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2ZU6
Asym. Unit
Info
Asym.Unit (313 KB)
Biol.Unit 1 (161 KB)
Biol.Unit 2 (148 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE EIF4A-PDCD4 COMPLEX
Authors
:
Y. Cho, J. H. Chang, S. Y. Sohn
Date
:
13 Oct 08 (Deposition) - 24 Feb 09 (Release) - 17 Mar 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Protein-Protein Complex, Atp-Binding, Helicase, Hydrolase, Initiation Factor, Nucleotide-Binding, Protein Biosynthesis, Rna-Binding, Anti-Oncogene, Apoptosis, Cell Cycle, Cytoplasm, Nucleus, Phosphoprotein, Polymorphism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. H. Chang, Y. H. Cho, S. Y. Sohn, J. M. Choi, A. Kim, Y. C. Kim, S. K. Jang, Y. Cho
Crystal Structure Of The Eif4A-Pdcd4 Complex
Proc. Natl. Acad. Sci. Usa V. 106 3148 2009
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 23)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
2
Ligand/Ion
ACETIC ACID
2
EDO
3
Ligand/Ion
1,2-ETHANEDIOL
3
MSE
18
Mod. Amino Acid
SELENOMETHIONINE
[
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:218 , GLU A:222 , LYS A:225
BINDING SITE FOR RESIDUE EDO A 2
2
AC2
SOFTWARE
ALA A:76 , GLN A:77 , SER A:78 , THR A:80 , ASP A:182 , GLU A:183 , ASP A:185 , SER A:213 , ALA A:214
BINDING SITE FOR RESIDUE EDO A 3
3
AC3
SOFTWARE
SER A:89
BINDING SITE FOR RESIDUE ACY A 1
4
AC4
SOFTWARE
SER D:89 , GLN D:93
BINDING SITE FOR RESIDUE EDO D 1
5
AC5
SOFTWARE
ARG D:141 , TYR D:170
BINDING SITE FOR RESIDUE ACY D 2
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 10)
Info
All PROSITE Patterns/Profiles
1: Q_MOTIF (C:32-60,D:60-60)
2: MI (B:163-284,E:163-284|B:326-449,E:32...)
3: DEAD_ATP_HELICASE (A:180-188,C:180-188,D:180-188,F:18...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
Q_MOTIF
PS51195
DEAD-box RNA helicase Q motif profile.
IF4A1_HUMAN
32-60
2
C:32-60
D:60-60
2
MI
PS51366
MI domain profile.
PDCD4_HUMAN
163-284
326-449
4
B:163-284
E:163-284
B:326-449
E:326-449
3
DEAD_ATP_HELICASE
PS00039
DEAD-box subfamily ATP-dependent helicases signature.
IF4A1_HUMAN
180-188
4
A:180-188
C:180-188
D:180-188
F:180-188
[
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]
Exons
(18, 53)
Info
All Exons
Exon 1.8c (B:163-185 | E:163-185)
Exon 1.9e (B:186-259 | E:186-259)
Exon 1.10 (B:260-292 | E:260-292)
Exon 1.11a (B:292-330 (gaps) | E:292-330 (gaps...)
Exon 1.12b (B:331-366 | E:331-366)
Exon 1.13 (B:367-403 | E:367-403)
Exon 1.14b (B:404-450 | E:404-450)
Exon 1.15e (B:450-450 | E:450-450)
Exon 2.2 (A:19-24 | - | D:19-24 | -)
Exon 2.3 (A:25-69 (gaps) | C:25-69 (gaps) | ...)
Exon 2.4a (A:69-115 | C:69-115 (gaps) | D:69-...)
Exon 2.5 (A:116-172 | C:116-172 (gaps) | D:1...)
Exon 2.6 (A:172-208 | C:172-208 | D:172-208 ...)
Exon 2.7 (A:209-256 | C:209-256 (gaps) | D:2...)
Exon 2.8 (A:257-302 | C:257-302 | D:257-302 ...)
Exon 2.9 (A:303-332 (gaps) | C:303-332 | D:3...)
Exon 2.10 (A:333-359 | C:333-359 | D:333-359 ...)
