PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2VUM
Asym. Unit
Info
Asym.Unit (666 KB)
Biol.Unit 1 (653 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ALPHA-AMANITIN INHIBITED COMPLETE RNA POLYMERASE II ELONGATION COMPLEX
Authors
:
F. Brueckner, P. Cramer
Date
:
27 May 08 (Deposition) - 17 Jun 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,P,T
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,P,T (1x)
Keywords
:
Transferase-Toxin Complex, Alpha Amanitin, Toxin, Inhibitor, Polymerase, Transferase, Dna Binding, Zinc-Finger, Phosphoprotein, Transcription, Ubl Transcription-Toxin Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Brueckner, P. Cramer
Structural Basis Of Transcription Inhibition By Alpha-Amanitin And Implications For Rna Polymerase Ii Translocation.
Nat. Struct. Mol. Biol. V. 15 811 2008
[
close entry info
]
Hetero Components
(7, 14)
Info
All Hetero Components
1a: 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHO... (BRUa)
2a: S-OXY CYSTEINE (CSXa)
3a: 4-HYDROXYPROLINE (HYPa)
4a: 4,5-DIHYDROXYISOLEUCINE (ILXa)
5a: MAGNESIUM ION (MGa)
6a: 6-HYDROXYTRYPTOPHAN (TRXa)
7a: ZINC ION (ZNa)
7b: ZINC ION (ZNb)
7c: ZINC ION (ZNc)
7d: ZINC ION (ZNd)
7e: ZINC ION (ZNe)
7f: ZINC ION (ZNf)
7g: ZINC ION (ZNg)
7h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BRU
1
Mod. Nucleotide
5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2
CSX
1
Mod. Amino Acid
S-OXY CYSTEINE
3
HYP
1
Mod. Amino Acid
4-HYDROXYPROLINE
4
ILX
1
Mod. Amino Acid
4,5-DIHYDROXYISOLEUCINE
5
MG
1
Ligand/Ion
MAGNESIUM ION
6
TRX
1
Mod. Amino Acid
6-HYDROXYTRYPTOPHAN
7
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:107 , MET A:108 , CYS A:110 , CYS A:148 , GLY A:166 , CYS A:167
BINDING SITE FOR RESIDUE ZN A2456
02
AC2
SOFTWARE
CYS A:67 , CYS A:70 , CYS A:77 , HIS A:80
BINDING SITE FOR RESIDUE ZN A2457
03
AC3
SOFTWARE
ASP A:481 , ASP A:483 , ASP A:485 , C P:10
BINDING SITE FOR RESIDUE MG A2458
04
AC4
SOFTWARE
CYS B:1163 , CYS B:1166 , CYS B:1182 , CYS B:1185
BINDING SITE FOR RESIDUE ZN B2225
05
AC5
SOFTWARE
CYS C:86 , CYS C:88 , HIS C:91 , CYS C:92 , CYS C:95
BINDING SITE FOR RESIDUE ZN C1269
06
AC6
SOFTWARE
CYS I:7 , CYS I:10 , CYS I:29 , CYS I:32
BINDING SITE FOR RESIDUE ZN I1121
07
AC7
SOFTWARE
CYS I:75 , CYS I:78 , CYS I:106
BINDING SITE FOR RESIDUE ZN I1122
08
AC8
SOFTWARE
CYS J:7 , CYS J:10 , CYS J:45 , CYS J:46
BINDING SITE FOR RESIDUE ZN J1066
09
AC9
SOFTWARE
CYS L:31 , CYS L:34 , CYS L:48 , CYS L:51
BINDING SITE FOR RESIDUE ZN L1071
10
BC1
SOFTWARE
ASN A:723 , ARG A:726 , ALA A:759 , GLN A:760 , CYS A:764 , VAL A:765 , GLY A:766 , GLN A:767 , GLN A:768 , SER A:769 , GLY A:772 , GLY A:819 , GLY A:820 , GLU A:822 , HIS A:1085 , GLN B:763
BINDING SITE FOR CHAIN M OF ALPHA-AMANITIN
[
close Site info
]
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)
[
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
(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
[
close EXON info
]
SCOP Domains
(6, 9)
Info
All SCOP Domains
1a: SCOP_d2vumj1 (J:1-65)
2a: SCOP_d2vumf1 (F:72-155)
3a: SCOP_d2vumh1 (H:2-146)
4a: SCOP_d2vuma1 (A:2-1455)
4b: SCOP_d2vumd1 (D:4-221)
4c: SCOP_d2vumg1 (G:1-171)
4d: SCOP_d2vumk1 (K:1-114)
5a: SCOP_d2vumb1 (B:20-1224)
6a: SCOP_d2vuml1 (L:25-70)
View:
Select:
Label:
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)
1a
d2vumj1
