PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2HYE
Asym. Unit
Info
Asym.Unit (329 KB)
Biol.Unit 1 (319 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF THE DDB1-CUL4A-RBX1-SV5V COMPLEX
Authors
:
S. Angers, T. Li, X. Yi, M. J. Maccoss, R. T. Moon, N. Zheng
Date
:
05 Aug 06 (Deposition) - 03 Oct 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Beta Propeller, Ring Finger, Zinc Finger, Propeller Cluster, Helical Repeats, Cullin Repeats, Protein Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Angers, T. Li, X. Yi, M. J. Maccoss, R. T. Moon, N. Zheng
Molecular Architecture And Assembly Of The Ddb1-Cul4A Ubiquitin Ligase Machinery.
Nature V. 443 590 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 5)
Info
All Hetero Components
1a: ZINC ION (ZNa)
1b: ZINC ION (ZNb)
1c: ZINC ION (ZNc)
1d: ZINC ION (ZNd)
1e: ZINC ION (ZNe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ZN
5
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS B:194 , CYS B:206 , CYS B:208 , CYS B:211
BINDING SITE FOR RESIDUE ZN B 3001
2
AC2
SOFTWARE
HIS B:171 , CYS B:190 , CYS B:215 , CYS B:218
BINDING SITE FOR RESIDUE ZN B 3002
3
AC3
SOFTWARE
CYS D:42 , CYS D:45 , HIS D:80 , CYS D:83
BINDING SITE FOR RESIDUE ZN D 4001
4
AC4
SOFTWARE
CYS D:53 , CYS D:56 , CYS D:68 , HIS D:82
BINDING SITE FOR RESIDUE ZN D 4003
5
AC5
SOFTWARE
CYS D:75 , HIS D:77 , CYS D:94 , ASP D:97
BINDING SITE FOR RESIDUE ZN D 4002
[
close Site info
]
SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_023074 (L427F, chain A, )
2: VAR_020341 (K644R, chain C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_023074
L
427
F
DDB1_HUMAN
Polymorphism
28720299
A
L
427
F
2
UniProt
VAR_020341
K
644
R
CUL4A_HUMAN
Polymorphism
2302757
C
K
644
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: ZF_RING_2 (D:53-98)
2: CULLIN_2 (C:404-632)
3: CULLIN_1 (C:732-759)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ZF_RING_2
PS50089
Zinc finger RING-type profile.
RBX1_HUMAN
53-98
1
D:53-98
2
CULLIN_2
PS50069
Cullin family profile.
CUL4A_HUMAN
404-632
1
C:404-632
3
CULLIN_1
PS01256
Cullin family signature.
CUL4A_HUMAN
732-759
1
C:732-759
[
close PROSITE info
]
Exons
(52, 52)
Info
All Exons
Exon 1.1b (D:19-26)
Exon 1.2 (D:27-53)
Exon 1.3a (D:53-76)
Exon 1.4b (D:77-105)
Exon 1.5b (D:105-108)
Exon 2.1a (A:1-21)
Exon 2.2 (A:21-70)
Exon 2.3c (A:71-109)
Exon 2.4 (A:110-183)
Exon 2.5 (A:184-222)
Exon 2.6a (A:222-254)
Exon 2.7 (A:255-307)
Exon 2.8 (A:308-335)
Exon 2.9 (A:336-374)
Exon 2.10a (A:375-409)
Exon 2.11 (A:409-434)
Exon 2.12 (A:434-470)
Exon 2.13 (A:471-530)
Exon 2.14 (A:530-585)
Exon 2.15 (A:585-621)
Exon 2.16 (A:621-690)
Exon 2.17 (A:690-722)
Exon 2.18 (A:722-759)
Exon 2.19 (A:760-801)
Exon 2.20 (A:801-856)
Exon 2.21 (A:856-887)
Exon 2.22 (A:888-944)
Exon 2.23 (A:945-981)
Exon 2.24 (A:981-1038)
Exon 2.25 (A:1038-1072)
Exon 2.26 (A:1072-1113)
Exon 2.27b (A:1114-1140)
Exon 3.2a (C:41-50)
Exon 3.3d (C:50-88)
Exon 3.4a (C:89-123)
Exon 3.6b (C:123-146)
Exon 3.7 (C:147-171)
Exon 3.9 (C:171-225)
Exon 3.10 (C:226-255)
