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2P9K
Asym. Unit
Info
Asym.Unit (298 KB)
Biol.Unit 1 (291 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BOVINE ARP2/3 COMPLEX CO-CRYSTALLIZED WITH ATP AND CROSSLINKED WITH GLUTARALDEHYDE
Authors
:
B. J. Nolen, T. D. Pollard
Date
:
26 Mar 07 (Deposition) - 29 May 07 (Release) - 24 Mar 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.59
Chains
:
Asym. Unit : A,B,C,D,E,F,G
Biol. Unit 1: A,B,C,D,E,F,G (1x)
Keywords
:
Complex, Actin, Wd Repeat, Structural Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. J. Nolen, T. D. Pollard
Insights Into The Influence Of Nucleotides On Actin Family Proteins From Seven Structures Of Arp2/3 Complex.
Mol. Cell V. 26 449 2007
(for further references see the
PDB file header
)
[
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]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
2
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
CA
2
Ligand/Ion
CALCIUM ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ATP B:602
BINDING SITE FOR RESIDUE CA B 501
2
AC2
SOFTWARE
ATP A:601 , HOH A:619 , HOH A:620
BINDING SITE FOR RESIDUE CA A 500
3
AC3
SOFTWARE
GLY A:13 , THR A:14 , GLY A:15 , TYR A:16 , LYS A:18 , GLY A:171 , ASP A:172 , GLY A:173 , GLY A:197 , LYS A:225 , LYS A:228 , GLU A:229 , GLY A:323 , GLY A:324 , SER A:325 , MET A:327 , PHE A:328 , CA A:500 , HOH A:602 , HOH A:616 , HOH A:621 , HOH A:624
BINDING SITE FOR RESIDUE ATP A 601
4
AC4
SOFTWARE
GLY B:14 , THR B:15 , GLY B:16 , PHE B:17 , LYS B:19 , GLY B:160 , ASP B:161 , GLY B:162 , GLY B:186 , ARG B:214 , LYS B:217 , GLU B:218 , GLY B:305 , GLY B:306 , SER B:307 , MET B:309 , TYR B:310 , CA B:501 , HOH B:606 , HOH B:607 , HOH B:612 , HOH B:620
BINDING SITE FOR RESIDUE ATP B 602
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: ACTINS_ACT_LIKE (B:108-120,A:111-123)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ACTINS_ACT_LIKE
PS01132
Actins and actin-related proteins signature.
ARP2_BOVIN
108-120
1
B:108-120
ARP3_BOVIN
111-123
1
A:111-123
[
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Exons
(21, 21)
Info
All Exons
Exon 1.1 (E:2-2)
Exon 1.2 (E:3-36)
Exon 1.3 (E:36-61)
Exon 1.4 (E:62-84)
Exon 1.5 (E:85-127)
Exon 1.6 (E:127-158)
Exon 1.7 (E:159-175)
Exon 2.2 (F:2-41)
Exon 2.3 (F:41-78)
Exon 2.4 (F:79-110)
Exon 2.5 (F:111-167)
Exon 2.6 (F:168-168)
Exon 3.2 (D:1-25)
Exon 3.3 (D:25-37)
Exon 3.4 (D:37-74)
Exon 3.5 (D:75-90)
Exon 3.6 (D:90-152)
Exon 3.7 (D:152-183)
Exon 3.8 (D:184-226 (gaps))
Exon 3.9 (D:226-259)
Exon 3.10 (D:260-282)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/-
09: Boundary 2.1/2.2
10: Boundary 2.2/2.3
11: Boundary 2.3/2.4
12: Boundary 2.4/2.5
13: Boundary 2.5/2.6
14: Boundary 2.6/-
15: Boundary 3.1/3.2
16: Boundary 3.2/3.3
17: Boundary 3.3/3.4
18: Boundary 3.4/3.5
19: Boundary 3.5/3.6
20: Boundary 3.6/3.7
21: Boundary 3.7/3.8
22: Boundary 3.8/3.9
23: Boundary 3.9/3.10
24: Boundary 3.10/3.11
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
1.1
ENSBTAT00000007028
1
ENSBTAE00000241202
chr17:
57102599-57102554
46
ARPC3_BOVIN
1-2
2
1
E:2-2
1
1.2
ENSBTAT00000007028
2
ENSBTAE00000056315
chr17:
57099957-57099858
100
ARPC3_BOVIN
3-36
34
1
E:3-36
34
1.3
ENSBTAT00000007028
3
ENSBTAE00000056318
chr17:
57097356-57097280
77
ARPC3_BOVIN
36-61
26
1
E:36-61
26
1.4
ENSBTAT00000007028
4
ENSBTAE00000056321
chr17:
57094013-57093945
69
ARPC3_BOVIN
62-84
23
1
E:62-84
23
1.5
ENSBTAT00000007028
