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Asym. Unit
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Asym.Unit (112 KB)
Biol.Unit 1 (105 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RNASE III FROM AQUIFEX AEOLICUS COMPLEXED WITH DS-RNA AT 1.7-ANGSTROM RESOLUTION
Authors
:
J. H. Gan, G. Shaw, J. E. Tropea, D. S. Waugh, D. L. Court, X. Ji
Date
:
09 Nov 06 (Deposition) - 20 Nov 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Ribonuclease Iii, Dsrna, Rna Interference, Endonucleolytic Cleavage, Hydrolase/Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Gan, G. Shaw, J. E. Tropea, D. S. Waugh, D. L. Court, X. Ji
A Stepwise Model For Double-Stranded Rna Processing By Ribonuclease Iii.
Mol. Microbiol. V. 67 143 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 19)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
1g: MAGNESIUM ION (MGg)
1h: MAGNESIUM ION (MGh)
1i: MAGNESIUM ION (MGi)
1j: MAGNESIUM ION (MGj)
1k: MAGNESIUM ION (MGk)
1l: MAGNESIUM ION (MGl)
1m: MAGNESIUM ION (MGm)
1n: MAGNESIUM ION (MGn)
1o: MAGNESIUM ION (MGo)
1p: MAGNESIUM ION (MGp)
1q: MAGNESIUM ION (MGq)
1r: MAGNESIUM ION (MGr)
1s: MAGNESIUM ION (MGs)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
19
Ligand/Ion
MAGNESIUM ION
[
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Sites
(19, 19)
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 (SOFTWAR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:44 , GLU A:110 , HOH A:518 , HOH A:519 , G D:12 , HOH D:517 , A E:17
BINDING SITE FOR RESIDUE MG A 501
02
AC2
SOFTWARE
GLU A:40 , GLU A:110 , MG A:503 , HOH A:519 , HOH A:520 , HOH A:531 , A E:17 , HOH E:506
BINDING SITE FOR RESIDUE MG A 502
03
AC3
SOFTWARE
ASP A:107 , MG A:502 , HOH A:521 , HOH A:522 , HOH A:523 , HOH E:506 , HOH E:507
BINDING SITE FOR RESIDUE MG A 503
04
AC4
SOFTWARE
GLU A:37 , GLU A:40 , HOH A:524 , HOH A:525 , HOH B:519 , G E:18 , HOH E:508
BINDING SITE FOR RESIDUE MG A 504
05
AC5
SOFTWARE
A E:17 , G E:18 , HOH E:509 , HOH E:510 , HOH E:511 , HOH E:512
BINDING SITE FOR RESIDUE MG E 505
06
AC6
SOFTWARE
HOH A:526 , HOH A:527 , HOH A:528 , HOH A:529 , HOH C:520 , HOH C:521
BINDING SITE FOR RESIDUE MG A 506
07
AC7
SOFTWARE
ASP B:44 , GLU B:110 , HOH B:520 , G C:12 , HOH C:522 , HOH C:523 , A F:17
BINDING SITE FOR RESIDUE MG B 507
08
AC8
SOFTWARE
GLU B:40 , GLU B:110 , HOH B:521 , HOH B:530 , HOH C:523 , A F:17 , HOH F:514
BINDING SITE FOR RESIDUE MG B 508
09
AC9
SOFTWARE
ASP B:107 , HOH B:521 , HOH B:522 , HOH B:523 , HOH B:524 , HOH B:530 , HOH F:515
BINDING SITE FOR RESIDUE MG B 509
10
BC1
SOFTWARE
HOH A:530 , GLU B:37 , GLU B:40 , HOH B:525 , HOH B:526 , HOH F:516
BINDING SITE FOR RESIDUE MG B 510
11
BC2
SOFTWARE
A F:17 , G F:18 , HOH F:517 , HOH F:518 , HOH F:519 , HOH F:520
BINDING SITE FOR RESIDUE MG F 511
12
BC3
SOFTWARE
HOH B:527 , HOH B:528 , HOH B:529 , HOH D:518 , HOH D:519 , HOH D:563
BINDING SITE FOR RESIDUE MG B 512
13
BC4
SOFTWARE
HOH E:522 , HOH F:542 , HOH F:543 , HOH F:544 , HOH F:545 , HOH F:552
BINDING SITE FOR RESIDUE MG F 513