Exon 2.11 (A:359-401 (gaps) | C:359-398 (gaps...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.7/1.8c
02: Boundary 1.8c/1.9e
03: Boundary 1.9e/1.10
04: Boundary 1.10/1.11a
05: Boundary 1.11a/1.12b
06: Boundary 1.12b/1.13
07: Boundary 1.13/1.14b
08: Boundary 1.14b/1.15e
09: Boundary 1.15e/-
10: Boundary 2.1a/2.2
11: Boundary 2.2/2.3
12: Boundary 2.3/2.4a
13: Boundary 2.4a/2.5
14: Boundary 2.5/2.6
15: Boundary 2.6/2.7
16: Boundary 2.7/2.8
17: Boundary 2.8/2.9
18: Boundary 2.9/2.10
19: Boundary 2.10/2.11
20: Boundary 2.11/-
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
1.1a
ENST00000280154
1a
ENSE00001922986
chr10:
112631565-112631776
212
PDCD4_HUMAN
-
0
0
-
-
1.2
ENST00000280154
2
ENSE00002190882
chr10:
112635724-112635828
105
PDCD4_HUMAN
1-15
15
0
-
-
1.6a
ENST00000280154
6a
ENSE00001380538
chr10:
112640991-112641293
303
PDCD4_HUMAN
15-116
102
0
-
-
1.7
ENST00000280154
7
ENSE00000995567
chr10:
112642761-112642855
95
PDCD4_HUMAN
116-147
32
0
-
-
1.8c
ENST00000280154
8c
ENSE00001094657
chr10:
112645011-112645124
114
PDCD4_HUMAN
148-185
38
2
B:163-185
E:163-185
23
23
1.9e
ENST00000280154
9e
ENSE00002200197
chr10:
112647423-112647644
222
PDCD4_HUMAN
186-259
74
2
B:186-259
E:186-259
74
74
1.10
ENST00000280154
10
ENSE00001788034
chr10:
112649291-112649388
98
PDCD4_HUMAN
260-292
33
2
B:260-292
E:260-292
33
33
1.11a
ENST00000280154
11a
ENSE00001772839
chr10:
112650314-112650428
115
PDCD4_HUMAN
292-330
39
2
B:292-330 (gaps)
E:292-330 (gaps)
39
39
1.12b
ENST00000280154
12b
ENSE00001599108
chr10:
112653849-112653956
108
PDCD4_HUMAN
331-366
36
2
B:331-366
E:331-366
36
36
1.13
ENST00000280154
13
ENSE00001674744
chr10:
112654170-112654280
111
PDCD4_HUMAN
367-403
37
2
B:367-403
E:367-403
37
37
1.14b
ENST00000280154
14b
ENSE00001636249
chr10:
112655706-112655845
140
PDCD4_HUMAN
404-450
47
2
B:404-450
E:404-450
47
47
1.15e
ENST00000280154
15e
ENSE00001840051
chr10:
112657786-112659764
1979
PDCD4_HUMAN
450-469
20
2
B:450-450
E:450-450
1
1
2.1a
ENST00000293831
1a
ENSE00001710114
chr17:
7476024-7476182
159
IF4A1_HUMAN
1-8
8
0
-
-
2.2
ENST00000293831
2
ENSE00001631751
chr17:
7477578-7477626
49
IF4A1_HUMAN
8-24
17
2
A:19-24
-
D:19-24
-
6
-
6
-
2.3
ENST00000293831
3
ENSE00001762686
chr17:
7477864-7477996
133
IF4A1_HUMAN
25-69
45
3
A:25-69 (gaps)
C:25-69 (gaps)
D:25-69 (gaps)
-
45
45
45
-
2.4a
ENST00000293831
4a
ENSE00001726391
chr17:
7478437-7478576
140
IF4A1_HUMAN
69-115
47
4
A:69-115
C:69-115 (gaps)
D:69-115
F:87-115
47
47
47
29
2.5
ENST00000293831
5
ENSE00001061690
chr17:
7479842-7480010
169
IF4A1_HUMAN
116-172
57
4
A:116-172
C:116-172 (gaps)
D:116-172
F:116-172 (gaps)
57
57
57
57
2.6
ENST00000293831
6
ENSE00001061689
chr17:
