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1SFO
Asym. Unit
Info
Asym.Unit (538 KB)
Biol.Unit 1 (517 KB)
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(1)
Title
:
RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX
Authors
:
K. D. Westover, D. A. Bushnell, R. D. Kornberg
Date
:
20 Feb 04 (Deposition) - 02 Mar 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.61
Chains
:
Asym. Unit : A,B,C,E,F,H,I,J,K,L,R,T
Biol. Unit 1: A,B,C,E,F,H,I,J,K,L,R,T (1x)
Keywords
:
Transcription, Mrna, Multiprotein Complex, Molecular Machine, Dna, 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: Separation Of Rna From Dna By Rna Polymerase Ii
Science V. 303 1014 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 9)
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:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
1
Ligand/Ion
MAGNESIUM ION
2
ZN
8
Ligand/Ion
ZINC ION
[
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]
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
CYS A:107 , MET A:108 , CYS A:110 , CYS A:148 , CYS A:167
BINDING SITE FOR RESIDUE ZN A 1734
2
AC2
SOFTWARE
CYS A:67 , GLN A:68 , CYS A:70 , CYS A:77 , HIS A:80
BINDING SITE FOR RESIDUE ZN A 1735
3
AC3
SOFTWARE
CYS B:1163 , CYS B:1166 , CYS B:1182
BINDING SITE FOR RESIDUE ZN B 1307
4
AC4
SOFTWARE
CYS C:86 , CYS C:88 , HIS C:91 , CYS C:92 , CYS C:95
BINDING SITE FOR RESIDUE ZN C 319
5
AC5
SOFTWARE
CYS I:7 , ARG I:8 , ASP I:9 , CYS I:10 , ASN I:11 , CYS I:29
BINDING SITE FOR RESIDUE ZN I 203
6
AC6
SOFTWARE
CYS I:75 , CYS I:78 , HIS I:79 , SER I:80 , CYS I:103
BINDING SITE FOR RESIDUE ZN I 204
7
AC7
SOFTWARE
CYS J:7 , SER J:9 , CYS J:10 , CYS J:45 , CYS J:46
BINDING SITE FOR RESIDUE ZN J 101
8
AC8
SOFTWARE
CYS L:31 , CYS L:34 , CYS L:48 , CYS L:51
BINDING SITE FOR RESIDUE ZN L 105
9
AC9
SOFTWARE
ASP A:481 , ASP A:483 , ASP A:485 , A R:10
BINDING SITE FOR RESIDUE MG A 2000
[
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]
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)
[
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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
(7, 7)
Info
All Exons
Exon 1.1 (E:2-215)
Exon 2.1 (A:3-1445 (gaps))
Exon 3.1 (L:25-70)
Exon 4.1 (C:3-268)
Exon 5.1 (B:20-1224 (gaps))
Exon 6.1 (J:1-65)
Exon 7.2 (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 7.1/7.2
14: Boundary 7.2/-
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:3-1445 (gaps)
1443
3.1
YHR143W-A
1
YHR143W-A.1
VIII:387236-387448
213
RPAB4_YEAST
1-70
70
1
L:25-70
46
4.1
YIL021W
1
YIL021W.1
IX:312903-313859
957
RPB3_YEAST
1-318
318
1
C:3-268
266
5.1
YOR151C
1
YOR151C.1
XV:616672-612998
3675
RPB2_YEAST
1-1224
1224
1
B:20-1224 (gaps)
1205
6.1
YOR210W
1
YOR210W.1
XV:738321-738533
213
RPAB5_YEAST
1-70
70
1
J:1-65
65
7.1
YPR187W
1
YPR187W.1
XVI:911253-911272
20
RPAB2_YEAST
1-7
7
0
-
-
7.2
YPR187W
2
YPR187W.2
XVI:911349-911796
448
RPAB2_YEAST
7-155
149
1
F:72-155
84
[
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]
SCOP Domains
(1, 10)
Info
All SCOP Domains
1a: SCOP_d1sfoa_ (A:)
1b: SCOP_d1sfob_ (B:)
1c: SCOP_d1sfoc_ (C:)
1d: SCOP_d1sfoe_ (E:)
1e: SCOP_d1sfof_ (F:)
1f: SCOP_d1sfoh_ (H:)
1g: SCOP_d1sfoi_ (I:)
1h: SCOP_d1sfoj_ (J:)
1i: SCOP_d1sfok_ (K:)
1j: SCOP_d1sfol_ (L:)
View:
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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
d1sfoa_
A:
1b
d1sfob_
B:
1c
d1sfoc_
C:
1d
d1sfoe_
E:
1e
d1sfof_
F:
1f
d1sfoh_
H:
1g
d1sfoi_
I:
1h
d1sfoj_
J:
1i
d1sfok_
K:
1j
d1sfol_
L:
[
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CATH Domains
(11, 13)
Info
all CATH domains
01a: CATH_1sfoK00 (K:1-114)
01b: CATH_1sfoC02 (C:3-42,C:169-268)
02a: CATH_1sfoE01 (E:5-142)
03a: CATH_1sfoB04 (B:221-397)
04a: CATH_1sfoF00 (F:72-155)
05a: CATH_1sfoE02 (E:143-215)
06a: CATH_1sfoJ00 (J:1-65)
07a: CATH_1sfoB07 (B:783-798,B:853-973)
08a: CATH_1sfoH00 (H:2-146)
09a: CATH_1sfoC01 (C:43-168)
10a: CATH_1sfoI02 (I:2-46)
10b: CATH_1sfoI01 (I:47-120)
11a: CATH_1sfoL00 (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
1sfoK00
K:1-114
01b
1sfoC02
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
1sfoE01
E:5-142
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
1sfoB04
B:221-397
Topology
:
Eukaryotic RPB6 RNA polymerase subunit
(77)
Homologous Superfamily
:
[code=3.90.940.10, no name defined]
(71)
[unclassified]
(17)
04a
1sfoF00
F:72-155
Homologous Superfamily
:
[code=3.90.940.20, no name defined]
(58)
[unclassified]
(14)
05a
1sfoE02
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
1sfoJ00
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
1sfoB07
B:783-798,B:853-973
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
[unclassified]
(49)
08a
1sfoH00
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
1sfoC01
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
1sfoI02
I:2-46
10b
1sfoI01
I:47-120
Topology
:
Rubrerythrin, domain 2
(145)
Homologous Superfamily
:
RNA polymerase ii, chain L
(52)
[unclassified]
(14)
11a
1sfoL00
L:25-70
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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Chain F
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Chain J
Chain K
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Chain R
Chain T
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