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3S14
Asym. Unit
Info
Asym.Unit (1.2 MB)
Biol.Unit 1, α-C (1.2 MB)
Biol.Unit 1 (1.2 MB)
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(1)
Title
:
RNA POLYMERASE II INITIATION COMPLEX WITH A 6-NT RNA
Authors
:
X. Liu, D. A. Bushnell, D. A. Silva, X. Huang, R. D. Kornberg
Date
:
14 May 11 (Deposition) - 10 Aug 11 (Release) - 10 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.85
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
:
Rna Polymerase Ii, Initiation Complex, Transcription-Rna-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Liu, D. A. Bushnell, D. A. Silva, X. Huang, R. D. Kornberg
Initiation Complex Structure And Promoter Proofreading.
Science V. 333 633 2011
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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 , 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
ASP A:481 , ASP A:483 , ASP A:485 , G R:10
BINDING SITE FOR RESIDUE MG A 2001
4
AC4
SOFTWARE
CYS B:1163 , CYS B:1166 , CYS B:1182 , CYS B:1185
BINDING SITE FOR RESIDUE ZN B 1307
5
AC5
SOFTWARE
CYS C:86 , CYS C:88 , CYS C:92 , CYS C:95
BINDING SITE FOR RESIDUE ZN C 319
6
AC6
SOFTWARE
CYS I:7 , CYS I:10 , CYS I:29 , CYS I:32
BINDING SITE FOR RESIDUE ZN I 203
7
AC7
SOFTWARE
CYS I:75 , CYS I:78 , CYS I:103 , CYS I:106
BINDING SITE FOR RESIDUE ZN I 204
8
AC8
SOFTWARE
CYS J:7 , CYS J:10 , CYS J:45 , CYS J:46
BINDING SITE FOR RESIDUE ZN J 101
9
AC9
SOFTWARE
CYS L:31 , CYS L:34 , CYS L:48 , CYS L:51
BINDING SITE FOR RESIDUE ZN L 105
[
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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:71-155)
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:71-155
85
[
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]
SCOP Domains
(12, 13)
Info
All SCOP Domains
01a: SCOP_d3s14j_ (J:)
02a: SCOP_d3s14f_ (F:)
03a: SCOP_d3s14h_ (H:)
04a: SCOP_d3s14k_ (K:)
05a: SCOP_d3s14c1 (C:3-41,C:173-268)
06a: SCOP_d3s14c2 (C:42-172)
07a: SCOP_d3s14e2 (E:144-215)
08a: SCOP_d3s14e1 (E:2-143)
09a: SCOP_d3s14b_ (B:)
10a: SCOP_d3s14a_ (A:)
11a: SCOP_d3s14l_ (L:)
12a: SCOP_d3s14i1 (I:2-49)
12b: SCOP_d3s14i2 (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: 559292]
(1)
01a
d3s14j_
J:
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: 559292]
(1)
02a
d3s14f_
F:
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: 559292]
(2)
03a
d3s14h_
H:
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: 559292]
(1)
04a
d3s14k_
K:
Family
:
RNA polymerase alpha subunit dimerisation domain
(43)
Protein domain
:
RPB3
(25)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 559292]
(1)
05a
d3s14c1
C:3-41,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: 559292]
(1)
06a
d3s14c2
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: 559292]
(1)
07a
d3s14e2
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: 559292]
(1)
08a
d3s14e1
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: 559292]
(1)
09a
d3s14b_
B:
Family
:
RNA-polymerase beta-prime
(49)
Protein domain
:
RBP1
(25)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 559292]
(1)
10a
d3s14a_
A:
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: 559292]
(1)
11a
d3s14l_
L:
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: 559292]
(1)
12a
d3s14i1
I:2-49
12b
d3s14i2
I:50-120
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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