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2OJ3
Asym. Unit
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Asym.Unit (55 KB)
Biol.Unit 1 (49 KB)
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(1)
Title
:
HEPATITIS DELTA VIRUS RIBOZYME PRECURSOR STRUCTURE, WITH C75U MUTATION, BOUND TO TL+ AND COBALT HEXAMMINE (CO(NH3) 63+)
Authors
:
A. Ke, F. Ding, J. D. Batchelor, J. A. Doudna
Date
:
12 Jan 07 (Deposition) - 27 Mar 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Tl+ And Cobalt Hexammine Compete For Binding Sites. , Structural Protein/Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
A. Ke, F. Ding, J. D. Batchelor, J. A. Doudna
Structural Roles Of Monovalent Cations In The Hdv Ribozyme.
Structure V. 15 281 2007
(for further references see the
PDB file header
)
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Hetero Components
(2, 11)
Info
All Hetero Components
1a: COBALT HEXAMMINE(III) (NCOa)
1b: COBALT HEXAMMINE(III) (NCOb)
2a: THALLIUM (I) ION (TLa)
2b: THALLIUM (I) ION (TLb)
2c: THALLIUM (I) ION (TLc)
2d: THALLIUM (I) ION (TLd)
2e: THALLIUM (I) ION (TLe)
2f: THALLIUM (I) ION (TLf)
2g: THALLIUM (I) ION (TLg)
2h: THALLIUM (I) ION (TLh)
2i: THALLIUM (I) ION (TLi)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NCO
2
Ligand/Ion
COBALT HEXAMMINE(III)
2
TL
9
Ligand/Ion
THALLIUM (I) ION
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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:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
G B:101 , U B:120 , C B:122 , U B:123 , C B:124 , G B:125 , U B:163
BINDING SITE FOR RESIDUE NCO B 301
02
AC2
SOFTWARE
ARG A:47 , ARG A:52 , C B:141 , G B:158 , G B:159
BINDING SITE FOR RESIDUE NCO B 302
03
AC3
SOFTWARE
G B:110 , C B:157
BINDING SITE FOR RESIDUE TL B 202
04
AC4
SOFTWARE
G B:169
BINDING SITE FOR RESIDUE TL B 204
05
AC5
SOFTWARE
U B:100 , G B:101 , G B:102 , U B:163
BINDING SITE FOR RESIDUE TL B 207
06
AC6
SOFTWARE
G B:134
BINDING SITE FOR RESIDUE TL B 209
07
AC7
SOFTWARE
G B:110 , TL B:212
BINDING SITE FOR RESIDUE TL B 210
08
AC8
SOFTWARE
G B:125 , G B:128
BINDING SITE FOR RESIDUE TL B 211
09
AC9
SOFTWARE
G B:111 , TL B:210
BINDING SITE FOR RESIDUE TL B 212
10
BC1
SOFTWARE
G B:105
BINDING SITE FOR RESIDUE TL B 213
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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, 1)
Info
All PROSITE Patterns/Profiles
1: RRM (A:10-89|-)
;
View:
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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
1
A:10-89
-
[
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Exons
(3, 3)
Info
All Exons
Exon 1.1 (A:4-25)
Exon 1.2 (A:25-82)
Exon 1.3 (A:83-98)
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
1
A:4-25
22
1.2
ENST00000243563
2
ENSE00000707951
chr19:
41263237-41263409
173
SNRPA_HUMAN
25-82
58
1
A:25-82
58
1.3
ENST00000243563
3
ENSE00000707956
chr19:
41265336-41265515
180
SNRPA_HUMAN
83-142
60
1
A:83-98
16
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, 1)
Info
All SCOP Domains
1a: SCOP_d2oj3a_ (A:)
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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
:
Splicesomal U1A protein
(46)
Human (Homo sapiens) [TaxId: 9606]
(43)
1a
d2oj3a_
A:
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2oj3A00 (A:4-98)
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)
Organisms
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)
(
)
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)
[unclassified]
(45)
1a
2oj3A00
A:4-98
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_RRM_1_2oj3A01 (A:12-83)
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Clans
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)
Clan
:
RRM
(206)
Family
:
RRM_1
(131)
Homo sapiens (Human)
(94)
1a
RRM_1-2oj3A01
A:12-83
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