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3HHN
Asym. Unit
Info
Asym.Unit (163 KB)
Biol.Unit 1 (154 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CLASS I LIGASE RIBOZYME SELF-LIGATION PRODUCT, IN COMPLEX WITH U1A RBD
Authors
:
D. M. Shechner, R. A. Grant, S. C. Bagby, D. P. Bartel
Date
:
15 May 09 (Deposition) - 24 Nov 09 (Release) - 12 Jan 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.99
Chains
:
Asym. Unit : B,C,D,E
Biol. Unit 1: B,C,D,E (1x)
Keywords
:
Ligase Ribozyme, Ribozyme, Catalytic Rna, Protein-Rna Complex, Ribonucleoprotein, Rna-Binding, Ligase/Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. M. Shechner, R. A. Grant, S. C. Bagby, Y. Koldobskaya, J. A. Piccirilli, D. P. Bartel
Crystal Structure Of The Catalytic Core Of An Rna-Polymerase Ribozyme.
Science V. 326 1271 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 36)
Info
All Hetero Components
1a: ADENOSINE-5'-PHOSPHATE-2',3'-CYCLI... (A23a)
1b: ADENOSINE-5'-PHOSPHATE-2',3'-CYCLI... (A23b)
2a: MAGNESIUM ION (MGa)
2aa: MAGNESIUM ION (MGaa)
2ab: MAGNESIUM ION (MGab)
2ac: MAGNESIUM ION (MGac)
2ad: MAGNESIUM ION (MGad)
2ae: MAGNESIUM ION (MGae)
2af: MAGNESIUM ION (MGaf)
2ag: MAGNESIUM ION (MGag)
2ah: MAGNESIUM ION (MGah)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
2i: MAGNESIUM ION (MGi)
2j: MAGNESIUM ION (MGj)
2k: MAGNESIUM ION (MGk)
2l: MAGNESIUM ION (MGl)
2m: MAGNESIUM ION (MGm)
2n: MAGNESIUM ION (MGn)
2o: MAGNESIUM ION (MGo)
2p: MAGNESIUM ION (MGp)
2q: MAGNESIUM ION (MGq)
2r: MAGNESIUM ION (MGr)
2s: MAGNESIUM ION (MGs)
2t: MAGNESIUM ION (MGt)
2u: MAGNESIUM ION (MGu)
2v: MAGNESIUM ION (MGv)
2w: MAGNESIUM ION (MGw)
2x: MAGNESIUM ION (MGx)
2y: MAGNESIUM ION (MGy)
2z: MAGNESIUM ION (MGz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
A23
2
Mod. Nucleotide
ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2
MG
34
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(34, 34)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH B:183 , HOH B:185 , HOH B:186 , HOH B:187 , HOH B:188 , HOH B:189
BINDING SITE FOR RESIDUE MG B 184
02
AC2
SOFTWARE
A C:31 , A C:32 , HOH C:1027 , HOH C:1028 , HOH C:1029 , HOH C:1030
BINDING SITE FOR RESIDUE MG C 1019
03
AC3
SOFTWARE
HOH C:1031 , HOH C:1032 , HOH C:1033 , HOH C:1034 , HOH C:1035 , HOH C:1036
BINDING SITE FOR RESIDUE MG C 1020
04
AC4
SOFTWARE
C C:70 , G C:72 , U C:106 , HOH C:1037 , HOH C:1038 , HOH C:1039 , HOH C:1040
BINDING SITE FOR RESIDUE MG C 1021
05
AC5
SOFTWARE
G C:77 , HOH C:1041 , HOH C:1042 , HOH C:1043 , HOH C:1044 , HOH C:1045
BINDING SITE FOR RESIDUE MG C 1022
06
AC6
SOFTWARE
A C:4 , A C:115 , HOH C:1046 , HOH C:1047 , HOH C:1048 , HOH C:1049 , HOH C:1050
BINDING SITE FOR RESIDUE MG C 1023
07
AC7
SOFTWARE
HOH C:59 , HOH C:61 , HOH C:62 , HOH C:63 , HOH C:64 , HOH C:65
BINDING SITE FOR RESIDUE MG C 60
08
AC8
SOFTWARE
HOH C:1051 , HOH C:1052 , HOH C:1053 , HOH C:1054 , HOH C:1055 , HOH C:1056
BINDING SITE FOR RESIDUE MG C 1024
09
AC9
SOFTWARE
HOH C:1057 , HOH C:1058 , HOH C:1059 , HOH C:1060 , HOH C:1061 , HOH C:1062
BINDING SITE FOR RESIDUE MG C 1025
10
BC1
SOFTWARE
HOH C:1063 , HOH C:1064 , HOH C:1065 , HOH C:1066 , HOH C:1067 , HOH C:1068
BINDING SITE FOR RESIDUE MG C 1026
11
BC2
SOFTWARE
HOH C:122 , HOH C:124 , HOH C:125 , HOH C:126 , HOH C:127 , HOH C:128
BINDING SITE FOR RESIDUE MG C 123
12
BC3
SOFTWARE
HOH C:136 , HOH C:138 , HOH C:139 , HOH C:140 , HOH C:141 , HOH C:142
BINDING SITE FOR RESIDUE MG C 137
13
BC4
SOFTWARE
HOH C:143 , HOH C:145 , HOH C:146 , HOH C:147 , HOH C:148 , HOH C:149
BINDING SITE FOR RESIDUE MG C 144
14
BC5
SOFTWARE
HOH C:150 , HOH C:152 , HOH C:153 , HOH C:154 , HOH C:155 , HOH C:156
