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3KQU
Biol. Unit 1
Info
Asym.Unit (464 KB)
Biol.Unit 1 (232 KB)
Biol.Unit 2 (233 KB)
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(1)
Title
:
THREE CONFORMATIONAL SNAPSHOTS OF THE HEPATITIS C VIRUS NS3 HELICASE REVEAL A RATCHET TRANSLOCATION MECHANISM
Authors
:
M. Gu, C. M. Rice
Date
:
17 Nov 09 (Deposition) - 26 Jan 10 (Release) - 26 Jan 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F,M,N
Biol. Unit 1: A,B,C,M (1x)
Biol. Unit 2: D,E,F,N (1x)
Keywords
:
Helicase-Substrate Ground-State Complex, Hcv, Ns3 Protein, Helicase, Dna-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Gu, C. M. Rice
Inaugural Article: Three Conformational Snapshots Of The Hepatitis C Virus Ns3 Helicase Reveal A Ratchet Translocation Mechanism.
Proc. Natl. Acad. Sci. Usa V. 107 521 2010
(for further references see the
PDB file header
)
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Hetero Components
(2, 6)
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)
2a: BERYLLIUM TRIFLUORIDE ION (BEFa)
2b: BERYLLIUM TRIFLUORIDE ION (BEFb)
2c: BERYLLIUM TRIFLUORIDE ION (BEFc)
2d: BERYLLIUM TRIFLUORIDE ION (BEFd)
2e: BERYLLIUM TRIFLUORIDE ION (BEFe)
2f: BERYLLIUM TRIFLUORIDE ION (BEFf)
3a: MANGANESE (II) ION (MNa)
3b: MANGANESE (II) ION (MNb)
3c: MANGANESE (II) ION (MNc)
3d: MANGANESE (II) ION (MNd)
3e: MANGANESE (II) ION (MNe)
3f: MANGANESE (II) ION (MNf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
3
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
BEF
3
Ligand/Ion
BERYLLIUM TRIFLUORIDE ION
3
MN
-1
Ligand/Ion
MANGANESE (II) ION
[
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ADP A:2 , MN A:3 , HOH A:4 , THR A:206 , GLY A:207 , LYS A:210 , GLU A:291 , ALA A:323 , ARG A:464 , ARG A:467 , HOH A:626 , HOH A:627 , HOH A:628
BINDING SITE FOR RESIDUE BEF A 1
2
AC2
SOFTWARE
BEF A:1 , MN A:3 , HOH A:4 , HOH A:5 , GLY A:207 , SER A:208 , GLY A:209 , LYS A:210 , SER A:211 , THR A:212 , GLY A:237 , TYR A:241 , THR A:419 , ARG A:467 , GLY A:468 , HOH A:628
BINDING SITE FOR RESIDUE ADP A 2
3
AC3
SOFTWARE
BEF A:1 , ADP A:2 , HOH A:4 , SER A:211 , ASP A:290 , GLU A:291 , HOH A:628
BINDING SITE FOR RESIDUE MN A 3
4
AC4
SOFTWARE
ADP B:2 , MN B:3 , HOH B:6 , HOH B:7 , HOH B:8 , HOH B:9 , THR B:206 , LYS B:210 , GLU B:291 , ALA B:323 , ARG B:464 , ARG B:467
BINDING SITE FOR RESIDUE BEF B 1
5
AC5
SOFTWARE
BEF B:1 , MN B:3 , HOH B:8 , HOH B:9 , HOH B:10 , GLY B:207 , SER B:208 , GLY B:209 , LYS B:210 , SER B:211 , THR B:212 , GLY B:237 , TYR B:241 , THR B:419 , ARG B:467 , GLY B:468 , HOH B:633 , HOH B:662
BINDING SITE FOR RESIDUE ADP B 2
6
AC6
SOFTWARE
BEF B:1 , ADP B:2 , HOH B:8 , HOH B:9 , SER B:211 , ASP B:290 , GLU B:291
BINDING SITE FOR RESIDUE MN B 3
7
AC7
SOFTWARE
ADP C:2 , MN C:3 , HOH C:11 , HOH C:12 , HOH C:13 , HOH C:14 , THR C:206 , GLY C:207 , LYS C:210 , GLU C:291 , ALA C:323 , ARG C:464 , ARG C:467
BINDING SITE FOR RESIDUE BEF C 1
8
AC8
SOFTWARE
BEF C:1 , MN C:3 , HOH C:13 , HOH C:14 , HOH C:15 , GLY C:207 , SER C:208 , GLY C:209 , LYS C:210 , SER C:211 , THR C:212 , GLY C:237 , TYR C:241 , THR C:419 , ARG C:467 , GLY C:468
BINDING SITE FOR RESIDUE ADP C 2
9
AC9
SOFTWARE
BEF C:1 , ADP C:2 , HOH C:13 , HOH C:14 , SER C:211 , ASP C:290 , GLU C:291
BINDING SITE FOR RESIDUE MN C 3
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
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;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
