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1Y1W
Asym. Unit
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Asym.Unit (668 KB)
Biol.Unit 1 (648 KB)
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(1)
Title
:
COMPLETE RNA POLYMERASE II ELONGATION COMPLEX
Authors
:
P. Cramer, H. Kettenberger, K. -J. Armache
Date
:
19 Nov 04 (Deposition) - 04 Jan 05 (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,N,P,T
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,N,P,T (1x)
Keywords
:
Rna Polymerase Ii, Transcription Bubble, Transcription, Elongation Complex, Transcription, Transferase/Dna-Rna Hybrid Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Kettenberger, K. -J. Armache, P. Cramer
Complete Rna Polymerase Ii Elongation Complex Structure And Its Interactions With Ntp And Tfiis
Mol. Cell V. 16 955 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
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 , 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 , CYS B:1185
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 , CYS I:10 , CYS I:29 , CYS I:32
BINDING SITE FOR RESIDUE ZN I 203
6
AC6
SOFTWARE
CYS I:75 , CYS I:78 , CYS I:103 , CYS I:106
BINDING SITE FOR RESIDUE ZN I 204
7
AC7
SOFTWARE
CYS J:7 , 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 , C P:10
BINDING SITE FOR RESIDUE MG A 1736
[
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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
[
close PROSITE info
]
Exons
(9, 9)
Info
All Exons
Exon 1.1 (E:2-215)
Exon 2.1 (A:2-1455 (gaps))
Exon 3.1 (G:1-171)
Exon 4.1 (L:25-70)
Exon 5.1 (C:3-268)
Exon 6.1 (D:4-221 (gaps))
Exon 7.1 (B:20-1224 (gaps))
Exon 8.1 (J:1-65)
Exon 9.2 (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
14: Boundary 7.1/-
15: Boundary -/8.1
16: Boundary 8.1/-
17: Boundary 9.1/9.2
18: Boundary 9.2/-
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:2-1455 (gaps)
1454
3.1
YDR404C
1
YDR404C.1
IV:1277162-1276647
516
RPB7_YEAST
1-171
171
1
G:1-171
171
4.1
YHR143W-A
1
YHR143W-A.1
VIII:387236-387448
213
RPAB4_YEAST
1-70
70
1
L:25-70
46
5.1
YIL021W
1
YIL021W.1
IX:312903-313859
957
RPB3_YEAST
1-318
318
1
C:3-268
266
6.1
YJL140W
1
YJL140W.1
X:150957-151622
666
RPB4_YEAST
1-221
221
1
D:4-221 (gaps)
218
7.1
YOR151C
1
YOR151C.1
XV:616672-612998
3675
RPB2_YEAST
1-1224
1224
1
B:20-1224 (gaps)
1205
8.1
YOR210W
1
YOR210W.1
XV:738321-738533
213
RPAB5_YEAST
1-70
70
1
J:1-65
65
9.1
YPR187W
1
YPR187W.1
XVI:911253-911272
20
RPAB2_YEAST
1-7
7
0
-
-
9.2
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, 12)
Info
All SCOP Domains
1a: SCOP_d1y1wa_ (A:)
1b: SCOP_d1y1wb_ (B:)
1c: SCOP_d1y1wc_ (C:)
1d: SCOP_d1y1wd_ (D:)
1e: SCOP_d1y1we_ (E:)
1f: SCOP_d1y1wf_ (F:)
1g: SCOP_d1y1wg_ (G:)
1h: SCOP_d1y1wh_ (H:)
1i: SCOP_d1y1wi_ (I:)
1j: SCOP_d1y1wj_ (J:)
1k: SCOP_d1y1wk_ (K:)
1l: SCOP_d1y1wl_ (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
d1y1wa_
A:
1b
d1y1wb_
B:
1c
d1y1wc_
C:
1d
d1y1wd_
D:
1e
d1y1we_
E:
1f
d1y1wf_
F:
1g
d1y1wg_
G:
1h
d1y1wh_
H:
1i
d1y1wi_
I:
1j
d1y1wj_
J:
1k
d1y1wk_
K:
1l
d1y1wl_
L:
[
close SCOP info
]
CATH Domains
(12, 15)
Info
all CATH domains
01a: CATH_1y1wG01 (G:1-83)
02a: CATH_1y1wK00 (K:1-114)
02b: CATH_1y1wC01 (C:3-42,C:169-268)
03a: CATH_1y1wE01 (E:2-142)
04a: CATH_1y1wB04 (B:221-397)
05a: CATH_1y1wF00 (F:72-155)
06a: CATH_1y1wE02 (E:143-215)
07a: CATH_1y1wJ00 (J:1-65)
08a: CATH_1y1wB07 (B:783-798,B:853-973)
09a: CATH_1y1wG02 (G:84-171)
09b: CATH_1y1wH00 (H:2-146)
10a: CATH_1y1wC02 (C:43-168)
11a: CATH_1y1wI01 (I:2-46)
11b: CATH_1y1wI02 (I:47-120)
12a: CATH_1y1wL00 (L:25-70)
View:
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Classes
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)
(
)
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
1y1wG01
G:1-83
Topology
:
Gyrase A; domain 2
(166)
Homologous Superfamily
:
[code=3.30.1360.10, no name defined]
(72)
[unclassified]
(17)
02a
1y1wK00
K:1-114
02b
1y1wC01
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)
03a
1y1wE01
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
1y1wB04
B:221-397
Topology
:
Eukaryotic RPB6 RNA polymerase subunit
(77)
Homologous Superfamily
:
[code=3.90.940.10, no name defined]
(71)
[unclassified]
(17)
05a
1y1wF00
F:72-155
Homologous Superfamily
:
[code=3.90.940.20, no name defined]
(58)
[unclassified]
(14)
06a
1y1wE02
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
1y1wJ00
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
1y1wB07
B:783-798,B:853-973
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
[unclassified]
(49)
09a
1y1wG02
G:84-171
09b
1y1wH00
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
1y1wC02
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
1y1wI01
I:2-46
11b
1y1wI02
I:47-120
Topology
:
Rubrerythrin, domain 2
(145)
Homologous Superfamily
:
RNA polymerase ii, chain L
(52)
[unclassified]
(14)
12a
1y1wL00
L:25-70
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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