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2R93
Biol. Unit 1
Info
Asym.Unit (659 KB)
Biol.Unit 1 (641 KB)
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(1)
Title
:
ELONGATION COMPLEX OF RNA POLYMERASE II WITH A HEPATITIS DELTA VIRUS-DERIVED RNA STEM LOOP
Authors
:
E. Lehmann, F. Brueckner, P. Cramer
Date
:
12 Sep 07 (Deposition) - 27 Nov 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
4.00
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
:
Transferase/Dna/Rna, Dna-Binding, Phosphorylation, Rna Polymerase Ii, Metal-Binding, Nuclear Protein, Transcription Bubble, Elongation Complex, Transferase, Transcription, Rna-Dependent, Rna-Dependent Rna Synthesis, Rdrp, Ddrp, Rna-Binding, Hepatitis Delta Virus, Hdv, Dna- Directed Rna Polymerase, Magnesium, Nucleotidyltransferase, Nucleus, Ubl Conjugation, Zinc, Zinc-Finger, Polymorphism, Cytoplasm, Dna Damage, Dna Repair, Mrna Processing, Transferase/Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Lehmann, F. Brueckner, P. Cramer
Molecular Basis Of Rna-Dependent Rna Polymerase Ii Activity.
Nature V. 450 445 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
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:
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Sorry, no Info available
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Sites
(0, 0)
Info
All Sites
View:
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Label:
Sorry, no Info available
[
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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 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
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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
(6, 9)
Info
All SCOP Domains
1a: SCOP_d2r93j1 (J:1-65)
2a: SCOP_d2r93f1 (F:72-155)
3a: SCOP_d2r93h1 (H:2-146)
4a: SCOP_d2r93a1 (A:2-1455)
4b: SCOP_d2r93d1 (D:4-221)
4c: SCOP_d2r93g1 (G:1-171)
4d: SCOP_d2r93k1 (K:1-112)
5a: SCOP_d2r93b1 (B:20-1224)
6a: SCOP_d2r93l1 (L:25-70)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
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)
1a
d2r93j1
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)
2a
d2r93f1
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)
3a
d2r93h1
H:2-146
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)
4a
d2r93a1
A:2-1455
4b
d2r93d1
D:4-221
4c
d2r93g1
G:1-171
4d
d2r93k1
K:1-112
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)
5a
d2r93b1
B:20-1224
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)
6a
d2r93l1
L:25-70
[
close SCOP info
]
CATH Domains
(12, 15)
Info
all CATH domains
01a: CATH_2r93G01 (G:1-82)
02a: CATH_2r93K00 (K:1-112)
02b: CATH_2r93C01 (C:2-42,C:169-268)
03a: CATH_2r93E01 (E:2-142)
04a: CATH_2r93B04 (B:221-397)
05a: CATH_2r93F00 (F:68-155)
06a: CATH_2r93E02 (E:143-215)
07a: CATH_2r93J00 (J:1-65)
08a: CATH_2r93B07 (B:783-798,B:853-973)
09a: CATH_2r93G02 (G:83-171)
09b: CATH_2r93H00 (H:2-146)
10a: CATH_2r93C02 (C:43-168)
11a: CATH_2r93I01 (I:2-46)
11b: CATH_2r93I02 (I:47-117)
12a: CATH_2r93L00 (L:25-70)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
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
2r93G01
G:1-82
Topology
:
Gyrase A; domain 2
(166)
Homologous Superfamily
:
[code=3.30.1360.10, no name defined]
(72)
[unclassified]
(17)
02a
2r93K00
K:1-112
02b