BINDING SITE FOR RESIDUE MG C 151
15
BC6
SOFTWARE
C C:47 , HOH C:157 , HOH C:159 , HOH C:160 , HOH C:161 , HOH C:162
BINDING SITE FOR RESIDUE MG C 158
16
BC7
SOFTWARE
HOH C:163 , HOH C:165 , HOH C:166 , HOH C:167 , HOH C:168 , C C:1009
BINDING SITE FOR RESIDUE MG C 164
17
BC8
SOFTWARE
HOH C:169 , HOH C:171 , HOH C:172 , HOH C:173 , HOH C:174 , HOH C:175
BINDING SITE FOR RESIDUE MG C 170
18
BC9
SOFTWARE
HOH C:176 , HOH C:178 , HOH C:179 , HOH C:180 , HOH C:181 , HOH C:182
BINDING SITE FOR RESIDUE MG C 177
19
CC1
SOFTWARE
HOH C:197 , HOH C:199 , HOH C:200 , HOH C:201 , HOH C:202 , G C:1008
BINDING SITE FOR RESIDUE MG C 198
20
CC2
SOFTWARE
C C:47 , G C:74
BINDING SITE FOR RESIDUE MG C 204
21
CC3
SOFTWARE
A C:31
BINDING SITE FOR RESIDUE MG C 222
22
CC4
SOFTWARE
A E:31 , A E:32 , HOH E:1029 , HOH E:1030 , HOH E:1031 , HOH E:1032
BINDING SITE FOR RESIDUE MG E 1019
23
CC5
SOFTWARE
HOH E:1033 , HOH E:1034 , HOH E:1035 , HOH E:1036 , HOH E:1037 , HOH E:1038
BINDING SITE FOR RESIDUE MG E 1020
24
CC6
SOFTWARE
G E:69 , C E:70 , U E:106 , HOH E:1039 , HOH E:1040 , HOH E:1041 , HOH E:1042
BINDING SITE FOR RESIDUE MG E 1021
25
CC7
SOFTWARE
G E:77 , HOH E:1043 , HOH E:1044 , HOH E:1045 , HOH E:1046 , HOH E:1047
BINDING SITE FOR RESIDUE MG E 1022
26
CC8
SOFTWARE
HOH E:58 , A E:115 , HOH E:1048 , HOH E:1049 , HOH E:1050 , HOH E:1051
BINDING SITE FOR RESIDUE MG E 1023
27
CC9
SOFTWARE
HOH E:66 , HOH E:1052 , HOH E:1053 , HOH E:1054 , HOH E:1055 , HOH E:1056
BINDING SITE FOR RESIDUE MG E 1024
28
DC1
SOFTWARE
HOH E:1057 , HOH E:1058 , HOH E:1059 , HOH E:1060 , HOH E:1061 , HOH E:1062
BINDING SITE FOR RESIDUE MG E 1025
29
DC2
SOFTWARE
HOH E:1063 , HOH E:1064 , HOH E:1065 , HOH E:1066 , HOH E:1067 , HOH E:1068
BINDING SITE FOR RESIDUE MG E 1026
30
DC3
SOFTWARE
HOH E:1069 , HOH E:1070 , HOH E:1071 , HOH E:1072 , HOH E:1073 , HOH E:1074
BINDING SITE FOR RESIDUE MG E 1027
31
DC4
SOFTWARE
HOH E:1075 , HOH E:1076 , HOH E:1077 , HOH E:1078 , HOH E:1079 , HOH E:1080
BINDING SITE FOR RESIDUE MG E 1028
32
DC5
SOFTWARE
HOH E:129 , HOH E:131 , HOH E:132 , HOH E:133 , HOH E:134 , HOH E:135
BINDING SITE FOR RESIDUE MG E 130
33
DC6
SOFTWARE
HOH E:190 , HOH E:192 , HOH E:193 , HOH E:194 , HOH E:195 , HOH E:196
BINDING SITE FOR RESIDUE MG E 191
34
DC7
SOFTWARE
A E:4 , A E:6
BINDING SITE FOR RESIDUE MG E 203
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: RRM (B:10-89,D:10-89|-)
;
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
2
B:10-89
D:10-89
-
[
close PROSITE info
]
Exons
(3, 6)
Info
All Exons
Exon 1.1 (B:7-25 | D:6-25)
Exon 1.2 (B:25-82 | D:25-82)
Exon 1.3 (B:83-98 | D:83-98)
View:
Select:
Label:
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
2
B:7-25
D:6-25
19
20
1.2
ENST00000243563
2
ENSE00000707951
chr19:
41263237-41263409
173
SNRPA_HUMAN
25-82
58
2
B:25-82
D:25-82
58
58
1.3
ENST00000243563
3
ENSE00000707956
chr19:
41265336-41265515
180
SNRPA_HUMAN
83-142
60
2
B:83-98
D:83-98
16
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
-
-
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3hhnb_ (B:)
1b: SCOP_d3hhnd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d3hhnb_
B:
1b
d3hhnd_
D:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3hhnB00 (B:7-98)
1b: CATH_3hhnD00 (D:6-98)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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)
[unclassified]
(45)
1a
3hhnB00
B:7-98
1b
3hhnD00
D:6-98
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
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 B
Chain C
Chain D
Chain E
Asymmetric Unit 1
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Asym.Unit (163 KB)
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