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3K0J
Asym. Unit
Info
Asym.Unit (136 KB)
Biol.Unit 1 (68 KB)
Biol.Unit 2 (66 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE E. COLI THIM RIBOSWITCH IN COMPLEX WITH THIAMINE PYROPHOSPHATE AND THE U1A CRYSTALLIZATION MODULE
Authors
:
N. Kulshina, T. E. Edwards, A. R. Ferre-D'Amare
Date
:
24 Sep 09 (Deposition) - 22 Dec 09 (Release) - 12 Jan 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,C,E (1x)
Biol. Unit 2: B,D,F (1x)
Keywords
:
Riboswitch, Rna, Thi-Box, Thim, U1A Protein, Acetylation, Mrna Processing, Mrna Splicing, Nucleus, Phosphoprotein, Ribonucleoprotein, Rna-Binding, Spliceosome, Rna/Rna Binding Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Kulshina, T. E. Edwards, A. R. Ferre-D'Amare
Thermodynamic Analysis Of Ligand Binding And Ligand Binding-Induced Tertiary Structure Formation By The Thiamine Pyrophosphate Riboswitch.
Rna V. 16 186 2010
(for further references see the
PDB file header
)
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Hetero Components
(2, 10)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
1g: MAGNESIUM ION (MGg)
1h: MAGNESIUM ION (MGh)
2a: THIAMINE DIPHOSPHATE (TPPa)
2b: THIAMINE DIPHOSPHATE (TPPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
8
Ligand/Ion
MAGNESIUM ION
2
TPP
2
Ligand/Ion
THIAMINE DIPHOSPHATE
[
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]
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
G E:14 , U E:15 , G E:40 , G E:42 , A E:43 , C E:57 , G E:72 , G E:76 , C E:77 , G E:78 , MG E:701 , MG E:702
BINDING SITE FOR RESIDUE TPP E 601
02
AC2
SOFTWARE
G F:114 , G F:140 , G F:142 , A F:143 , C F:157 , C F:158 , G F:172 , A F:175 , G F:176 , C F:177 , MG F:703 , MG F:708
BINDING SITE FOR RESIDUE TPP F 602
03
AC3
SOFTWARE
TPP E:601
BINDING SITE FOR RESIDUE MG E 701
04
AC4
SOFTWARE
G E:60 , G E:78 , TPP E:601
BINDING SITE FOR RESIDUE MG E 702
05
AC5
SOFTWARE
U F:159 , G F:160 , G F:178 , TPP F:602 , MG F:708
BINDING SITE FOR RESIDUE MG F 703
06
AC6
SOFTWARE
C E:74
BINDING SITE FOR RESIDUE MG E 704
07
AC7
SOFTWARE
G E:36
BINDING SITE FOR RESIDUE MG E 705
08
AC8
SOFTWARE
A E:80 , G E:81
BINDING SITE FOR RESIDUE MG E 706
09
AC9
SOFTWARE
U E:64 , G E:65 , G E:66
BINDING SITE FOR RESIDUE MG E 707
10
BC1
SOFTWARE
G F:178 , TPP F:602 , MG F:703
BINDING SITE FOR RESIDUE MG F 708
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: RRM (A:210-289,B:310-389,C:410-489,D:51...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RRM
PS50102
Eukaryotic RNA Recognition Motif (RRM) profile.
SNRPA_HUMAN
10-89
208-282
4
A:210-289
B:310-389
C:410-489
D:510-589
-
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Exons
(3, 12)
Info
All Exons
Exon 1.1 (A:206-225 | B:306-325 | C:404-425 ...)
Exon 1.2 (A:225-282 | B:325-382 | C:425-482 ...)
Exon 1.3 (A:283-297 | B:383-397 | C:483-489 ...)
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
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
ENST00000243563
1
ENSE00001052136
chr19:
41256779-41257386
608
SNRPA_HUMAN
1-25
25
4
A:206-225
B:306-325
C:404-425
D:506-525
20
20
22
20
1.2
ENST00000243563
2
ENSE00000707951
chr19:
41263237-41263409
173
SNRPA_HUMAN
25-82
58
4
A:225-282
B:325-382
C:425-482
D:525-582 (gaps)
58
58
58
58
1.3
ENST00000243563
3
ENSE00000707956
chr19:
41265336-41265515
180
SNRPA_HUMAN
83-142
60
4
A:283-297
B:383-397
C:483-489
D:583-589
15
15
7
7
1.4
ENST00000243563
4
ENSE00000707961
chr19:
41268806-41268979
174
SNRPA_HUMAN
143-200
58
0
-
-
1.5
ENST00000243563
5
ENSE00000842333
chr19:
41269492-41269580
89
SNRPA_HUMAN
201-230
30
0
-
-
1.6
ENST00000243563
6
ENSE00000842334
chr19:
41270913-41271290
378
SNRPA_HUMAN
230-282
53
0
-
-
[
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SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3k0ja_ (A:)
1b: SCOP_d3k0jb_ (B:)
1c: SCOP_d3k0jc_ (C:)
1d: SCOP_d3k0jd_ (D:)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
RNA-binding domain, RBD
(289)
Family
:
Canonical RBD
(214)
Protein domain
:
automated matches
(24)
Human (Homo sapiens) [TaxId: 9606]
(21)
1a
d3k0ja_
A:
1b
d3k0jb_
B:
1c
d3k0jc_
C:
1d
d3k0jd_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3k0jC00 (C:404-489)
1b: CATH_3k0jA00 (A:206-297)
1c: CATH_3k0jB00 (B:306-397)
1d: CATH_3k0jD00 (D:506-589)
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.330, no name defined]
(307)
Human (Homo sapiens)
(81)
1a
3k0jC00
C:404-489
1b
3k0jA00
A:206-297
1c
3k0jB00
B:306-397
1d
3k0jD00
D:506-589
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_RRM_1_3k0jD01 (D:512-583)
1b: PFAM_RRM_1_3k0jD02 (D:512-583)
1c: PFAM_RRM_1_3k0jD03 (D:512-583)
1d: PFAM_RRM_1_3k0jD04 (D:512-583)
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)
Clan
:
RRM
(206)
Family
:
RRM_1
(131)
Homo sapiens (Human)
(94)
1a
RRM_1-3k0jD01
D:512-583
1b
RRM_1-3k0jD02
D:512-583
1c
RRM_1-3k0jD03
D:512-583
1d
RRM_1-3k0jD04
D:512-583
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Asymmetric Unit 1
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