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2VNU
Biol. Unit 1
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Asym.Unit (132 KB)
Biol.Unit 1 (123 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF SC RRP44
Authors
:
E. Lorentzen, J. Basquin, E. Conti
Date
:
07 Feb 08 (Deposition) - 08 Apr 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : B,D
Biol. Unit 1: B,D (1x)
Keywords
:
Hydrolase-Rna Complex, Rna Degradation, Rna-Binding, Rna Processing
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
E. Lorentzen, J. Basquin, R. Tomecki, A. Dziembowski, E. Conti
Structure Of The Active Subunit Of The Yeast Exosome Core, Rrp44: Diverse Modes Of Substrate Recruitment In The Rnase Ii Nuclease Family
Mol. Cell V. 29 717 2008
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Hetero Components
(2, 19)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
2a: MAGNESIUM ION (MGa)
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)
4a: SODIUM ION (NAa)
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No.
Name
Count
Type
Full Name
1
1PE
1
Ligand/Ion
PENTAETHYLENE GLYCOL
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
MSE
18
Mod. Amino Acid
SELENOMETHIONINE
4
NA
-1
Ligand/Ion
SODIUM ION
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
A B:-2 , A B:-1 , ASP D:543 , ASP D:552 , HOH D:2168
BINDING SITE FOR RESIDUE MG D1500
2
AC2
SOFTWARE
SER D:541 , ASP D:543 , PHE D:652 , HOH D:2162
BINDING SITE FOR RESIDUE NA D1501
3
AC3
SOFTWARE
ALA D:556 , LYS D:558 , GLY D:562 , TRP D:564 , MSE D:672 , THR D:772 , ARG D:773 , LYS D:774 , ASN D:775 , TYR D:974 , HOH D:2173 , HOH D:2313 , HOH D:2314 , HOH D:2432
BINDING SITE FOR RESIDUE 1PE D1502
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: RIBONUCLEASE_II (D:831-855)
2: S1 (D:904-998)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIBONUCLEASE_II
PS01175
Ribonuclease II family signature.
RRP44_YEAST
831-855
1
D:831-855
2
S1
PS50126
S1 domain profile.
RRP44_YEAST
904-1001
1
D:904-998
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2vnud1 (D:400-494)
1b: SCOP_d2vnud2 (D:911-998)
1c: SCOP_d2vnud3 (D:252-399)
2a: SCOP_d2vnud4 (D:495-910)
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Class
:
All beta proteins
(24004)
Fold
:
OB-fold
(1179)
Superfamily
:
Nucleic acid-binding proteins
(590)
Family
:
Cold shock DNA-binding domain-like
(310)
Protein domain
:
Exosome complex exonuclease RRP44
(1)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
1a
d2vnud1
D:400-494
1b
d2vnud2
D:911-998
1c
d2vnud3
D:252-399
Family
:
RNB domain-like
(6)
Protein domain
:
Exosome complex exonuclease RRP44
(1)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
2a
d2vnud4
D:495-910
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_RNB_2vnuD01 (D:531-863)
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(
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Clan
:
no clan defined [family: RNB]
(4)
Family
:
RNB
(4)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
1a
RNB-2vnuD01
D:531-863
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Asymmetric Unit 1
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Asym.Unit (132 KB)
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