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Asym. Unit
Info
Asym.Unit (118 KB)
Biol.Unit 1 (59 KB)
Biol.Unit 2 (58 KB)
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(1)
Title
:
STRUCTURAL BASIS FOR E2-MEDIATED SUMO CONJUGATION REVEALED BY A COMPLEX BETWEEN UBIQUITIN CONJUGATING ENZYME UBC9 AND RANGAP1
Authors
:
V. Bernier-Villamor, D. A. Sampson, M. J. Matunis, C. D. Lima
Date
:
02 Jan 02 (Deposition) - 13 Feb 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Sumo, Ubiquitin, E2, Conjugating Enzyme, Ligase, Thioester, Small Ubiquitin-Like Modifier, Ligase/Protein Transport Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
V. Bernier-Villamor, D. A. Sampson, M. J. Matunis, C. D. Lima
Structural Basis For E2-Mediated Sumo Conjugation Revealed By A Complex Between Ubiquitin-Conjugating Enzyme Ubc9 And Rangap1.
Cell(Cambridge, Mass. ) V. 108 345 2002
(for further references see the
PDB file header
)
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
View:
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Label:
No.
Name
Count
Type
Full Name
1
SO4
4
Ligand/Ion
SULFATE ION
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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
SER D:536 , LEU D:537 , HIS D:538 , HOH D:681
BINDING SITE FOR RESIDUE SO4 D 601
2
AC2
SOFTWARE
GLY C:47 , LYS C:48 , LYS C:49 , GLN C:117 , HOH C:656 , HOH C:724
BINDING SITE FOR RESIDUE SO4 C 602
3
AC3
SOFTWARE
SER B:536 , LEU B:537 , HIS B:538
BINDING SITE FOR RESIDUE SO4 B 603
4
AC4
SOFTWARE
LYS B:502 , HOH B:660 , HOH B:683 , LYS D:502
BINDING SITE FOR RESIDUE SO4 B 604
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: UBIQUITIN_CONJUGAT_2 (A:7-146,C:7-146)
2: UBIQUITIN_CONJUGAT_1 (A:82-97,C:82-97)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UBIQUITIN_CONJUGAT_2
PS50127
Ubiquitin-conjugating enzymes family profile.
UBC9_HUMAN
7-146
2
A:7-146
C:7-146
2
UBIQUITIN_CONJUGAT_1
PS00183
Ubiquitin-conjugating enzymes active site.
UBC9_HUMAN
82-97
2
A:82-97
C:82-97
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Exons
(6, 12)
Info
All Exons
Exon 1.4b (A:1-22 | C:3-22)
Exon 1.5 (A:23-50 | C:23-50)
Exon 1.6a (A:51-75 | C:51-75)
Exon 1.7 (A:75-111 | C:75-111)
Exon 1.8a (A:112-138 | C:112-138)
Exon 1.9c (A:138-158 | C:138-158)
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All Exon Boundaries
1: Boundary 1.3c/1.4b
2: Boundary 1.4b/1.5
3: Boundary 1.5/1.6a
4: Boundary 1.6a/1.7
5: Boundary 1.7/1.8a
6: Boundary 1.8a/1.9c
7: Boundary 1.9c/-
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.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.2b
ENST00000397515
2b
ENSE00001529011
chr16:
1359636-1359774
139
UBC9_HUMAN
-
0
0
-
-
1.3c
ENST00000397515
3c
ENSE00001529008
chr16:
1362348-1362604
257
UBC9_HUMAN
-
0
0
-
-
1.4b
ENST00000397515
4b
ENSE00002200477
chr16:
1364021-1364097
77
UBC9_HUMAN
1-22
22
2
A:1-22
C:3-22
22
20
1.5
ENST00000397515
5
ENSE00000665751
chr16:
1364294-1364377
84
UBC9_HUMAN
23-50
28
2
A:23-50
C:23-50
28
28
1.6a
ENST00000397515
6a
ENSE00000873575
chr16:
1365655-1365727
73
UBC9_HUMAN
51-75
25
2
A:51-75
C:51-75
25
25
1.7
ENST00000397515
7
ENSE00000873577
chr16:
1370175-1370284
110
UBC9_HUMAN
75-111
37
2
A:75-111
C:75-111
37
37
1.8a
ENST00000397515
8a
ENSE00001287298
chr16:
1370439-1370518
80
UBC9_HUMAN
112-138
27
2
A:112-138
C:112-138
27
27
1.9c
ENST00000397515
9c
ENSE00001287274
chr16:
1374731-1377019
2289
UBC9_HUMAN
138-158
21
2
A:138-158
C:138-158
21
21
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SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1kpsb_ (B:)
1b: SCOP_d1kpsd_ (D:)
2a: SCOP_d1kpsa_ (A:)
2b: SCOP_d1kpsc_ (C:)
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Protein Domains
(
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(
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Organisms
(
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(
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Class
:
All alpha proteins
(14657)
Fold
:
alpha-alpha superhelix
(690)
Superfamily
:
Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain
(13)
Family
:
Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain
(13)
Protein domain
:
Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain
(10)
Mouse (Mus musculus) [TaxId: 10090]
(1)
1a
d1kpsb_
B:
1b
d1kpsd_
D:
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
UBC-like
(176)
Superfamily
:
UBC-like
(176)
Family
:
UBC-related
(135)
Protein domain
:
Ubiquitin conjugating enzyme, UBC
(84)
Human (Homo sapiens), ubc9 [TaxId: 9606]
(20)
2a
d1kpsa_
A:
2b
d1kpsc_
C:
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1kpsC00 (C:3-158)
1b: CATH_1kpsA00 (A:0-158)
2a: CATH_1kpsB00 (B:434-589)
2b: CATH_1kpsD00 (D:435-589)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin Conjugating Enzyme
(83)
Homologous Superfamily
:
Ubiquitin Conjugating Enzyme
(83)
Human (Homo sapiens)
(49)
1a
1kpsC00
C:3-158
1b
1kpsA00
A:0-158
Class
:
Mainly Alpha
(13335)
Architecture
:
Alpha Horseshoe
(399)
Topology
:
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
(320)
Homologous Superfamily
:
[code=1.25.40.200, no name defined]
(8)
Human (Homo sapiens)
(8)
2a
1kpsB00
B:434-589
2b
1kpsD00
D:435-589
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_UQ_con_1kpsC01 (C:8-152)
1b: PFAM_UQ_con_1kpsC02 (C:8-152)
2a: PFAM_RanGAP1_C_1kpsD01 (D:435-588)
2b: PFAM_RanGAP1_C_1kpsD02 (D:435-588)
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Clans
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(
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Families
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(
)
Organisms
(
)
(
)
Clan
:
UBC
(69)
Family
:
UQ_con
(55)
Homo sapiens (Human)
(36)
1a
UQ_con-1kpsC01
C:8-152
1b
UQ_con-1kpsC02
C:8-152
Clan
:
no clan defined [family: RanGAP1_C]
(2)
Family
:
RanGAP1_C
(2)
Mus musculus (Mouse)
(1)
2a
RanGAP1_C-1kpsD01
D:435-588
2b
RanGAP1_C-1kpsD02
D:435-588
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Asym.Unit (118 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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