14
BC5
SOFTWARE
HOH D:529 , HOH D:533 , HOH D:550 , HOH D:551 , HOH D:552
BINDING SITE FOR RESIDUE MG D 514
15
BC6
SOFTWARE
HOH C:535 , HOH C:538 , HOH C:559 , HOH C:563
BINDING SITE FOR RESIDUE MG C 515
16
BC7
SOFTWARE
HOH D:522 , HOH D:531 , HOH D:535 , HOH D:562 , HOH E:513 , HOH E:526
BINDING SITE FOR RESIDUE MG D 516
17
BC8
SOFTWARE
GLY A:12 , HOH A:534 , HOH A:620 , HOH A:632 , ARG B:194
BINDING SITE FOR RESIDUE MG A 517
18
BC9
SOFTWARE
HOH B:538 , HOH B:561 , HOH B:657
BINDING SITE FOR RESIDUE MG B 518
19
CC1
SOFTWAR
HOH C:526 , HOH C:530 , HOH C:540 , HOH C:546 , HOH C:562 , HOH F:551
BINDING SITE FOR RESIDUE MG C 519
[
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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, 6)
Info
All PROSITE Patterns/Profiles
1: RNASE_3_2 (A:4-121,B:4-121)
2: RNASE_3_1 (A:37-45,B:37-45)
3: DS_RBD (A:151-218,B:151-219)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RNASE_3_2
PS50142
Ribonuclease III family domain profile.
RNC_AQUAE
4-121
2
A:4-121
B:4-121
2
RNASE_3_1
PS00517
Ribonuclease III family signature.
RNC_AQUAE
37-45
2
A:37-45
B:37-45
3
DS_RBD
PS50137
Double stranded RNA-binding domain (dsRBD) profile.
RNC_AQUAE
151-219
2
A:151-218
B:151-219
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2nuga1 (A:3-150)
1b: SCOP_d2nugb1 (B:3-150)
2a: SCOP_d2nuga2 (A:151-218)
2b: SCOP_d2nugb2 (B:151-220)
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Classes
(
)
(
)
Folds
(
)
(
)
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(
)
(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
RNase III domain-like
(16)
Superfamily
:
RNase III domain-like
(16)
Family
:
RNase III catalytic domain-like
(14)
Protein domain
:
RNase III endonuclease catalytic domain
(13)
Aquifex aeolicus [TaxId: 63363]
(12)
1a
d2nuga1
A:3-150
1b
d2nugb1
B:3-150
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
dsRBD-like
(111)
Superfamily
:
dsRNA-binding domain-like
(98)
Family
:
Double-stranded RNA-binding domain (dsRBD)
(34)
Protein domain
:
RNase III, C-terminal domain
(13)
Aquifex aeolicus [TaxId: 63363]
(9)
2a
d2nuga2
A:151-218
2b
d2nugb2
B:151-220
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
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Sorry, no Info available
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_dsrm_2nugB01 (B:152-217)
1b: PFAM_dsrm_2nugB02 (B:152-217)
2a: PFAM_Ribonuclease_3_2nugB03 (B:37-121)
2b: PFAM_Ribonuclease_3_2nugB04 (B:37-121)
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Clans
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)
(
)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
DSRM
(45)
Family
:
dsrm
(27)
Aquifex aeolicus
(7)
1a
dsrm-2nugB01
B:152-217
1b
dsrm-2nugB02
B:152-217
Clan
:
no clan defined [family: Ribonuclease_3]
(11)
Family
:
Ribonuclease_3
(11)
Aquifex aeolicus
(9)
2a
Ribonuclease_3-2nugB03
B:37-121
2b
Ribonuclease_3-2nugB04
B:37-121
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]
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