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2C39
Asym. Unit
Info
Asym.Unit (915 KB)
Biol.Unit 1 (235 KB)
Biol.Unit 2 (234 KB)
Biol.Unit 3 (237 KB)
Biol.Unit 4 (233 KB)
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(1)
Title
:
RNASE PH CORE OF THE ARCHAEAL EXOSOME IN COMPLEX WITH ADP
Authors
:
E. Lorentzen, E. Conti
Date
:
05 Oct 05 (Deposition) - 23 Nov 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Biol. Unit 3: M,N,O,P,Q,R (1x)
Biol. Unit 4: S,T,U,V,W,X (1x)
Keywords
:
Exosome, Rnase Ph, Rrp41, Rrp42, Phosphorolytic, Exoribonuclease, Rna Degradation, Archaeal, Hydrolase, Exonuclease, Nuclease
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Lorentzen, E. Conti
Structural Basis Of 3' End Rna Recognition And Exoribonucleolytic Cleavage By An Exosome Rnase Ph Core.
Mol. Cell V. 20 473 2005
[
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Hetero Components
(1, 12)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
1e: ADENOSINE-5'-DIPHOSPHATE (ADPe)
1f: ADENOSINE-5'-DIPHOSPHATE (ADPf)
1g: ADENOSINE-5'-DIPHOSPHATE (ADPg)
1h: ADENOSINE-5'-DIPHOSPHATE (ADPh)
1i: ADENOSINE-5'-DIPHOSPHATE (ADPi)
1j: ADENOSINE-5'-DIPHOSPHATE (ADPj)
1k: ADENOSINE-5'-DIPHOSPHATE (ADPk)
1l: ADENOSINE-5'-DIPHOSPHATE (ADPl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
12
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
[
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Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG B:99 , ALA B:134 , ASP B:135 , ALA B:136 , GLY B:137 , SER B:138 , ARG B:139 , ASP B:182
BINDING SITE FOR RESIDUE ADP B 404
02
AC2
SOFTWARE
THR D:88 , ARG D:99 , ALA D:134 , ASP D:135 , ALA D:136 , GLY D:137 , SER D:138 , ARG D:139 , GLU D:179 , ASP D:182 , ASP D:188
BINDING SITE FOR RESIDUE ADP D 404
03
AC3
SOFTWARE
ARG F:99 , ALA F:134 , ASP F:135 , ALA F:136 , GLY F:137 , SER F:138 , ARG F:139 , GLU F:179 , ASP F:182 , ASP F:188
BINDING SITE FOR RESIDUE ADP F 404
04
AC4
SOFTWARE
THR H:88 , ARG H:99 , ALA H:134 , ALA H:136 , GLY H:137 , SER H:138 , ARG H:139 , ASP H:182 , ASP H:188
BINDING SITE FOR RESIDUE ADP H 404
05
AC5
SOFTWARE
ARG J:99 , ALA J:136 , GLY J:137 , SER J:138 , ARG J:139 , ASP J:182 , ASP J:188
BINDING SITE FOR RESIDUE ADP J 404
06
AC6
SOFTWARE
ARG D:2 , MET L:83 , THR L:88 , ARG L:99 , ALA L:134 , ASP L:135 , ALA L:136 , GLY L:137 , SER L:138 , ARG L:139 , GLU L:179 , ASP L:182 , ASP L:188
BINDING SITE FOR RESIDUE ADP L 404
07
AC7
SOFTWARE
THR N:88 , ARG N:99 , ALA N:134 , ALA N:136 , GLY N:137 , SER N:138 , ARG N:139 , ASP N:182
BINDING SITE FOR RESIDUE ADP N 404
08
AC8
SOFTWARE
ARG P:2 , THR P:88 , ARG P:99 , ALA P:134 , ALA P:136 , GLY P:137 , SER P:138 , ARG P:139 , ASP P:182 , ASP P:188
BINDING SITE FOR RESIDUE ADP P 404
09
AC9
SOFTWARE
THR R:88 , ARG R:99 , ALA R:134 , ALA R:136 , GLY R:137 , SER R:138 , ARG R:139 , ASP R:182 , ASP R:188 , MET T:1 , ARG T:2
BINDING SITE FOR RESIDUE ADP R 404
10
BC1
SOFTWARE
MET R:1 , ARG R:2 , THR T:88 , ARG T:99 , LEU T:103 , ALA T:134 , ASP T:135 , ALA T:136 , GLY T:137 , SER T:138 , ARG T:139 , GLU T:179 , ASP T:182 , ASP T:188
BINDING SITE FOR RESIDUE ADP T 404
11
BC2
SOFTWARE
ARG V:99 , ALA V:134 , ALA V:136 , GLY V:137 , SER V:138 , ARG V:139 , GLU V:179 , ASP V:182
BINDING SITE FOR RESIDUE ADP V 404
12
BC3
SOFTWARE
THR X:88 , ARG X:99 , ALA X:136 , GLY X:137 , SER X:138 , ARG X:139 , ASP X:182 , ASP X:188
BINDING SITE FOR RESIDUE ADP X 404
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Exons
(0, 0)
Info
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(4, 46)
Info
All SCOP Domains