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
(1, 12)
Info
All SCOP Domains
1a: SCOP_d3kqua1 (A:189-325)
1b: SCOP_d3kqua2 (A:326-625)
1c: SCOP_d3kqub1 (B:189-325)
1d: SCOP_d3kqub2 (B:326-625)
1e: SCOP_d3kquc1 (C:189-325)
1f: SCOP_d3kquc2 (C:326-625)
1g: SCOP_d3kqud1 (D:189-325)
1h: SCOP_d3kqud2 (D:326-625)
1i: SCOP_d3kque1 (E:189-325)
1j: SCOP_d3kque2 (E:326-625)
1k: SCOP_d3kquf1 (F:189-325)
1l: SCOP_d3kquf2 (F:326-625)
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)
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)
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)
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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
:
RNA helicase
(31)
Protein domain
:
HCV helicase domain
(16)
Human hepatitis C virus (HCV), different isolates [TaxId: 11103]
(16)
1a
d3kqua1
A:189-325
1b
d3kqua2
A:326-625
1c
d3kqub1
B:189-325
1d
d3kqub2
B:326-625
1e
d3kquc1
C:189-325
1f
d3kquc2
C:326-625
1g
d3kqud1
D:189-325
1h
d3kqud2
D:326-625
1i
d3kque1
E:189-325
1j
d3kque2
E:326-625
1k
d3kquf1
F:189-325
1l
d3kquf2
F:326-625
[
close SCOP info
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CATH Domains
(2, 18)
Info
all CATH domains
1a: CATH_3kquA01 (A:189-326)
1b: CATH_3kquA02 (A:327-430,A:452-483)
1c: CATH_3kquB02 (B:327-430,B:452-483)
1d: CATH_3kquC02 (C:327-430,C:452-483)
1e: CATH_3kquD02 (D:327-430,D:452-483)
1f: CATH_3kquE02 (E:327-430,E:452-483)
1g: CATH_3kquF02 (F:327-430,F:452-483)
1h: CATH_3kquB01 (B:189-326)
1i: CATH_3kquC01 (C:189-326)
1j: CATH_3kquD01 (D:189-326)
1k: CATH_3kquE01 (E:189-326)
1l: CATH_3kquF01 (F:189-326)
2a: CATH_3kquA03 (A:431-451,A:484-625)
2b: CATH_3kquB03 (B:431-451,B:484-625)
2c: CATH_3kquC03 (C:431-451,C:484-625)
2d: CATH_3kquD03 (D:431-451,D:484-625)
2e: CATH_3kquE03 (E:431-451,E:484-625)
2f: CATH_3kquF03 (F:431-451,F:484-625)
View:
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)
(
)
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Hcv (Hepatitis c virus)
(5)
1a
3kquA01
A:189-326
1b
3kquA02
A:327-430,A:452-483
1c
3kquB02
B:327-430,B:452-483
1d
3kquC02
C:327-430,C:452-483
1e
3kquD02
D:327-430,D:452-483
1f
3kquE02
E:327-430,E:452-483
1g
3kquF02
F:327-430,F:452-483
1h
3kquB01
B:189-326
1i
3kquC01
C:189-326
1j
3kquD01
D:189-326
1k
3kquE01
E:189-326
1l
3kquF01
F:189-326
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
RNA Helicase; Chain A, domain 3
(11)
Homologous Superfamily
:
RNA Helicase Chain A , domain 3
(11)
Hcv (Hepatitis c virus)
(5)
2a
3kquA03
A:431-451,A:484-625
2b
3kquB03
B:431-451,B:484-625
2c
3kquC03
C:431-451,C:484-625
2d
3kquD03
D:431-451,D:484-625
2e
3kquE03
E:431-451,E:484-625
2f
3kquF03
F:431-451,F:484-625
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Flavi_DEAD_3kquF01 (F:255-336)
1b: PFAM_Flavi_DEAD_3kquF02 (F:255-336)
1c: PFAM_Flavi_DEAD_3kquF03 (F:255-336)
1d: PFAM_Flavi_DEAD_3kquF04 (F:255-336)
1e: PFAM_Flavi_DEAD_3kquF05 (F:255-336)
1f: PFAM_Flavi_DEAD_3kquF06 (F:255-336)
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(
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)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
Flavi_DEAD
(27)
Hepatitis C virus genotype 1b (isolate Con1) (HCV)
(5)
1a
Flavi_DEAD-3kquF01
F:255-336
1b
Flavi_DEAD-3kquF02
F:255-336
1c
Flavi_DEAD-3kquF03
F:255-336
1d
Flavi_DEAD-3kquF04
F:255-336
1e
Flavi_DEAD-3kquF05
F:255-336
1f
Flavi_DEAD-3kquF06
F:255-336
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Asym.Unit (464 KB)
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