Exon 3.11 (C:256-283)
Exon 3.12b (C:283-306)
Exon 3.13 (C:306-345)
Exon 3.14 (C:346-410)
Exon 3.15b (C:410-445)
Exon 3.16 (C:445-482)
Exon 3.17 (C:482-510)
Exon 3.18 (C:511-546)
Exon 3.19 (C:547-584)
Exon 3.20b (C:585-620)
Exon 3.21 (C:620-677)
Exon 3.22 (C:678-728)
Exon 3.23b (C:729-759)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1b
02: Boundary 1.1b/1.2
03: Boundary 1.2/1.3a
04: Boundary 1.3a/1.4b
05: Boundary 1.4b/1.5b
06: Boundary 1.5b/-
07: Boundary -/2.1a
08: Boundary 2.1a/2.2
09: Boundary 2.2/2.3c
10: Boundary 2.3c/2.4
11: Boundary 2.4/2.5
12: Boundary 2.5/2.6a
13: Boundary 2.6a/2.7
14: Boundary 2.7/2.8
15: Boundary 2.8/2.9
16: Boundary 2.9/2.10a
17: Boundary 2.10a/2.11
18: Boundary 2.11/2.12
19: Boundary 2.12/2.13
20: Boundary 2.13/2.14
21: Boundary 2.14/2.15
22: Boundary 2.15/2.16
23: Boundary 2.16/2.17
24: Boundary 2.17/2.18
25: Boundary 2.18/2.19
26: Boundary 2.19/2.20
27: Boundary 2.20/2.21
28: Boundary 2.21/2.22
29: Boundary 2.22/2.23
30: Boundary 2.23/2.24
31: Boundary 2.24/2.25
32: Boundary 2.25/2.26
33: Boundary 2.26/2.27b
34: Boundary 2.27b/-
35: Boundary -/3.2a
36: Boundary 3.2a/3.3d
37: Boundary 3.3d/3.4a
38: Boundary 3.4a/3.6b
39: Boundary 3.6b/3.7
40: Boundary 3.7/3.9
41: Boundary 3.9/3.10
42: Boundary 3.10/3.11
43: Boundary 3.11/3.12b
44: Boundary 3.12b/3.13
45: Boundary 3.13/3.14
46: Boundary 3.14/3.15b
47: Boundary 3.15b/3.16
48: Boundary 3.16/3.17
49: Boundary 3.17/3.18
50: Boundary 3.18/3.19
51: Boundary 3.19/3.20b
52: Boundary 3.20b/3.21
53: Boundary 3.21/3.22
54: Boundary 3.22/3.23b
55: Boundary 3.23b/-
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
1.1b
ENST00000216225
1b
ENSE00000880432
chr22:
41347363-41347480
118
RBX1_HUMAN
1-26
26
1
D:19-26
8
1.2
ENST00000216225
2
ENSE00000654972
chr22:
41349559-41349637
79
RBX1_HUMAN
27-53
27
1
D:27-53
27
1.3a
ENST00000216225
3a
ENSE00000654975
chr22:
41360051-41360121
71
RBX1_HUMAN
53-76
24
1
D:53-76
24
1.4b
ENST00000216225
4b
ENSE00000654978
chr22:
41363803-41363888
86
RBX1_HUMAN
77-105
29
1
D:77-105
29
1.5b
ENST00000216225
5b
ENSE00001814441
chr22:
41368480-41369313
834
RBX1_HUMAN
105-108
4
1
D:105-108
4
2.1a
ENST00000301764
1a
ENSE00001766096
chr11:
61100666-61100380
287
DDB1_HUMAN
1-21
21
1
A:1-21
21
2.2
ENST00000301764
2
ENSE00001244589
chr11:
61099163-61099015
149
DDB1_HUMAN
21-70
50
1
A:21-70
50
2.3c
ENST00000301764
3c
ENSE00001244580
chr11:
61097546-61097430
117
DDB1_HUMAN
71-109
39
1
A:71-109
39
2.4
ENST00000301764
4
ENSE00001244572
chr11:
61097056-61096835
222
DDB1_HUMAN
110-183
74
1
A:110-183
74
2.5
ENST00000301764
5
ENSE00001119057
chr11:
61094365-61094251
115
DDB1_HUMAN
184-222
39
1
A:184-222
39
2.6a
ENST00000301764
6a
ENSE00001119056
chr11:
61093180-61093083
98
DDB1_HUMAN
222-254
33
1
A:222-254
33
2.7
ENST00000301764
7
ENSE00001119058
chr11:
61091609-61091451
159
DDB1_HUMAN
255-307
53
1
A:255-307
53
2.8
ENST00000301764
8
ENSE00001119055
chr11:
61090566-61090483
84
DDB1_HUMAN
308-335
28
1
A:308-335
28
2.9
ENST00000301764
9
ENSE00001119053
chr11:
