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2YJY
Asym. Unit
Info
Asym.Unit (127 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (62 KB)
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(1)
Title
:
A SPECIFIC AND MODULAR BINDING CODE FOR CYTOSINE RECOGNITION IN PUF DOMAINS
Authors
:
S. Dong, Y. Wang, C. Cassidy-Amstutz, G. Lu, C. Qiu, R. Bigler, M. Jezyk, T. M. T. Hall, Z. Wang
Date
:
24 May 11 (Deposition) - 08 Jun 11 (Release) - 28 Oct 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: B,D (1x)
Biol. Unit 2: A,C (1x)
Keywords
:
Rna Binding Protein-Rna Complex, Nanos Response Element
(Keyword Search:
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Reference
:
S. Dong, Y. Wang, C. Cassidy-Amstutz, G. Lu, R. Bigler, M. R. Jezyk, C. Li, T. M. Hall, Z. Wang
Specific And Modular Binding Code For Cytosine Recognition In Pumilio/Fbf (Puf) Rna-Binding Domains.
J. Biol. Chem. V. 286 26732 2011
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Hetero Components
(0, 0)
Info
All Hetero Components
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Sorry, no Info available
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Sites
(0, 0)
Info
All Sites
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Sorry, no Info available
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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
(2, 18)
Info
All PROSITE Patterns/Profiles
1: PUM_HD (A:828-1164,B:828-1168)
2: PUM (A:848-883,B:848-883|A:884-919,B:88...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PUM_HD
PS50303
Pumilio homology domain (PUM-HD) profile.
PUM1_HUMAN
828-1168
2
A:828-1164
B:828-1168
2
PUM
PS50302
Pumilio RNA-binding repeat profile.
PUM1_HUMAN
848-883
884-919
920-955
956-991
992-1027
1028-1063
1064-1099
1103-1142
16
A:848-883
B:848-883
A:884-919
B:884-919
A:920-955
B:920-955
A:956-991
B:956-991
A:992-1027
B:992-1027
A:1028-1063
B:1028-1063
A:1064-1099
B:1064-1099
A:1103-1142
B:1103-1142
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Exons
(8, 16)
Info
All Exons
Exon 1.18a (A:828-864 | B:828-864)
Exon 1.19 (A:864-907 | B:864-907)
Exon 1.20a (A:908-950 | B:908-950)
Exon 1.21b (A:951-996 | B:951-996)
Exon 1.22a (A:997-1038 | B:997-1038)
Exon 1.23 (A:1039-1079 | B:1039-1079)
Exon 1.24c (A:1079-1143 | B:1079-1143)
Exon 1.25g (A:1144-1164 | B:1144-1168)
View:
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All Exon Boundaries
1: Boundary 1.17b/1.18a
2: Boundary 1.18a/1.19
3: Boundary 1.19/1.20a
4: Boundary 1.20a/1.21b
5: Boundary 1.21b/1.22a
6: Boundary 1.22a/1.23
7: Boundary 1.23/1.24c
8: Boundary 1.24c/1.25g
9: Boundary 1.25g/-
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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
1.1f
ENST00000257075
1f
ENSE00001830352
chr1:
31538545-31538463
83
PUM1_HUMAN
-
0
0
-
-
1.3c
ENST00000257075
3c
ENSE00002154901
chr1:
31532424-31532051
374
PUM1_HUMAN
1-121
121
0
-
-
1.5a
ENST00000257075
5a
ENSE00001171922
chr1:
31501711-31501643
69
PUM1_HUMAN
122-144
23
0
-
-
1.6
ENST00000257075
6
ENSE00001171914
chr1:
31479949-31479841
109
PUM1_HUMAN
145-181
37
0
-
-
1.7
ENST00000257075
7
ENSE00001171904
chr1:
31478878-31478700
179
PUM1_HUMAN
181-240
60
0
-
-
1.8b
ENST00000257075
8b
ENSE00000916523
chr1:
31468067-31467901
167
PUM1_HUMAN
241-296
56
0
-
-
1.9b
ENST00000257075
9b
ENSE00000916522
chr1:
31465507-31465237
271
PUM1_HUMAN
296-386
91
0
-
-
1.11b
ENST00000257075
11b
ENSE00000916520
chr1:
31454252-31454159
94
PUM1_HUMAN
387-418
32
0
-
-
1.12c
ENST00000257075