2r93C01
C:2-42,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
2r93E01
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
2r93B04
B:221-397
Topology
:
Eukaryotic RPB6 RNA polymerase subunit
(77)
Homologous Superfamily
:
[code=3.90.940.10, no name defined]
(71)
[unclassified]
(17)
05a
2r93F00
F:68-155
Homologous Superfamily
:
[code=3.90.940.20, no name defined]
(58)
[unclassified]
(14)
06a
2r93E02
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
2r93J00
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
2r93B07
B:783-798,B:853-973
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
[unclassified]
(49)
09a
2r93G02
G:83-171
09b
2r93H00
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
2r93C02
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
2r93I01
I:2-46
11b
2r93I02
I:47-117
Topology
:
Rubrerythrin, domain 2
(145)
Homologous Superfamily
:
RNA polymerase ii, chain L
(52)
[unclassified]
(14)
12a
2r93L00
L:25-70
[
close CATH info
]
Pfam Domains
(28, 28)
Info
all PFAM domains
01a: PFAM_RNA_pol_Rpb4_2r93D01 (D:49-218)
02a: PFAM_RNA_pol_Rpb2_6_2r93B01 (B:750-1124)
03a: PFAM_RNA_pol_Rpb8_2r93H01 (H:7-146)
04a: PFAM_S1_2r93G01 (G:80-161)
05a: PFAM_RNA_pol_L_2r93C01 (C:18-256)
06a: PFAM_RNA_pol_L_2_2r93K01 (K:29-105)
07a: PFAM_SHS2_Rpb7_N_2r93G02 (G:8-79)
08a: PFAM_DNA_RNApol_7kD_2r93L01 (L:29-60)
09a: PFAM_RNA_POL_M_15KD_2r93I01 (I:4-41)
10a: PFAM_TFIIS_C_2r93I02 (I:73-111)
11a: PFAM_RNA_pol_A_bac_2r93C02 (C:49-171)
12a: PFAM_RNA_pol_N_2r93J01 (J:1-61)
13a: PFAM_RNA_pol_Rpb1_1_2r93A01 (A:11-340)
14a: PFAM_RNA_pol_Rpb1_2_2r93A02 (A:342-507)
15a: PFAM_RNA_pol_Rpb1_3_2r93A03 (A:510-669)
16a: PFAM_RNA_pol_Rpb1_4_2r93A04 (A:693-800)
17a: PFAM_RNA_pol_Rpb1_5_2r93A05 (A:807-1398)
18a: PFAM_RNA_pol_Rpb1_6_2r93A06 (A:873-1056)
19a: PFAM_RNA_pol_Rpb1_7_2r93A07 (A:1141-1274)
20a: PFAM_RNA_pol_Rpb2_1_2r93B02 (B:42-464)
21a: PFAM_RNA_pol_Rpb2_2_2r93B03 (B:219-407)
22a: PFAM_RNA_pol_Rpb2_3_2r93B04 (B:481-546)
23a: PFAM_RNA_pol_Rpb2_4_2r93B05 (B:580-642)
24a: PFAM_RNA_pol_Rpb2_5_2r93B06 (B:681-745)
25a: PFAM_RNA_pol_Rpb2_7_2r93B07 (B:1126-1219)
26a: PFAM_RNA_pol_Rpb5_C_2r93E01 (E:142-215)
27a: PFAM_RNA_pol_Rpb5_N_2r93E02 (E:2-101)
28a: PFAM_RNA_pol_Rpb6_2r93F01 (F:78-134)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HRDC-like
(19)
Family
:
RNA_pol_Rpb4
(11)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(9)
01a
RNA_pol_Rpb4-2r93D01
D:49-218
Clan
:
LEF-8-like
(36)
Family
:
RNA_pol_Rpb2_6
(36)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
02a
RNA_pol_Rpb2_6-2r93B01
B:750-1124
Clan
:
OB
(224)
Family
:
RNA_pol_Rpb8
(26)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
03a
RNA_pol_Rpb8-2r93H01
H:7-146
Family
:
S1
(23)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(10)
04a
S1-2r93G01
G:80-161
Clan
:
RBP11-like
(36)
Family
:
RNA_pol_L
(36)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
05a
RNA_pol_L-2r93C01
C:18-256
Family
:
RNA_pol_L_2
(27)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
06a
RNA_pol_L_2-2r93K01
K:29-105
Clan
:
SHS2
(26)
Family
:
SHS2_Rpb7-N
(12)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(10)
07a
SHS2_Rpb7-N-2r93G02
G:8-79
Clan
:
Zn_Beta_Ribbon
(109)
Family
:
DNA_RNApol_7kD
(28)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
08a
DNA_RNApol_7kD-2r93L01
L:29-60
Family
:
RNA_POL_M_15KD