5
ENSBTAE00000056324
chr17:
57093166-57093040
127
ARPC3_BOVIN
85-127
43
1
E:85-127
43
1.6
ENSBTAT00000007028
6
ENSBTAE00000056327
chr17:
57092682-57092588
95
ARPC3_BOVIN
127-158
32
1
E:127-158
32
1.7
ENSBTAT00000007028
7
ENSBTAE00000241201
chr17:
57092098-57091788
311
ARPC3_BOVIN
159-178
20
1
E:159-175
17
2.1
ENSBTAT00000010469
1
ENSBTAE00000356147
chr22:
17348655-17348634
22
ARPC4_BOVIN
1-1
1
0
-
-
2.2
ENSBTAT00000010469
2
ENSBTAE00000085160
chr22:
17346149-17346031
119
ARPC4_BOVIN
2-41
40
1
F:2-41
40
2.3
ENSBTAT00000010469
3
ENSBTAE00000085162
chr22:
17344816-17344705
112
ARPC4_BOVIN
41-78
38
1
F:41-78
38
2.4
ENSBTAT00000010469
4
ENSBTAE00000085166
chr22:
17343409-17343314
96
ARPC4_BOVIN
79-110
32
1
F:79-110
32
2.5
ENSBTAT00000010469
5
ENSBTAE00000085168
chr22:
17342368-17342198
171
ARPC4_BOVIN
111-167
57
1
F:111-167
57
2.6
ENSBTAT00000010469
6
ENSBTAE00000356140
chr22:
17339867-17339499
369
ARPC4_BOVIN
168-168
1
1
F:168-168
1
3.1
ENSBTAT00000013707
1
ENSBTAE00000297026
chr2:
110657742-110657775
34
ARPC2_BOVIN
-
0
0
-
-
3.2
ENSBTAT00000013707
2
ENSBTAE00000111802
chr2:
110657989-110658070
82
ARPC2_BOVIN
1-25
25
1
D:1-25
25
3.3
ENSBTAT00000013707
3
ENSBTAE00000111805
chr2:
110666097-110666131
35
ARPC2_BOVIN
25-37
13
1
D:25-37
13
3.4
ENSBTAT00000013707
4
ENSBTAE00000111808
chr2:
110667349-110667461
113
ARPC2_BOVIN
37-74
38
1
D:37-74
38
3.5
ENSBTAT00000013707
5
ENSBTAE00000111810
chr2:
110671447-110671492
46
ARPC2_BOVIN
75-90
16
1
D:75-90
16
3.6
ENSBTAT00000013707
6
ENSBTAE00000111812
chr2:
110673846-110674032
187
ARPC2_BOVIN
90-152
63
1
D:90-152
63
3.7
ENSBTAT00000013707
7
ENSBTAE00000111814
chr2:
110674626-110674719
94
ARPC2_BOVIN
152-183
32
1
D:152-183
32
3.8
ENSBTAT00000013707
8
ENSBTAE00000111816
chr2:
110680171-110680297
127
ARPC2_BOVIN
184-226
43
1
D:184-226 (gaps)
43
3.9
ENSBTAT00000013707
9
ENSBTAE00000111818
chr2:
110681805-110681905
101
ARPC2_BOVIN
226-259
34
1
D:226-259
34
3.10
ENSBTAT00000013707
10
ENSBTAE00000111819
chr2:
110682214-110682314
101
ARPC2_BOVIN
260-293
34
1
D:260-282
23
3.11
ENSBTAT00000013707
11
ENSBTAE00000111821
chr2:
110684909-110685359
451
ARPC2_BOVIN
293-300
8
0
-
-
[
close EXON info
]
SCOP Domains
(6, 8)
Info
All SCOP Domains
1a: SCOP_d2p9kg_ (G:)
2a: SCOP_d2p9ke_ (E:)
3a: SCOP_d2p9kc_ (C:)
4a: SCOP_d2p9kd1 (D:1-120)
4b: SCOP_d2p9kd2 (D:121-282)
5a: SCOP_d2p9kf_ (F:)
6a: SCOP_d2p9ka1 (A:3-160)
6b: SCOP_d2p9ka2 (A:161-413)
View:
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Classes
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)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
alpha-alpha superhelix
(690)
Superfamily
:
Arp2/3 complex 16 kDa subunit ARPC5
(17)
Family
:
Arp2/3 complex 16 kDa subunit ARPC5
(17)
Protein domain
:
automated matches
(14)
Cow (Bos taurus) [TaxId: 9913]
(14)
1a
d2p9kg_
G:
Fold
:
Arp2/3 complex 21 kDa subunit ARPC3
(17)
Superfamily
:
Arp2/3 complex 21 kDa subunit ARPC3
(17)
Family
:
Arp2/3 complex 21 kDa subunit ARPC3
(17)
Protein domain
:
automated matches
(12)
Cow (Bos taurus) [TaxId: 9913]
(12)
2a
d2p9ke_
E:
Class
:
All beta proteins
(24004)
Fold
:
7-bladed beta-propeller
(245)
Superfamily
:
WD40 repeat-like
(95)
Family
:
WD40-repeat
(53)
Protein domain
:
automated matches
(14)
Cow (Bos taurus) [TaxId: 9913]
(14)
3a
d2p9kc_
C:
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Secretion chaperone-like
(60)
Superfamily
:
Arp2/3 complex subunits
(34)
Family
:
Arp2/3 complex subunits
