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3II6
Asym. Unit
Info
Asym.Unit (231 KB)
Biol.Unit 1 (114 KB)
Biol.Unit 2 (114 KB)
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(1)
Title
:
STRUCTURE OF HUMAN XRCC4 IN COMPLEX WITH THE TANDEM BRCT DOMAINS OF DNA LIGASEIV.
Authors
:
S. Meesala, M. Junop
Date
:
31 Jul 09 (Deposition) - 11 Aug 09 (Release) - 11 Aug 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,X,Y
Biol. Unit 1: A,B,X (1x)
Biol. Unit 2: C,D,Y (1x)
Keywords
:
Xrcc4, Dna Ligase Iv, Nhej, Dna Repair, Brct, Alternative Splicing, Coiled Coil, Dna Damage, Dna Recombination, Isopeptide Bond, Nucleus, Phosphoprotein, Polymorphism, Ubl Conjugation, Atp-Binding, Cell Cycle, Cell Division, Disease Mutation, Dna Replication, Ligase, Magnesium, Metal-Binding, Nucleotide-Binding, Scid, Ligase/Dna Binding Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Y. Wu, P. Frit, S. Meesala, S. Dauvillier, M. Modesti, S. N. Andres, Y. Huang, J. Sekiguchi, P. Calsou, B. Salles, M. S. Junop
Structural And Functional Interaction Between The Human Dna Repair Proteins Dna Ligase Iv And Xrcc4
Mol. Cell. Biol. V. 11 3163 2009
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
2
Ligand/Ion
CHLORIDE ION
[
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY Y:669 , LYS Y:675
BINDING SITE FOR RESIDUE CL Y 301
2
AC2
SOFTWARE
TRP Y:738
BINDING SITE FOR RESIDUE CL Y 302
[
close Site info
]
SAPs(SNPs)/Variants
(6, 20)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_022310 (S12C, chain A/B/C/D, )
2: VAR_022311 (A56T, chain A/B/C/D, )
3: VAR_022312 (T134T, chain A/B/C/D, )
4: VAR_022313 (E142Q, chain A/B/C/D, )
5: VAR_016772 (I658V, chain X/Y, )
6: VAR_016773 (A857T, chain X/Y, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_022310
S
12
C
XRCC4_HUMAN
Polymorphism
28383138
A/B/C/D
S
12
C
2
UniProt
VAR_022311
A
56
T
XRCC4_HUMAN
Polymorphism
28383151
A/B/C/D
A
56
T
3
UniProt
VAR_022312
I
134
T
XRCC4_HUMAN
Polymorphism
28360135
A/B/C/D
T
134
T
4
UniProt
VAR_022313
E
142
Q
XRCC4_HUMAN
Polymorphism
28360136
A/B/C/D
E
142
Q
5
UniProt
VAR_016772
I
658
V
DNLI4_HUMAN
Polymorphism
2232641
X/Y
I
658
V
6
UniProt
VAR_016773
A
857
T
DNLI4_HUMAN
Polymorphism
2232642
X/Y
A
857
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: BRCT (X:654-743,Y:654-743|X:808-911,Y:80...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BRCT
PS50172
BRCT domain profile.
DNLI4_HUMAN
654-743
808-911
4
X:654-743
Y:654-743
X:808-911
Y:808-911
[
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Exons
(5, 18)
Info
All Exons
Exon 1.2b (A:1-47 | B:1-47 | C:1-47 | D:1-47)
Exon 1.3a (A:47-105 | B:47-105 (gaps) | C:47-...)
Exon 1.4 (A:106-161 | B:106-161 | C:106-161 ...)
Exon 1.5 (A:161-201 | B:161-201 | C:161-201 ...)
