESIDUE ZN B 3007
08
AC8
SOFTWARE
CYS A:67 , CYS A:70 , CYS A:77 , HIS A:80
BINDING SITE FOR RESIDUE ZN A 3008
09
AC9
SOFTWARE
ASP A:481 , ASP A:483 , ASP A:485 , UTP B:3571
BINDING SITE FOR RESIDUE MN A 3009
10
BC1
SOFTWARE
ASP A:481 , ASP A:483 , ASP B:837 , UTP B:3571
BINDING SITE FOR RESIDUE MN A 3010
11
BC2
SOFTWARE
ASP A:481 , ASP A:483 , ASP A:485 , MN A:3009 , MN A:3010 , ARG B:766 , GLN B:986 , LYS B:987 , ARG B:1020
BINDING SITE FOR RESIDUE UTP B 3571
[
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SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are only available for the asymmetric unit)
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, 18)
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
2
J:2-11
2
RNA_POL_M_15KD
PS01030
RNA polymerases M / 15 Kd subunits signature.
RPB9_YEAST
6-32
2
I:6-32
3
RNA_POL_D_30KD
PS00446
RNA polymerases D / 30 to 40 Kd subunits signature.
RPB3_YEAST
31-71
2
C:31-71
4
RNA_POL_L_13KD
PS01154
RNA polymerases L / 13 to 16 Kd subunits signature.
RPB11_YEAST
35-66
2
K:35-66
5
ZF_TFIIS_2
PS51133
Zinc finger TFIIS-type profile.
RPB9_YEAST
71-111
2
I:71-111
6
ZF_TFIIS_1
PS00466
Zinc finger TFIIS-type signature.
RPB9_YEAST
75-110
2
I:75-110
7
RNA_POL_K_14KD
PS01111
RNA polymerases K / 14 to 18 Kd subunits signature.
RPAB2_YEAST
86-100
2
F:86-100
8
RNA_POL_H_23KD
PS01110
RNA polymerases H / 23 Kd subunits signature.
RPAB1_YEAST
147-160
2
E:147-160
9
RNA_POL_BETA
PS01166
RNA polymerases beta chain signature.
RPB2_YEAST
977-989
2
B:977-989
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(12, 13)
Info
All SCOP Domains
01a: SCOP_d1twfj_ (J:)
02a: SCOP_d1twff_ (F:)
03a: SCOP_d1twfh_ (H:)
04a: SCOP_d1twfk_ (K:)
05a: SCOP_d1twfc1 (C:3-41,C:173-268)
06a: SCOP_d1twfc2 (C:42-172)
07a: SCOP_d1twfe2 (E:144-215)
08a: SCOP_d1twfe1 (E:1-143)
09a: SCOP_d1twfb_ (B:)
10a: SCOP_d1twfa_ (A:)
11a: SCOP_d1twfl_ (L:)
12a: SCOP_d1twfi1 (I:1-49)
12b: SCOP_d1twfi2 (I:50-121)
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Classes
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)
Folds
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d1twfj_
J:
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
d1twff_
F:
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
d1twfh_
H:
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
d1twfk_
K:
Family
:
RNA polymerase alpha subunit dimerisation domain
(43)
Protein domain
:
RPB3
(25)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(24)
05a
d1twfc1
C:3-41,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
d1twfc2
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
d1twfe2
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
d1twfe1
E:1-143
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)
09a
d1twfb_
B:
Family
:
RNA-polymerase beta-prime
(49)
Protein domain
:
RBP1
(25)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(24)
10a
d1twfa_
A:
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)
11a
d1twfl_
L:
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)
12a
d1twfi1
I:1-49
12b
d1twfi2
I:50-121
[
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CATH Domains
(11, 13)
Info
all CATH domains
01a: CATH_1twfK00 (K:1-114)
01b: CATH_1twfC01 (C:3-42,C:169-268)
02a: CATH_1twfE01 (E:1-142)
03a: CATH_1twfB04 (B:221-397)
04a: CATH_1twfF00 (F:72-155)
05a: CATH_1twfE02 (E:143-215)
06a: CATH_1twfJ00 (J:1-65)
07a: CATH_1twfB07 (B:783-798,B:853-973)
08a: CATH_1twfH00 (H:2-146)
09a: CATH_1twfC02 (C:43-168)
10a: CATH_1twfI01 (I:1-46)
10b: CATH_1twfI02 (I:47-122)
11a: CATH_1twfL00 (L:25-70)
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(
)
(
)
Architectures
(
)
(
)
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)
Baker's yeast (Saccharomyces cerevisiae)
(19)
01a
1twfK00
K:1-114
01b
1twfC01
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)
Baker's yeast (Saccharomyces cerevisiae)
(19)
02a
1twfE01
E:1-142
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)
Baker's yeast (Saccharomyces cerevisiae)
(11)
03a
1twfB04
B:221-397
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
1twfF00
F:72-155
Homologous Superfamily
:
[code=3.90.940.20, no name defined]
(58)
Baker's yeast (Saccharomyces cerevisiae)
(19)
05a
1twfE02
E: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
1twfJ00
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)
Baker's yeast (Saccharomyces cerevisiae)
(11)
07a
1twfB07
B:783-798,B:853-973
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
Baker's yeast (Saccharomyces cerevisiae)
(28)
08a
1twfH00
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)
Baker's yeast (Saccharomyces cerevisiae)
(19)
09a
1twfC02
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)
Baker's yeast (Saccharomyces cerevisiae)
(19)
10a
1twfI01
I:1-46
10b
1twfI02
I:47-122
Topology
:
Rubrerythrin, domain 2
(145)
Homologous Superfamily
:
RNA polymerase ii, chain L
(52)
Baker's yeast (Saccharomyces cerevisiae)
(19)
11a
1twfL00
L:25-70
[
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Pfam Domains
(0, 0)
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all PFAM domains
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Asym.Unit (587 KB)
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