(34)
Protein domain
:
ARPC2 (34 kDa subunit)
(16)
Cow (Bos taurus) [TaxId: 9913]
(16)
4a
d2p9kd1
D:1-120
4b
d2p9kd2
D:121-282
Protein domain
:
ARPC4 (20 kDa subunit)
(17)
Cow (Bos taurus) [TaxId: 9913]
(17)
5a
d2p9kf_
F:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Actin-like ATPase domain
(426)
Family
:
Actin/HSP70
(199)
Protein domain
:
Actin-related protein 3, Arp3
(16)
Cow (Bos taurus) [TaxId: 9913]
(16)
6a
d2p9ka1
A:3-160
6b
d2p9ka2
A:161-413
[
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]
CATH Domains
(6, 9)
Info
all CATH domains
1a: CATH_2p9kA01 (A:3-144,A:377-411)
1b: CATH_2p9kA02 (A:145-194,A:294-376)
2a: CATH_2p9kD02 (D:133-282)
2b: CATH_2p9kD01 (D:1-131)
2c: CATH_2p9kF00 (F:2-168)
3a: CATH_2p9kA03 (A:195-293)
4a: CATH_2p9kG00 (G:9-151)
5a: CATH_2p9kE00 (E:2-175)
6a: CATH_2p9kC00 (C:2-372)
View:
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)
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)
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(
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.40, no name defined]
(217)
Cattle (Bos taurus)
(47)
1a
2p9kA01
A:3-144,A:377-411
1b
2p9kA02
A:145-194,A:294-376
Topology
:
Yope Regulator; Chain: A,
(26)
Homologous Superfamily
:
[code=3.30.1460.20, no name defined]
(13)
Cattle (Bos taurus)
(10)
2a
2p9kD02
D:133-282
2b
2p9kD01
D:1-131
2c
2p9kF00
F:2-168
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Actin; Chain A, domain 4
(156)
Homologous Superfamily
:
Actin; Chain A, domain 4
(155)
Cattle (Bos taurus)
(47)
3a
2p9kA03
A:195-293
Class
:
Mainly Alpha
(13335)
Architecture
:
Alpha Horseshoe
(399)
Topology
:
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
(320)
Homologous Superfamily
:
[code=1.25.40.190, no name defined]
(12)
Cattle (Bos taurus)
(10)
4a
2p9kG00
G:9-151
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arp2/3 complex 21 kDa subunit ARPC3
(12)
Homologous Superfamily
:
Arp2/3 complex 21 kDa subunit ARPC3
(12)
Cattle (Bos taurus)
(10)
5a
2p9kE00
E:2-175
Class
:
Mainly Beta
(13760)
Architecture
:
7 Propellor
(136)
Topology
:
Methylamine Dehydrogenase; Chain H
(136)
Homologous Superfamily
:
YVTN repeat-like/Quinoprotein amine dehydrogenase
(76)
Cattle (Bos taurus)
(18)
6a
2p9kC00
C:2-372
[
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]
Pfam Domains
(6, 8)
Info
all PFAM domains
1a: PFAM_Actin_2p9kB01 (B:9-364)
1b: PFAM_Actin_2p9kA01 (A:3-412)
2a: PFAM_WD40_2p9kC01 (C:132-170)
2b: PFAM_WD40_2p9kC02 (C:132-170)
3a: PFAM_ARPC4_2p9kF01 (F:2-168)
4a: PFAM_P16_Arc_2p9kG01 (G:9-151)
5a: PFAM_P21_Arc_2p9kE01 (E:2-173)
6a: PFAM_P34_Arc_2p9kD01 (D:56-282)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Actin_ATPase
(173)
Family
:
Actin
(70)
Bos taurus (Bovine)
(11)
1a
Actin-2p9kB01
B:9-364
1b
Actin-2p9kA01
A:3-412
Clan
:
Beta_propeller
(192)
Family
:
WD40
(64)
Bos taurus (Bovine)
(19)
2a
WD40-2p9kC01
C:132-170
2b
WD40-2p9kC02
C:132-170
Clan
:
no clan defined [family: ARPC4]
(10)
Family
:
ARPC4
(10)
Bos taurus (Bovine)
(10)
3a
ARPC4-2p9kF01
F:2-168
Clan
:
no clan defined [family: P16-Arc]
(10)
Family
:
P16-Arc
(10)
Bos taurus (Bovine)
(10)
4a
P16-Arc-2p9kG01
G:9-151
Clan
:
no clan defined [family: P21-Arc]
(10)
Family
:
P21-Arc
(10)
Bos taurus (Bovine)
(10)
5a
P21-Arc-2p9kE01
E:2-173
Clan
:
no clan defined [family: P34-Arc]
(10)
Family
:
P34-Arc
(10)
Bos taurus (Bovine)
(10)
6a
P34-Arc-2p9kD01
D:56-282
[
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