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1R9T
Biol. Unit 1
Info
Asym.Unit (625 KB)
Biol.Unit 1 (598 KB)
(using Jmol or JSmol)
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(1)
Title
:
RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDE
Authors
:
K. D. Westover, D. A. Bushnell, R. D. Kornberg
Date
:
30 Oct 03 (Deposition) - 16 Nov 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
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, Mrna, Multiprotein Complex, Molecular Machine, Dna, Transcription/Dna/Rna Complex, Transcription/Dna-Rna Hybrid Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
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
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
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
ATP
1
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
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 A:107 , MET A:108 , CYS A:110 , CYS A:148 , CYS A:167
BINDING SITE FOR RESIDUE ZN A 1734
02
AC2
SOFTWARE
CYS A:67 , GLN A:68 , CYS A:70 , CYS A:77 , HIS A:80
BINDING SITE FOR RESIDUE ZN A 1735
03
AC3
SOFTWARE
CYS B:1163 , CYS B:1166 , CYS B:1182 , CYS B:1185
BINDING SITE FOR RESIDUE ZN B 1307
04
AC4
SOFTWARE
CYS C:86 , CYS C:88 , HIS C:91 , CYS C:92 , CYS C:95
BINDING SITE FOR RESIDUE ZN C 319
05
AC5
SOFTWARE
CYS I:7 , ARG I:8 , CYS I:10 , CYS I:29 , THR I:31 , CYS I:32
BINDING SITE FOR RESIDUE ZN I 203
06
AC6
SOFTWARE
CYS I:75 , CYS I:78 , CYS I:103 , CYS I:106
BINDING SITE FOR RESIDUE ZN I 204
07
AC7
SOFTWARE
CYS J:7 , CYS J:10 , CYS J:45 , CYS J:46
BINDING SITE FOR RESIDUE ZN J 101
08
AC8
SOFTWARE
CYS L:31 , CYS L:34 , CYS L:48 , CYS L:51
BINDING SITE FOR RESIDUE ZN L 105
09
AC9
SOFTWARE
ASP A:481 , ASP A:483 , ASP A:485 , A R:10
BINDING SITE FOR RESIDUE MG A 2001
10
BC1
SOFTWARE
ASP A:481 , ASP A:483 , ASP B:837 , ATP B:1308
BINDING SITE FOR RESIDUE MG A 2002
11
BC2
SOFTWARE
LYS A:752 , MG A:2002 , ARG B:766 , LYS B:987 , SER B:1019 , ARG B:1020
BINDING SITE FOR RESIDUE ATP B 1308
[
close Site info
]
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
[
close PROSITE info
]
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
(1, 10)
Info
All SCOP Domains
1a: SCOP_d1r9ta_ (A:)
1b: SCOP_d1r9tb_ (B:)
1c: SCOP_d1r9tc_ (C:)
1d: SCOP_d1r9te_ (E:)
1e: SCOP_d1r9tf_ (F:)
1f: SCOP_d1r9th_ (H:)
1g: SCOP_d1r9ti_ (I:)
1h: SCOP_d1r9tj_ (J:)
1i: SCOP_d1r9tk_ (K:)
1j: SCOP_d1r9tl_ (L:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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)
1a
d1r9ta_
A:
1b
d1r9tb_
B:
1c
d1r9tc_
C:
1d
d1r9te_
E:
1e
d1r9tf_
F:
1f
d1r9th_
H:
1g
d1r9ti_
I:
1h
d1r9tj_
J:
1i
d1r9tk_
K:
1j
d1r9tl_
L:
[
close SCOP info
]
CATH Domains
(11, 13)
Info
all CATH domains
01a: CATH_1r9tK00 (K:1-114)
01b: CATH_1r9tC01 (C:3-42,C:169-268)
02a: CATH_1r9tE01 (E:2-142)
03a: CATH_1r9tB04 (B:221-397)
04a: CATH_1r9tF00 (F:72-155)
05a: CATH_1r9tE02 (E:143-215)
06a: CATH_1r9tJ00 (J:1-65)
07a: CATH_1r9tB07 (B:783-798,B:853-973)
08a: CATH_1r9tH00 (H:2-146)
09a: CATH_1r9tC02 (C:43-168)
10a: CATH_1r9tI01 (I:2-46)
10b: CATH_1r9tI02 (I:47-120)
11a: CATH_1r9tL00 (L:25-70)
View:
Select:
Label:
Classes
(
)
(
)
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)
[unclassified]
(17)
01a
1r9tK00
K:1-114
01b
1r9tC01
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)
02a
1r9tE01
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)
03a
1r9tB04
B:221-397
Topology
:
Eukaryotic RPB6 RNA polymerase subunit
(77)
Homologous Superfamily
:
[code=3.90.940.10, no name defined]
(71)
[unclassified]
(17)
04a
1r9tF00
F:72-155
Homologous Superfamily
:
[code=3.90.940.20, no name defined]
(58)
[unclassified]
(14)
05a
1r9tE02
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)
06a
1r9tJ00
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)
07a
1r9tB07
B:783-798,B:853-973
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
[unclassified]
(49)
08a
1r9tH00
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)