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)
2a
d2vumf1
F:72-155
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)
3a
d2vumh1
H:2-146
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)
4a
d2vuma1
A:2-1455
4b
d2vumd1
D:4-221
4c
d2vumg1
G:1-171
4d
d2vumk1
K:1-114
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)
5a
d2vumb1
B:20-1224
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)
6a
d2vuml1
L:25-70
[
close SCOP info
]
CATH Domains
(10, 13)
Info
all CATH domains
01a: CATH_2vumG01 (G:1-82)
02a: CATH_2vumK00 (K:1-114)
02b: CATH_2vumC01 (C:3-42,C:169-268)
03a: CATH_2vumE01 (E:2-142)
04a: CATH_2vumF00 (F:72-155)
05a: CATH_2vumE02 (E:143-215)
06a: CATH_2vumJ00 (J:1-65)
07a: CATH_2vumG02 (G:83-171)
07b: CATH_2vumH00 (H:2-146)
08a: CATH_2vumC02 (C:43-168)
09a: CATH_2vumI01 (I:2-46)
09b: CATH_2vumI02 (I:47-120)
10a: CATH_2vumL00 (L:25-70)
View:
Select:
Label:
Classes
(
)
(
)
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)
Bakers' yeast (Saccharomyces cerevisiae)
(5)
01a
2vumG01
G:1-82
Topology
:
Gyrase A; domain 2
(166)
Homologous Superfamily
:
[code=3.30.1360.10, no name defined]
(72)
Bakers' yeast (Saccharomyces cerevisiae)
(5)
02a
2vumK00
K:1-114
02b
2vumC01
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)
Bakers' yeast (Saccharomyces cerevisiae)
(5)
03a
2vumE01
E:2-142
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Eukaryotic RPB6 RNA polymerase subunit
(77)
Homologous Superfamily
:
[code=3.90.940.10, no name defined]
(71)
Bakers' yeast (Saccharomyces cerevisiae)
(5)
04a
2vumF00
F:72-155
Homologous Superfamily
:
[code=3.90.940.20, no name defined]
(58)
Bakers' yeast (Saccharomyces cerevisiae)
(5)
05a
2vumE02
E:143-215
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
Homeodomain-like
(288)
Bakers' yeast (Saccharomyces cerevisiae)
(5)
06a
2vumJ00
J:1-65
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
Bakers' yeast (Saccharomyces cerevisiae)
(5)
07a
2vumG02
G:83-171
07b
2vumH00
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)
Bakers' yeast (Saccharomyces cerevisiae)
(5)
08a
2vumC02
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)
Bakers' yeast (Saccharomyces cerevisiae)
(5)
09a
2vumI01
I:2-46
09b
2vumI02
I:47-120
Topology
:
Rubrerythrin, domain 2
(145)
Homologous Superfamily
:
RNA polymerase ii, chain L
(52)
Bakers' yeast (Saccharomyces cerevisiae)
(5)
10a
2vumL00
L:25-70
[
close CATH info
]
Pfam Domains
(28, 28)
Info
all PFAM domains
01a: PFAM_RNA_pol_Rpb4_2vumD01 (D:49-218)
02a: PFAM_RNA_pol_Rpb2_6_2vumB01 (B:750-1124)
03a: PFAM_RNA_pol_Rpb8_2vumH01 (H:7-146)
04a: PFAM_S1_2vumG01 (G:80-161)
05a: PFAM_RNA_pol_L_2vumC01 (C:18-256)
06a: PFAM_RNA_pol_L_2_2vumK01 (K:29-105)
07a: PFAM_SHS2_Rpb7_N_2vumG02 (G:8-79)
08a: PFAM_DNA_RNApol_7kD_2vumL01 (L:29-60)
09a: PFAM_RNA_POL_M_15KD_2vumI01 (I:4-41)
10a: PFAM_TFIIS_C_2vumI02 (I:73-111)
11a: PFAM_RNA_pol_A_bac_2vumC02 (C:49-171)
12a: PFAM_RNA_pol_N_2vumJ01 (J:1-61)
13a: PFAM_RNA_pol_Rpb1_1_2vumA01 (A:11-340)
14a: PFAM_RNA_pol_Rpb1_2_2vumA02 (A:342-507)
15a: PFAM_RNA_pol_Rpb1_3_2vumA03 (A:510-669)
16a: PFAM_RNA_pol_Rpb1_4_2vumA04 (A:693-800)
17a: PFAM_RNA_pol_Rpb1_5_2vumA05 (A:807-1398)
18a: PFAM_RNA_pol_Rpb1_6_2vumA06 (A:873-1056)
19a: PFAM_RNA_pol_Rpb1_7_2vumA07 (A:1141-1274)
20a: PFAM_RNA_pol_Rpb2_1_2vumB02 (B:42-464)
21a: PFAM_RNA_pol_Rpb2_2_2vumB03 (B:219-407)
22a: PFAM_RNA_pol_Rpb2_3_2vumB04 (B:481-546)
