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3DQV
Asym. Unit
Info
Asym.Unit (189 KB)
Biol.Unit 1 (93 KB)
Biol.Unit 2 (91 KB)
Biol.Unit 3 (180 KB)
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(1)
Title
:
STRUCTURAL INSIGHTS INTO NEDD8 ACTIVATION OF CULLIN-RING LIGASES: CONFORMATIONAL CONTROL OF CONJUGATION
Authors
:
D. M. Duda, L. A. Borg, D. C. Scott, H. W. Hunt, M. Hammel, B. A. Schulman
Date
:
09 Jul 08 (Deposition) - 30 Sep 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,R,Y
Biol. Unit 1: A,C,R (1x)
Biol. Unit 2: B,D,Y (1x)
Biol. Unit 3: A,B,C,D,R,Y (1x)
Keywords
:
Ubiquitin, Nedd8, Scf, Cullin-Ring Ligase, Cullin, Nucleus, Ubl Conjugation Pathway, Host-Virus Interaction, Receptor, Ubl Conjugation, Acetylation, Cytoplasm, Dna Damage, Dna Repair, Metal-Binding, Zinc, Zinc-Finger, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. M. Duda, L. A. Borg, D. C. Scott, H. W. Hunt, M. Hammel, B. A. Schulman
Structural Insights Into Nedd8 Activation Of Cullin-Ring Ligases: Conformational Control Of Conjugation.
Cell(Cambridge, Mass. ) V. 134 995 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 40)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1aa: SELENOMETHIONINE (MSEaa)
1ab: SELENOMETHIONINE (MSEab)
1ac: SELENOMETHIONINE (MSEac)
1ad: SELENOMETHIONINE (MSEad)
1ae: SELENOMETHIONINE (MSEae)
1af: SELENOMETHIONINE (MSEaf)
1ag: SELENOMETHIONINE (MSEag)
1ah: SELENOMETHIONINE (MSEah)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
1i: SELENOMETHIONINE (MSEi)
1j: SELENOMETHIONINE (MSEj)
1k: SELENOMETHIONINE (MSEk)
1l: SELENOMETHIONINE (MSEl)
1m: SELENOMETHIONINE (MSEm)
1n: SELENOMETHIONINE (MSEn)
1o: SELENOMETHIONINE (MSEo)
1p: SELENOMETHIONINE (MSEp)
1q: SELENOMETHIONINE (MSEq)
1r: SELENOMETHIONINE (MSEr)
1s: SELENOMETHIONINE (MSEs)
1t: SELENOMETHIONINE (MSEt)
1u: SELENOMETHIONINE (MSEu)
1v: SELENOMETHIONINE (MSEv)
1w: SELENOMETHIONINE (MSEw)
1x: SELENOMETHIONINE (MSEx)
1y: SELENOMETHIONINE (MSEy)
1z: SELENOMETHIONINE (MSEz)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
34
Mod. Amino Acid
SELENOMETHIONINE
2
ZN
6
Ligand/Ion
ZINC ION
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS R:53 , CYS R:56 , CYS R:68 , HIS R:82
BINDING SITE FOR RESIDUE ZN R 4004
2
AC2
SOFTWARE
CYS R:42 , CYS R:45 , HIS R:80 , CYS R:83
BINDING SITE FOR RESIDUE ZN R 4005
3
AC3
SOFTWARE
CYS R:75 , HIS R:77 , CYS R:94 , ASP R:97
BINDING SITE FOR RESIDUE ZN R 4006
4
AC4
SOFTWARE
CYS Y:75 , HIS Y:77 , ASP Y:97
BINDING SITE FOR RESIDUE ZN Y 4001
5
AC5
SOFTWARE
CYS Y:42 , CYS Y:45 , HIS Y:80 , CYS Y:83
BINDING SITE FOR RESIDUE ZN Y 4002
6
AC6
SOFTWARE
CYS Y:53 , CYS Y:56 , CYS Y:68 , HIS Y:82
BINDING SITE FOR RESIDUE ZN Y 4003
[
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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
(5, 10)
Info
All PROSITE Patterns/Profiles
1: UBIQUITIN_2 (A:101-176,B:101-176)
2: UBIQUITIN_1 (A:127-152,B:127-152)
3: ZF_RING_2 (R:53-98,Y:53-98)
4: CULLIN_2 (C:1403-1638,D:1403-1638)
5: CULLIN_1 (C:1753-1780,D:1753-1780)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UBIQUITIN_2
PS50053
Ubiquitin domain profile.