Exon 2.4b (X:654-911 (gaps) | Y:654-911)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1b/1.2b
2: Boundary 1.2b/1.3a
3: Boundary 1.3a/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6
6: Boundary 2.3/2.4b
7: Boundary 2.4b/-
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
ENST00000338635
1b
ENSE00001556292
chr5:
82373346-82373434
89
XRCC4_HUMAN
-
0
0
-
-
1.2b
ENST00000338635
2b
ENSE00002174590
chr5:
82400729-82400877
149
XRCC4_HUMAN
1-47
47
4
A:1-47
B:1-47
C:1-47
D:1-47
47
47
47
47
1.3a
ENST00000338635
3a
ENSE00000971597
chr5:
82406847-82407022
176
XRCC4_HUMAN
47-105
59
4
A:47-105
B:47-105 (gaps)
C:47-105
D:47-105 (gaps)
59
59
59
59
1.4
ENST00000338635
4
ENSE00001005114
chr5:
82491589-82491755
167
XRCC4_HUMAN
106-161
56
4
A:106-161
B:106-161
C:106-161
D:106-161
56
56
56
56
1.5
ENST00000338635
5
ENSE00001005109
chr5:
82499371-82499526
156
XRCC4_HUMAN
161-213
53
4
A:161-201
B:161-201
C:161-201
D:161-201
41
41
41
41
1.6
ENST00000338635
6
ENSE00001005110
chr5:
82500634-82500740
107
XRCC4_HUMAN
213-249
37
0
-
-
1.7a
ENST00000338635
7a
ENSE00001005113
chr5:
82554349-82554496
148
XRCC4_HUMAN
249-298
50
0
-
-
1.8a
ENST00000338635
8a
ENSE00001932573
chr5:
82648944-82649530
587
XRCC4_HUMAN
298-336
39
0
-
-
2.3
ENST00000356922
3
ENSE00001263649
chr13:
108867130-108866886
245
DNLI4_HUMAN
-
0
0
-
-
2.4b
ENST00000356922
4b
ENSE00001930844
chr13:
108863644-108860565
3080
DNLI4_HUMAN
1-921
921
2
X:654-911 (gaps)
Y:654-911
258
258
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d3ii6a1 (A:1-117)
1b: SCOP_d3ii6b1 (B:1-117)
1c: SCOP_d3ii6c1 (C:1-117)
1d: SCOP_d3ii6d1 (D:1-117)
2a: SCOP_d3ii6a2 (A:118-201)
2b: SCOP_d3ii6b2 (B:118-201)
2c: SCOP_d3ii6c2 (C:118-201)
2d: SCOP_d3ii6d2 (D:118-201)
View:
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Classes
(
)
(
)
Folds
(
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(
)
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
XRCC4, N-terminal domain
(3)
Superfamily
:
XRCC4, N-terminal domain
(3)
Family
:
XRCC4, N-terminal domain
(3)
Protein domain
:
XRCC4, N-terminal domain
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d3ii6a1
A:1-117
1b
d3ii6b1
B:1-117
1c
d3ii6c1
C:1-117
1d
d3ii6d1
D:1-117
Class
:
Coiled coil proteins
(689)
Fold
:
Parallel coiled-coil
(407)
Superfamily
:
XRCC4, C-terminal oligomerization domain
(3)
Family
:
XRCC4, C-terminal oligomerization domain
(3)
Protein domain
:
XRCC4, C-terminal oligomerization domain
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
2a
d3ii6a2
A:118-201
2b
d3ii6b2
B:118-201
2c
d3ii6c2
C:118-201
2d
d3ii6d2
D:118-201
[
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]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_3ii6A02 (A:119-176)
1b: CATH_3ii6B02 (B:119-176)
1c: CATH_3ii6C02 (C:119-176)
1d: CATH_3ii6D02 (D:119-176)
2a: CATH_3ii6A01 (A:1-118)
2b: CATH_3ii6C01 (C:1-118)
2c: CATH_3ii6B01 (B:1-118)
2d: CATH_3ii6D01 (D:1-118)
View:
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(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
[code=1.20.5.370, no name defined]
(3)
Human (Homo sapiens)
(3)
1a
3ii6A02
A:119-176
1b
3ii6B02
B:119-176
1c
3ii6C02
C:119-176
1d
3ii6D02
D:119-176
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
Dna Repair Protein Xrcc4; Chain: A, domain 1
(5)
Homologous Superfamily
:
[code=2.170.210.10, no name defined]
(5)
Human (Homo sapiens)
(5)
2a
3ii6A01
A:1-118
2b
3ii6C01
C:1-118
2c
3ii6B01
B:1-118
2d
3ii6D01
D:1-118
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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