61089884-61089768
117
DDB1_HUMAN
336-374
39
1
A:336-374
39
2.10a
ENST00000301764
10a
ENSE00001119059
chr11:
61089169-61089067
103
DDB1_HUMAN
375-409
35
1
A:375-409
35
2.11
ENST00000301764
11
ENSE00001145160
chr11:
61084039-61083964
76
DDB1_HUMAN
409-434
26
1
A:409-434
26
2.12
ENST00000301764
12
ENSE00001145157
chr11:
61083865-61083757
109
DDB1_HUMAN
434-470
37
1
A:434-470
37
2.13
ENST00000301764
13
ENSE00001198138
chr11:
61081958-61081780
179
DDB1_HUMAN
471-530
60
1
A:471-530
60
2.14
ENST00000301764
14
ENSE00001063042
chr11:
61081682-61081519
164
DDB1_HUMAN
530-585
56
1
A:530-585
56
2.15
ENST00000301764
15
ENSE00001063027
chr11:
61081441-61081334
108
DDB1_HUMAN
585-621
37
1
A:585-621
37
2.16
ENST00000301764
16
ENSE00001063028
chr11:
61081178-61080971
208
DDB1_HUMAN
621-690
70
1
A:621-690
70
2.17
ENST00000301764
17
ENSE00001145124
chr11:
61079556-61079461
96
DDB1_HUMAN
690-722
33
1
A:690-722
33
2.18
ENST00000301764
18
ENSE00001198106
chr11:
61079367-61079256
112
DDB1_HUMAN
722-759
38
1
A:722-759
38
2.19
ENST00000301764
19
ENSE00001063044
chr11:
61077890-61077767
124
DDB1_HUMAN
760-801
42
1
A:760-801
42
2.20
ENST00000301764
20
ENSE00001063040
chr11:
61077432-61077268
165
DDB1_HUMAN
801-856
56
1
A:801-856
56
2.21
ENST00000301764
21
ENSE00001063041
chr11:
61076549-61076455
95
DDB1_HUMAN
856-887
32
1
A:856-887
32
2.22
ENST00000301764
22
ENSE00001145096
chr11:
61071507-61071337
171
DDB1_HUMAN
888-944
57
1
A:888-944
57
2.23
ENST00000301764
23
ENSE00001145090
chr11:
61070627-61070518
110
DDB1_HUMAN
945-981
37
1
A:945-981
37
2.24
ENST00000301764
24
ENSE00001198074
chr11:
61070223-61070054
170
DDB1_HUMAN
981-1038
58
1
A:981-1038
58
2.25
ENST00000301764
25
ENSE00001506453
chr11:
61069831-61069729
103
DDB1_HUMAN
1038-1072
35
1
A:1038-1072
35
2.26
ENST00000301764
26
ENSE00001506452
chr11:
61068404-61068281
124
DDB1_HUMAN
1072-1113
42
1
A:1072-1113
42
2.27b
ENST00000301764
27b
ENSE00001798842
chr11:
61067691-61066920
772
DDB1_HUMAN
1114-1140
27
1
A:1114-1140
27
3.2a
ENST00000375440
2a
ENSE00001953061
chr13:
113863858-113864089
232
CUL4A_HUMAN
1-50
50
1
C:41-50
10
3.3d
ENST00000375440
3d
ENSE00001615761
chr13:
113864287-113864402
116
CUL4A_HUMAN
50-88
39
1
C:50-88
39
3.4a
ENST00000375440
4a
ENSE00001725141
chr13:
113873259-113873362
104
CUL4A_HUMAN
89-123
35
1
C:89-123
35
3.6b
ENST00000375440
6b
ENSE00001133644
chr13:
113882290-113882359
70
CUL4A_HUMAN
123-146
24
1
C:123-146
24
3.7
ENST00000375440
7
ENSE00000940402
chr13:
113883760-113883833
74
CUL4A_HUMAN
147-171
25
1
C:147-171
25
3.9
ENST00000375440
9
ENSE00001133507
chr13:
113887491-113887653
163
CUL4A_HUMAN
171-225
55
1
C:171-225
55
3.10
ENST00000375440
10
ENSE00000940404
chr13:
113888211-113888300
90
CUL4A_HUMAN
226-255
30
1
C:226-255
30
3.11
ENST00000375440
11
ENSE00000940405
chr13:
113889377-113889459
83
CUL4A_HUMAN
256-283
28
1
C:256-283
28
3.12b
ENST00000375440
12b
ENSE00001630009
chr13:
113891137-113891204
68
CUL4A_HUMAN
283-306
24
1
C:283-306
24
3.13
ENST00000375440
13
ENSE00001133496
chr13:
113893747-113893865
119