NEDD8_HUMAN
1-76
2
A:101-176
B:101-176
2
UBIQUITIN_1
PS00299
Ubiquitin domain signature.
NEDD8_HUMAN
27-52
2
A:127-152
B:127-152
3
ZF_RING_2
PS50089
Zinc finger RING-type profile.
RBX1_HUMAN
53-98
2
R:53-98
Y:53-98
4
CULLIN_2
PS50069
Cullin family profile.
CUL5_HUMAN
403-638
2
C:1403-1638
D:1403-1638
5
CULLIN_1
PS01256
Cullin family signature.
CUL5_HUMAN
753-780
2
C:1753-1780
D:1753-1780
[
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]
Exons
(9, 18)
Info
All Exons
Exon 1.1b (R:20-26 | Y:19-26)
Exon 1.2 (R:27-53 | Y:27-53 (gaps))
Exon 1.3a (R:53-76 | Y:53-76)
Exon 1.4b (R:77-105 | Y:77-105)
Exon 1.5b (R:105-105 | Y:105-105)
Exon 2.1a (A:101-106 | B:101-106)
Exon 2.4 (A:107-122 | B:107-122)
Exon 2.5a (A:123-150 | B:123-150)
Exon 2.6e (A:150-176 | B:150-176)
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/2.4
09: Boundary 2.4/2.5a
10: Boundary 2.5a/2.6e
11: Boundary 2.6e/-
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
2
R:20-26
Y:19-26
7
8
1.2
ENST00000216225
2
ENSE00000654972
chr22:
41349559-41349637
79
RBX1_HUMAN
27-53
27
2
R:27-53
Y:27-53 (gaps)
27
27
1.3a
ENST00000216225
3a
ENSE00000654975
chr22:
41360051-41360121
71
RBX1_HUMAN
53-76
24
2
R:53-76
Y:53-76
24
24
1.4b
ENST00000216225
4b
ENSE00000654978
chr22:
41363803-41363888
86
RBX1_HUMAN
77-105
29
2
R:77-105
Y:77-105
29
29
1.5b
ENST00000216225
5b
ENSE00001814441
chr22:
41368480-41369313
834
RBX1_HUMAN
105-108
4
2
R:105-105
Y:105-105
1
1
2.1a
ENST00000250495
1a
ENSE00001101093
chr14:
24701660-24701456
205
NEDD8_HUMAN
1-6
6
2
A:101-106
B:101-106
6
6
2.4
ENST00000250495
4
ENSE00002175755
chr14:
24687637-24687590
48
NEDD8_HUMAN
7-22
16
2
A:107-122
B:107-122
16
16
2.5a
ENST00000250495
5a
ENSE00002178617
chr14:
24687421-24687339
83
NEDD8_HUMAN
23-50
28
2
A:123-150
B:123-150
28
28
2.6e
ENST00000250495
6e
ENSE00001549615
chr14:
24686429-24686058
372
NEDD8_HUMAN
50-81
32
2
A:150-176
B:150-176
27
27
[
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]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3dqva_ (A:)
1b: SCOP_d3dqvb_ (B:)
2a: SCOP_d3dqvr_ (R:)
2b: SCOP_d3dqvy_ (Y:)
View:
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(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
Ubiquitin-like
(546)
Family
:
Ubiquitin-related
(337)
Protein domain
:
Nedd8
(14)
Human (Homo sapiens) [TaxId: 9606]
(14)
1a
d3dqva_
A:
1b
d3dqvb_
B:
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)
2a
d3dqvr_
R:
2b
d3dqvy_
Y:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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