12c
ENSE00001171885
chr1:
31453010-31452909
102
PUM1_HUMAN
418-452
35
0
-
-
1.13b
ENST00000257075
13b
ENSE00000916518
chr1:
31447649-31447498
152
PUM1_HUMAN
452-502
51
0
-
-
1.14a
ENST00000257075
14a
ENSE00001171865
chr1:
31441339-31441201
139
PUM1_HUMAN
503-549
47
0
-
-
1.15b
ENST00000257075
15b
ENSE00000916516
chr1:
31440157-31440014
144
PUM1_HUMAN
549-597
49
0
-
-
1.16d
ENST00000257075
16d
ENSE00000916515
chr1:
31439125-31438829
297
PUM1_HUMAN
597-696
100
0
-
-
1.17b
ENST00000257075
17b
ENSE00000916514
chr1:
31437757-31437521
237
PUM1_HUMAN
696-775
80
0
-
-
1.18a
ENST00000257075
18a
ENSE00000916513
chr1:
31426828-31426561
268
PUM1_HUMAN
775-864
90
2
A:828-864
B:828-864
37
37
1.19
ENST00000257075
19
ENSE00000916512
chr1:
31425210-31425081
130
PUM1_HUMAN
864-907
44
2
A:864-907
B:864-907
44
44
1.20a
ENST00000257075
20a
ENSE00001234157
chr1:
31423108-31422980
129
PUM1_HUMAN
908-950
43
2
A:908-950
B:908-950
43
43
1.21b
ENST00000257075
21b
ENSE00000916510
chr1:
31418330-31418193
138
PUM1_HUMAN
951-996
46
2
A:951-996
B:951-996
46
46
1.22a
ENST00000257075
22a
ENSE00000916508
chr1:
31414970-31414845
126
PUM1_HUMAN
997-1038
42
2
A:997-1038
B:997-1038
42
42
1.23
ENST00000257075
23
ENSE00000916506
chr1:
31414119-31413998
122
PUM1_HUMAN
1039-1079
41
2
A:1039-1079
B:1039-1079
41
41
1.24c
ENST00000257075
24c
ENSE00001620412
chr1:
31409682-31409490
193
PUM1_HUMAN
1079-1143
65
2
A:1079-1143
B:1079-1143
65
65
1.25g
ENST00000257075
25g
ENSE00001065956
chr1:
31406189-31404353
1837
PUM1_HUMAN
1144-1186
43
2
A:1144-1164
B:1144-1168
21
25
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2yjya_ (A:)
1b: SCOP_d2yjyb_ (B:)
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Organisms
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Class
:
All alpha proteins
(14657)
Fold
:
alpha-alpha superhelix
(690)
Superfamily
:
ARM repeat
(317)
Family
:
Pumilio repeat
(19)
Protein domain
:
automated matches
(7)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d2yjya_
A:
1b
d2yjyb_
B:
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CATH Domains
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Pfam Domains
(1, 16)
Info
all PFAM domains
1a: PFAM_PUF_2yjyB01 (B:1110-1141)
1b: PFAM_PUF_2yjyB02 (B:1110-1141)
1c: PFAM_PUF_2yjyB03 (B:1110-1141)
1d: PFAM_PUF_2yjyB04 (B:1110-1141)
1e: PFAM_PUF_2yjyB05 (B:1110-1141)
1f: PFAM_PUF_2yjyB06 (B:1110-1141)
1g: PFAM_PUF_2yjyB07 (B:1110-1141)
1h: PFAM_PUF_2yjyB08 (B:1110-1141)
1i: PFAM_PUF_2yjyB09 (B:1110-1141)
1j: PFAM_PUF_2yjyB10 (B:1110-1141)
1k: PFAM_PUF_2yjyB11 (B:1110-1141)
1l: PFAM_PUF_2yjyB12 (B:1110-1141)
1m: PFAM_PUF_2yjyB13 (B:1110-1141)
1n: PFAM_PUF_2yjyB14 (B:1110-1141)
1o: PFAM_PUF_2yjyB15 (B:1110-1141)
1p: PFAM_PUF_2yjyB16 (B:1110-1141)
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Families
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Organisms
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)
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)
Clan
:
TPR
(230)
Family
:
PUF
(24)
Homo sapiens (Human)
(13)
1a
PUF-2yjyB01
B:1110-1141
1b
PUF-2yjyB02
B:1110-1141
1c
PUF-2yjyB03
B:1110-1141
1d
PUF-2yjyB04
B:1110-1141
1e
PUF-2yjyB05
B:1110-1141
1f
PUF-2yjyB06
B:1110-1141
1g
PUF-2yjyB07
B:1110-1141
1h
PUF-2yjyB08
B:1110-1141
1i
PUF-2yjyB09
B:1110-1141
1j
PUF-2yjyB10
B:1110-1141
1k
PUF-2yjyB11
B:1110-1141
1l
PUF-2yjyB12
B:1110-1141
1m
PUF-2yjyB13
B:1110-1141
1n
PUF-2yjyB14
B:1110-1141
1o
PUF-2yjyB15
B:1110-1141
1p
PUF-2yjyB16
B:1110-1141
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