7480374-7480483
110
IF4A1_HUMAN
172-208
37
4
A:172-208
C:172-208
D:172-208
F:172-208
37
37
37
37
2.7
ENST00000293831
7
ENSE00001061692
chr17:
7480662-7480805
144
IF4A1_HUMAN
209-256
48
4
A:209-256
C:209-256 (gaps)
D:209-256
F:209-256 (gaps)
48
48
48
48
2.8
ENST00000293831
8
ENSE00001799518
chr17:
7480887-7481024
138
IF4A1_HUMAN
257-302
46
4
A:257-302
C:257-302
D:257-302 (gaps)
F:257-302 (gaps)
46
46
46
46
2.9
ENST00000293831
9
ENSE00001061685
chr17:
7481145-7481234
90
IF4A1_HUMAN
303-332
30
4
A:303-332 (gaps)
C:303-332
D:303-332 (gaps)
F:303-332 (gaps)
30
30
30
30
2.10
ENST00000293831
10
ENSE00001061694
chr17:
7481483-7481562
80
IF4A1_HUMAN
333-359
27
4
A:333-359
C:333-359
D:333-359
F:333-359
27
27
27
27
2.11
ENST00000293831
11
ENSE00001485271
chr17:
7481660-7482324
665
IF4A1_HUMAN
359-406
48
4
A:359-401 (gaps)
C:359-398 (gaps)
D:359-402 (gaps)
F:359-398 (gaps)
43
40
44
40
[
close EXON info
]
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d2zu6a1 (A:19-239)
1b: SCOP_d2zu6a2 (A:246-401)
1c: SCOP_d2zu6c1 (C:25-239)
1d: SCOP_d2zu6c2 (C:246-398)
1e: SCOP_d2zu6d1 (D:19-239)
1f: SCOP_d2zu6d2 (D:246-402)
1g: SCOP_d2zu6f1 (F:245-398)
1h: SCOP_d2zu6f2 (F:87-231)
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Folds
(
)
(
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
Tandem AAA-ATPase domain
(59)
Protein domain
:
Initiation factor 4a
(6)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d2zu6a1
A:19-239
1b
d2zu6a2
A:246-401
1c
d2zu6c1
C:25-239
1d
d2zu6c2
C:246-398
1e
d2zu6d1
D:19-239
1f
d2zu6d2
D:246-402
1g
d2zu6f1
F:245-398
1h
d2zu6f2
F:87-231
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_DEAD_2zu6F01 (F:87-223)
1b: PFAM_DEAD_2zu6F02 (F:87-223)
1c: PFAM_DEAD_2zu6F03 (F:87-223)
1d: PFAM_DEAD_2zu6F04 (F:87-223)
2a: PFAM_Helicase_C_2zu6F05 (F:290-360)
2b: PFAM_Helicase_C_2zu6F06 (F:290-360)
2c: PFAM_Helicase_C_2zu6F07 (F:290-360)
2d: PFAM_Helicase_C_2zu6F08 (F:290-360)
3a: PFAM_MA3_2zu6E01 (E:327-440)
3b: PFAM_MA3_2zu6E02 (E:327-440)
3c: PFAM_MA3_2zu6E03 (E:327-440)
3d: PFAM_MA3_2zu6E04 (E:327-440)
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Clan
:
P-loop_NTPase
(1112)
Family
:
DEAD
(41)
Homo sapiens (Human)
(12)
1a
DEAD-2zu6F01
F:87-223
1b
DEAD-2zu6F02
F:87-223
1c
DEAD-2zu6F03
F:87-223
1d
DEAD-2zu6F04
F:87-223
Family
:
Helicase_C
(51)
Homo sapiens (Human)
(15)
2a
Helicase_C-2zu6F05
F:290-360
2b
Helicase_C-2zu6F06
F:290-360
2c
Helicase_C-2zu6F07
F:290-360
2d
Helicase_C-2zu6F08
F:290-360
Clan
:
TPR
(230)
Family
:
MA3
(5)
Homo sapiens (Human)
(5)
3a
MA3-2zu6E01
E:327-440
3b
MA3-2zu6E02
E:327-440
3c
MA3-2zu6E03
E:327-440
3d
MA3-2zu6E04
E:327-440
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