09a
1r9tC02
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)
10a
1r9tI01
I:2-46
10b
1r9tI02
I:47-120
Topology
:
Rubrerythrin, domain 2
(145)
Homologous Superfamily
:
RNA polymerase ii, chain L
(52)
[unclassified]
(14)
11a
1r9tL00
L:25-70
[
close CATH info
]
Pfam Domains
(25, 25)
Info
all PFAM domains
01a: PFAM_RNA_pol_Rpb2_6_1r9tB01 (B:750-1124)
02a: PFAM_RNA_pol_Rpb8_1r9tH01 (H:7-146)
03a: PFAM_RNA_pol_L_1r9tC01 (C:18-256)
04a: PFAM_RNA_pol_L_2_1r9tK01 (K:29-105)
05a: PFAM_DNA_RNApol_7kD_1r9tL01 (L:29-60)
06a: PFAM_RNA_POL_M_15KD_1r9tI01 (I:4-41)
07a: PFAM_TFIIS_C_1r9tI02 (I:73-111)
08a: PFAM_RNA_pol_A_bac_1r9tC02 (C:49-171)
09a: PFAM_RNA_pol_N_1r9tJ01 (J:1-61)
10a: PFAM_RNA_pol_Rpb1_1_1r9tA01 (A:11-340)
11a: PFAM_RNA_pol_Rpb1_2_1r9tA02 (A:342-507)
12a: PFAM_RNA_pol_Rpb1_3_1r9tA03 (A:510-669)
13a: PFAM_RNA_pol_Rpb1_4_1r9tA04 (A:693-800)
14a: PFAM_RNA_pol_Rpb1_5_1r9tA05 (A:807-1398)
15a: PFAM_RNA_pol_Rpb1_6_1r9tA06 (A:873-1056)
16a: PFAM_RNA_pol_Rpb1_7_1r9tA07 (A:1141-1274)
17a: PFAM_RNA_pol_Rpb2_1_1r9tB02 (B:42-464)
18a: PFAM_RNA_pol_Rpb2_2_1r9tB03 (B:219-407)
19a: PFAM_RNA_pol_Rpb2_3_1r9tB04 (B:481-546)
20a: PFAM_RNA_pol_Rpb2_4_1r9tB05 (B:580-642)
21a: PFAM_RNA_pol_Rpb2_5_1r9tB06 (B:681-745)
22a: PFAM_RNA_pol_Rpb2_7_1r9tB07 (B:1126-1219)
23a: PFAM_RNA_pol_Rpb5_C_1r9tE01 (E:142-215)
24a: PFAM_RNA_pol_Rpb5_N_1r9tE02 (E:2-101)
25a: PFAM_RNA_pol_Rpb6_1r9tF01 (F:78-134)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
LEF-8-like
(36)
Family
:
RNA_pol_Rpb2_6
(36)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
01a
RNA_pol_Rpb2_6-1r9tB01
B:750-1124
Clan
:
OB
(224)
Family
:
RNA_pol_Rpb8
(26)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
02a
RNA_pol_Rpb8-1r9tH01
H:7-146
Clan
:
RBP11-like
(36)
Family
:
RNA_pol_L
(36)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
03a
RNA_pol_L-1r9tC01
C:18-256
Family
:
RNA_pol_L_2
(27)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
04a
RNA_pol_L_2-1r9tK01
K:29-105
Clan
:
Zn_Beta_Ribbon
(109)
Family
:
DNA_RNApol_7kD
(28)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
05a
DNA_RNApol_7kD-1r9tL01
L:29-60
Family
:
RNA_POL_M_15KD
(26)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
06a
RNA_POL_M_15KD-1r9tI01
I:4-41
Family
:
TFIIS_C
(26)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(25)
07a
TFIIS_C-1r9tI02
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)
08a
RNA_pol_A_bac-1r9tC02
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)
09a
RNA_pol_N-1r9tJ01
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)
10a
RNA_pol_Rpb1_1-1r9tA01
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)
11a
RNA_pol_Rpb1_2-1r9tA02
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)
12a
RNA_pol_Rpb1_3-1r9tA03
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)
13a
RNA_pol_Rpb1_4-1r9tA04
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)
14a
RNA_pol_Rpb1_5-1r9tA05
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)
15a
RNA_pol_Rpb1_6-1r9tA06
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)
16a
RNA_pol_Rpb1_7-1r9tA07
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)
17a
RNA_pol_Rpb2_1-1r9tB02
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)
18a
RNA_pol_Rpb2_2-1r9tB03
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)
19a
RNA_pol_Rpb2_3-1r9tB04
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)
20a
RNA_pol_Rpb2_4-1r9tB05
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)
21a
RNA_pol_Rpb2_5-1r9tB06
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)
22a
RNA_pol_Rpb2_7-1r9tB07
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)
23a
RNA_pol_Rpb5_C-1r9tE01
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)
24a
RNA_pol_Rpb5_N-1r9tE02
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)
25a
RNA_pol_Rpb6-1r9tF01
F:78-134
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Asymmetric Unit 1
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