(26)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
09a
RNA_POL_M_15KD-2r93I01
I:4-41
Family
:
TFIIS_C
(26)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(25)
10a
TFIIS_C-2r93I02
I:73-111
Clan
:
no clan defined [family: RNA_pol_A_bac]
(36)
Family
:
RNA_pol_A_bac
(36)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
11a
RNA_pol_A_bac-2r93C02
C:49-171
Clan
:
no clan defined [family: RNA_pol_N]
(28)
Family
:
RNA_pol_N
(28)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
12a
RNA_pol_N-2r93J01
J:1-61
Clan
:
no clan defined [family: RNA_pol_Rpb1_1]
(37)
Family
:
RNA_pol_Rpb1_1
(37)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
13a
RNA_pol_Rpb1_1-2r93A01
A:11-340
Clan
:
no clan defined [family: RNA_pol_Rpb1_2]
(36)
Family
:
RNA_pol_Rpb1_2
(36)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
14a
RNA_pol_Rpb1_2-2r93A02
A:342-507
Clan
:
no clan defined [family: RNA_pol_Rpb1_3]
(36)
Family
:
RNA_pol_Rpb1_3
(36)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
15a
RNA_pol_Rpb1_3-2r93A03
A:510-669
Clan
:
no clan defined [family: RNA_pol_Rpb1_4]
(36)
Family
:
RNA_pol_Rpb1_4
(36)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
16a
RNA_pol_Rpb1_4-2r93A04
A:693-800
Clan
:
no clan defined [family: RNA_pol_Rpb1_5]
(36)
Family
:
RNA_pol_Rpb1_5
(36)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
17a
RNA_pol_Rpb1_5-2r93A05
A:807-1398
Clan
:
no clan defined [family: RNA_pol_Rpb1_6]
(26)
Family
:
RNA_pol_Rpb1_6
(26)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
18a
RNA_pol_Rpb1_6-2r93A06
A:873-1056
Clan
:
no clan defined [family: RNA_pol_Rpb1_7]
(26)
Family
:
RNA_pol_Rpb1_7
(26)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
19a
RNA_pol_Rpb1_7-2r93A07
A:1141-1274
Clan
:
no clan defined [family: RNA_pol_Rpb2_1]
(37)
Family
:
RNA_pol_Rpb2_1
(37)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
20a
RNA_pol_Rpb2_1-2r93B02
B:42-464
Clan
:
no clan defined [family: RNA_pol_Rpb2_2]
(36)
Family
:
RNA_pol_Rpb2_2
(36)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
21a
RNA_pol_Rpb2_2-2r93B03
B:219-407
Clan
:
no clan defined [family: RNA_pol_Rpb2_3]
(35)
Family
:
RNA_pol_Rpb2_3
(35)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
22a
RNA_pol_Rpb2_3-2r93B04
B:481-546
Clan
:
no clan defined [family: RNA_pol_Rpb2_4]
(28)
Family
:
RNA_pol_Rpb2_4
(28)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
23a
RNA_pol_Rpb2_4-2r93B05
B:580-642
Clan
:
no clan defined [family: RNA_pol_Rpb2_5]
(28)
Family
:
RNA_pol_Rpb2_5
(28)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
24a
RNA_pol_Rpb2_5-2r93B06
B:681-745
Clan
:
no clan defined [family: RNA_pol_Rpb2_7]
(36)
Family
:
RNA_pol_Rpb2_7
(36)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
25a
RNA_pol_Rpb2_7-2r93B07
B:1126-1219
Clan
:
no clan defined [family: RNA_pol_Rpb5_C]
(28)
Family
:
RNA_pol_Rpb5_C
(28)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
26a
RNA_pol_Rpb5_C-2r93E01
E:142-215
Clan
:
no clan defined [family: RNA_pol_Rpb5_N]
(26)
Family
:
RNA_pol_Rpb5_N
(26)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
27a
RNA_pol_Rpb5_N-2r93E02
E:2-101
Clan
:
no clan defined [family: RNA_pol_Rpb6]
(37)
Family
:
RNA_pol_Rpb6
(37)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
28a
RNA_pol_Rpb6-2r93F01
F:78-134
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