CUL4A_HUMAN
306-345
40
1
C:306-345
40
3.14
ENST00000375440
14
ENSE00000940408
chr13:
113897282-113897474
193
CUL4A_HUMAN
346-410
65
1
C:346-410
65
3.15b
ENST00000375440
15b
ENSE00001133490
chr13:
113898724-113898828
105
CUL4A_HUMAN
410-445
36
1
C:410-445
36
3.16
ENST00000375440
16
ENSE00001133483
chr13:
113899263-113899373
111
CUL4A_HUMAN
445-482
38
1
C:445-482
38
3.17
ENST00000375440
17
ENSE00001133476
chr13:
113899466-113899551
86
CUL4A_HUMAN
482-510
29
1
C:482-510
29
3.18
ENST00000375440
18
ENSE00000940412
chr13:
113900270-113900377
108
CUL4A_HUMAN
511-546
36
1
C:511-546
36
3.19
ENST00000375440
19
ENSE00000940413
chr13:
113907396-113907509
114
CUL4A_HUMAN
547-584
38
1
C:547-584
38
3.20b
ENST00000375440
20b
ENSE00000940414
chr13:
113909007-113909112
106
CUL4A_HUMAN
585-620
36
1
C:585-620
36
3.21
ENST00000375440
21
ENSE00001325525
chr13:
113909267-113909439
173
CUL4A_HUMAN
620-677
58
1
C:620-677
58
3.22
ENST00000375440
22
ENSE00001592368
chr13:
113914921-113915073
153
CUL4A_HUMAN
678-728
51
1
C:678-728
51
3.23b
ENST00000375440
23b
ENSE00001924609
chr13:
113917801-113917896
96
CUL4A_HUMAN
729-759
31
1
C:729-759
31
[
close EXON info
]
SCOP Domains
(5, 5)
Info
All SCOP Domains
1a: SCOP_d2hyec2 (C:55-401)
2a: SCOP_d2hyec1 (C:676-759)
3a: SCOP_d2hyeb_ (B:)
4a: SCOP_d2hyec3 (C:403-675)
5a: SCOP_d2hyed_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
alpha-alpha superhelix
(690)
Superfamily
:
Cullin repeat-like
(11)
Family
:
Cullin repeat
(4)
Protein domain
:
Cullin-4A
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d2hyec2
C:55-401
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
Winged helix DNA-binding domain
(576)
Family
:
SCF ubiquitin ligase complex WHB domain
(6)
Protein domain
:
Cullin-4A
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d2hyec1
C:676-759
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
SV5-V core-like
(2)
Superfamily
:
SV5-V core-like
(2)
Family
:
SV5-V core-like
(2)
Protein domain
:
SV5-V core
(2)
Simian virus 5 [TaxId: 11207]
(2)
3a
d2hyeb_
B:
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Cullin homology domain
(4)
Superfamily
:
Cullin homology domain
(4)
Family
:
Cullin homology domain
(4)
Protein domain
:
Cullin-4A
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
4a
d2hyec3
C:403-675
Class
:
Small proteins
(3458)
Fold
:
RING/U-box
(48)
Superfamily
:
RING/U-box
(48)
Family
:
RING finger domain, C3HC4
(23)
Protein domain
:
RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
(8)
Human (Homo sapiens) [TaxId: 9606]
(8)
5a
d2hyed_
D:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2hyeD00 (D:19-108)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Herpes Virus-1
(49)
Homologous Superfamily
:
Zinc/RING finger domain, C3HC4 (zinc finger)
(47)
Human (Homo sapiens)
(26)
1a
2hyeD00
D:19-108
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (329 KB)
Header - Asym.Unit
Biol.Unit 1 (319 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2HYE
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
