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2E2J
Biol. Unit 1
Info
Asym.Unit (605 KB)
Biol.Unit 1 (589 KB)
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(1)
Title
:
RNA POLYMERASE II ELONGATION COMPLEX IN 5 MM MG+2 WITH GMPCPP
Authors
:
D. Wang, D. A. Bushnell, K. D. Westover, C. D. Kaplan, R. D. Kornberg
Date
:
14 Nov 06 (Deposition) - 12 Dec 06 (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, Transferase/Dna-Rna Hybrid Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Wang, D. A. Bushnell, K. D. Westover, C. D. Kaplan, R. D. Kornberg
Structural Basis Of Transcription: Role Of The Trigger Loop In Substrate Specificity And Catalysis
Cell(Cambridge, Mass. ) V. 127 941 2006
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: PHOSPHOMETHYLPHOSPHONIC ACID GUANY... (G2Pa)
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
G2P
1
Ligand/Ion
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
2
MG
-1
Ligand/Ion
MAGNESIUM ION
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 A:107 , CYS A:110 , CYS A:148 , CYS A:167
BINDING SITE FOR RESIDUE ZN A 1734
02
AC2
SOFTWARE
CYS A:67 , 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 , CYS C:92 , CYS C:95
BINDING SITE FOR RESIDUE ZN C 319
05
AC5
SOFTWARE
CYS I:7 , 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 , G R:10 , G2P T:3000
BINDING SITE FOR RESIDUE MG A 2001
10
BC1
SOFTWARE
ASP A:481 , ASP A:483 , ASP B:837 , G2P T:3000
BINDING SITE FOR RESIDUE MG A 2002
11
BC2
SOFTWARE
ARG A:446 , PRO A:448 , ASN A:479 , MG A:2001 , MG A:2002 , ARG B:766 , ARG B:1020 , G R:10 , DC T:18 , DC T:19
BINDING SITE FOR RESIDUE G2P T 3000
[
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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)
[
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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
(0, 0)
Info
All Exons
View:
Select:
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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_d2e2jj1 (J:1-65)
02a: SCOP_d2e2jf1 (F:72-154)
03a: SCOP_d2e2jh1 (H:2-146)
04a: SCOP_d2e2jk1 (K:1-114)
05a: SCOP_d2e2jc1 (C:3-37,C:173-268)
06a: SCOP_d2e2jc2 (C:42-172)
07a: SCOP_d2e2je2 (E:144-215)
08a: SCOP_d2e2je1 (E:2-143)
09a: SCOP_d2e2jb1 (B:20-1222)
10a: SCOP_d2e2ja1 (A:3-1445)
11a: SCOP_d2e2jl1 (L:25-70)
12a: SCOP_d2e2ji1 (I:2-49)
12b: SCOP_d2e2ji2 (I:50-120)
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)
01a
d2e2jj1
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
d2e2jf1
F:72-154
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
d2e2jh1
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
d2e2jk1
K:1-114
Family
:
RNA polymerase alpha subunit dimerisation domain
(43)
Protein domain
:
RPB3
(25)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(24)
05a
d2e2jc1
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
d2e2jc2
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
d2e2je2
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
d2e2je1
E:2-143
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
d2e2jb1
B:20-1222
Family
:
RNA-polymerase beta-prime
(49)
Protein domain
:
RBP1
(25)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(24)
10a
d2e2ja1
A:3-1445
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
d2e2jl1
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)
12a
d2e2ji1
I:2-49
12b
d2e2ji2
I:50-120
[
close SCOP info
]
CATH Domains
(11, 13)
Info
all CATH domains
01a: CATH_2e2jK00 (K:1-114)
01b: CATH_2e2jC01 (C:2-42,C:169-268)
02a: CATH_2e2jE01 (E:2-142)
03a: CATH_2e2jB04 (B:221-397)
04a: CATH_2e2jF00 (F:69-154)
05a: CATH_2e2jE02 (E:143-215)
06a: CATH_2e2jJ00 (J:1-65)
07a: CATH_2e2jB07 (B:783-798,B:853-973)
08a: CATH_2e2jH00 (H:2-146)
09a: CATH_2e2jC02 (C:43-168)
10a: CATH_2e2jI01 (I:2-46)
10b: CATH_2e2jI02 (I:47-120)
11a: CATH_2e2jL00 (L:25-70)
View:
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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
2e2jK00
K:1-114
01b
2e2jC01
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)
02a
2e2jE01
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
2e2jB04
B:221-397
Topology
:
Eukaryotic RPB6 RNA polymerase subunit
(77)
Homologous Superfamily
:
[code=3.90.940.10, no name defined]
(71)
[unclassified]
(17)
04a
2e2jF00
F:69-154
Homologous Superfamily
:
[code=3.90.940.20, no name defined]
(58)
[unclassified]
(14)
05a
2e2jE02
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
2e2jJ00
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
2e2jB07
B:783-798,B:853-973
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
[unclassified]
(49)
08a
2e2jH00
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
2e2jC02
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
2e2jI01
I:2-46
10b
2e2jI02
I:47-120
Topology
:
Rubrerythrin, domain 2
(145)
Homologous Superfamily
:
RNA polymerase ii, chain L
(52)
[unclassified]
(14)
11a
2e2jL00
L:25-70
[
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Pfam Domains
(0, 0)
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all PFAM domains
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