1a: SCOP_d2c39b2 (B:156-248)
1b: SCOP_d2c39d2 (D:156-248)
1c: SCOP_d2c39f2 (F:156-248)
1d: SCOP_d2c39j2 (J:156-248)
1e: SCOP_d2c39l2 (L:156-248)
1f: SCOP_d2c39n2 (N:156-248)
1g: SCOP_d2c39p2 (P:156-248)
1h: SCOP_d2c39r2 (R:156-248)
1i: SCOP_d2c39t2 (T:156-248)
1j: SCOP_d2c39v2 (V:156-247)
1k: SCOP_d2c39x2 (X:156-248)
2a: SCOP_d2c39a2 (A:192-275)
2b: SCOP_d2c39k2 (K:192-275)
2c: SCOP_d2c39m2 (M:192-275)
2d: SCOP_d2c39o2 (O:192-275)
2e: SCOP_d2c39q2 (Q:192-275)
2f: SCOP_d2c39s2 (S:192-274)
2g: SCOP_d2c39u2 (U:192-274)
2h: SCOP_d2c39w2 (W:192-275)
2i: SCOP_d2c39c2 (C:192-275)
2j: SCOP_d2c39e2 (E:192-275)
2k: SCOP_d2c39g2 (G:192-275)
2l: SCOP_d2c39i2 (I:192-275)
3a: SCOP_d2c39b1 (B:8-155)
3b: SCOP_d2c39d1 (D:8-155)
3c: SCOP_d2c39f1 (F:8-155)
3d: SCOP_d2c39j1 (J:8-155)
3e: SCOP_d2c39l1 (L:8-155)
3f: SCOP_d2c39n1 (N:10-155)
3g: SCOP_d2c39p1 (P:8-155)
3h: SCOP_d2c39r1 (R:8-155)
3i: SCOP_d2c39t1 (T:8-155)
3j: SCOP_d2c39v1 (V:9-155)
3k: SCOP_d2c39x1 (X:8-155)
4a: SCOP_d2c39a1 (A:1-191)
4b: SCOP_d2c39k1 (K:1-191)
4c: SCOP_d2c39m1 (M:1-191)
4d: SCOP_d2c39o1 (O:1-191)
4e: SCOP_d2c39q1 (Q:1-191)
4f: SCOP_d2c39s1 (S:1-191)
4g: SCOP_d2c39u1 (U:1-191)
4h: SCOP_d2c39w1 (W:1-191)
4i: SCOP_d2c39c1 (C:1-191)
4j: SCOP_d2c39e1 (E:1-191)
4k: SCOP_d2c39g1 (G:1-191)
4l: SCOP_d2c39i1 (I:1-191)
View:
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(
)
(
)
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(
)
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ribonuclease PH domain 2-like
(52)
Superfamily
:
Ribonuclease PH domain 2-like
(52)
Family
:
Ribonuclease PH domain 2-like
(41)
Protein domain
:
Exosome complex exonuclease 1, ECX1
(11)
Sulfolobus solfataricus [TaxId: 2287]
(9)
1a
d2c39b2
B:156-248
1b
d2c39d2
D:156-248
1c
d2c39f2
F:156-248
1d
d2c39j2
J:156-248
1e
d2c39l2
L:156-248
1f
d2c39n2
N:156-248
1g
d2c39p2
P:156-248
1h
d2c39r2
R:156-248
1i
d2c39t2
T:156-248
1j
d2c39v2
V:156-247
1k
d2c39x2
X:156-248
Protein domain
:
Exosome complex exonuclease 2, ECX2
(10)
Sulfolobus solfataricus [TaxId: 2287]
(6)
2a
d2c39a2
A:192-275
2b
d2c39k2
K:192-275
2c
d2c39m2
M:192-275
2d
d2c39o2
O:192-275
2e
d2c39q2
Q:192-275
2f
d2c39s2
S:192-274
2g
d2c39u2
U:192-274
2h
d2c39w2
W:192-275
2i
d2c39c2
C:192-275
2j
d2c39e2
E:192-275
2k
d2c39g2
G:192-275
2l
d2c39i2
I:192-275
Fold
:
Ribosomal protein S5 domain 2-like
(306)
Superfamily
:
Ribosomal protein S5 domain 2-like
(306)
Family
:
Ribonuclease PH domain 1-like
(45)
Protein domain
:
Exosome complex exonuclease 1, ECX1
(11)
Sulfolobus solfataricus [TaxId: 2287]
(9)
3a
d2c39b1
B:8-155
3b
d2c39d1
D:8-155
3c
d2c39f1
F:8-155
3d
d2c39j1
J:8-155
3e
d2c39l1
L:8-155
3f
d2c39n1
N:10-155
3g
d2c39p1
P:8-155
3h
d2c39r1
R:8-155
3i
d2c39t1
T:8-155
3j
d2c39v1
V:9-155
3k
d2c39x1
X:8-155
Protein domain
:
Exosome complex exonuclease 2,ECX2
(10)
Sulfolobus solfataricus [TaxId: 2287]
(6)
4a
d2c39a1
A:1-191
4b
d2c39k1
K:1-191
4c
d2c39m1
M:1-191
4d
d2c39o1
O:1-191
4e
d2c39q1
Q:1-191
4f
d2c39s1
S:1-191
4g
d2c39u1
U:1-191
4h
d2c39w1
W:1-191
4i
d2c39c1
C:1-191
4j
d2c39e1
E:1-191
4k
d2c39g1
G:1-191
4l
d2c39i1
I:1-191
[
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CATH Domains
(0, 0)
Info
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Pfam Domains
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Asym.Unit (915 KB)
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Biol.Unit 1 (235 KB)
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Biol.Unit 2 (234 KB)
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Biol.Unit 3 (237 KB)
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