23a: PFAM_RNA_pol_Rpb2_4_2vumB05 (B:580-642)
24a: PFAM_RNA_pol_Rpb2_5_2vumB06 (B:681-745)
25a: PFAM_RNA_pol_Rpb2_7_2vumB07 (B:1126-1219)
26a: PFAM_RNA_pol_Rpb5_C_2vumE01 (E:142-215)
27a: PFAM_RNA_pol_Rpb5_N_2vumE02 (E:2-101)
28a: PFAM_RNA_pol_Rpb6_2vumF01 (F:78-134)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HRDC-like
(19)
Family
:
RNA_pol_Rpb4
(11)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(9)
01a
RNA_pol_Rpb4-2vumD01
D:49-218
Clan
:
LEF-8-like
(36)
Family
:
RNA_pol_Rpb2_6
(36)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
02a
RNA_pol_Rpb2_6-2vumB01
B:750-1124
Clan
:
OB
(224)
Family
:
RNA_pol_Rpb8
(26)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
03a
RNA_pol_Rpb8-2vumH01
H:7-146
Family
:
S1
(23)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(10)
04a
S1-2vumG01
G:80-161
Clan
:
RBP11-like
(36)
Family
:
RNA_pol_L
(36)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
05a
RNA_pol_L-2vumC01
C:18-256
Family
:
RNA_pol_L_2
(27)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
06a
RNA_pol_L_2-2vumK01
K:29-105
Clan
:
SHS2
(26)
Family
:
SHS2_Rpb7-N
(12)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(10)
07a
SHS2_Rpb7-N-2vumG02
G:8-79
Clan
:
Zn_Beta_Ribbon
(109)
Family
:
DNA_RNApol_7kD
(28)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
08a
DNA_RNApol_7kD-2vumL01
L:29-60
Family
:
RNA_POL_M_15KD
(26)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(26)
09a
RNA_POL_M_15KD-2vumI01
I:4-41
Family
:
TFIIS_C
(26)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(25)
10a
TFIIS_C-2vumI02
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)
11a
RNA_pol_A_bac-2vumC02
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)
12a
RNA_pol_N-2vumJ01
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)
13a
RNA_pol_Rpb1_1-2vumA01
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)
14a
RNA_pol_Rpb1_2-2vumA02
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)
15a
RNA_pol_Rpb1_3-2vumA03
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)
16a
RNA_pol_Rpb1_4-2vumA04
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)
17a
RNA_pol_Rpb1_5-2vumA05
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)
18a
RNA_pol_Rpb1_6-2vumA06
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)
19a
RNA_pol_Rpb1_7-2vumA07
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)
20a
RNA_pol_Rpb2_1-2vumB02
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)
21a
RNA_pol_Rpb2_2-2vumB03
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)
22a
RNA_pol_Rpb2_3-2vumB04
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)
23a
RNA_pol_Rpb2_4-2vumB05
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)
24a
RNA_pol_Rpb2_5-2vumB06
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)
25a
RNA_pol_Rpb2_7-2vumB07
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)
26a
RNA_pol_Rpb5_C-2vumE01
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)
27a
RNA_pol_Rpb5_N-2vumE02
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)
28a
RNA_pol_Rpb6-2vumF01
F:78-134
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Chain N
Chain P
Chain T
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (666 KB)
Header - Asym.Unit
Biol.Unit 1 (653 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2VUM
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
