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Asym. Unit
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Asym.Unit (760 KB)
Biol.Unit 1 (256 KB)
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Title
:
CRYSTAL STRUCTURE OF THE HUMAN XRCC4-XLF COMPLEX
Authors
:
S. N. Andres, M. S. Junop
Date
:
09 May 11 (Deposition) - 07 Dec 11 (Release) - 29 Oct 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.94
Chains
:
Asym. Unit : A,B,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y
Biol. Unit 1: A,B,D,E,F,G,H,I (1x)
Keywords
:
Complex-Filament, Non-Homologous End-Joining, Dna And Protein Binding, Dna Binding Protein-Protein Binding Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. S. Andres, C. Wyman, M. Modesti, M. S. Junop
Structure Of Human Xlf-Xrcc4: Assembly Of A Functional Dna Repair Complex
To Be Published
[
close entry info
]
Hetero Components
(1, 8)
Info
All Hetero Components
1a: HEXATANTALUM DODECABROMIDE (TBRa)
1b: HEXATANTALUM DODECABROMIDE (TBRb)
1c: HEXATANTALUM DODECABROMIDE (TBRc)
1d: HEXATANTALUM DODECABROMIDE (TBRd)
1e: HEXATANTALUM DODECABROMIDE (TBRe)
1f: HEXATANTALUM DODECABROMIDE (TBRf)
1g: HEXATANTALUM DODECABROMIDE (TBRg)
1h: HEXATANTALUM DODECABROMIDE (TBRh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
TBR
8
Ligand/Ion
HEXATANTALUM DODECABROMIDE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS D:122
BINDING SITE FOR RESIDUE TBR D 231
2
AC2
SOFTWARE
HIS H:122
BINDING SITE FOR RESIDUE TBR H 231
3
AC3
SOFTWARE
GLU M:560 , HIS M:622
BINDING SITE FOR RESIDUE TBR M 164
4
AC4
SOFTWARE
MET J:1 , VAL J:33 , THR J:44 , GLU J:125 , ARG T:176
BINDING SITE FOR RESIDUE TBR J 164
5
AC5
SOFTWARE
TRP J:155 , LEU K:651 , LEU K:652 , ARG K:653 , ASP K:654 , TRP K:655 , ASN K:656 , ASP P:557
BINDING SITE FOR RESIDUE TBR P 2
6
AC6
SOFTWARE
ALA V:560
BINDING SITE FOR RESIDUE TBR V 1
7
AC7
SOFTWARE
ILE X:605 , ARG X:607 , HIS X:622
BINDING SITE FOR RESIDUE TBR X 5
8
AC8
SOFTWARE
TYR Y:629 , ASP Y:632
BINDING SITE FOR RESIDUE TBR Y 10
[
close Site info
]
SAPs(SNPs)/Variants
(8, 94)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_022310 (S512C, chain A/F/J/N/R/U/B/G/K/P/V/Y, )
2: VAR_038790 (A514T, chain D/H/L/O/S/T/E/I/M/Q/W/X, )
3: VAR_022311 (A556T, chain A/F/J/N/R/U/B/G/K/P/V/Y, )
4: VAR_025704 (R557G, chain D/H/L/O/S/T/E/I/M/Q/W/X, )
5: VAR_038791 (H589R, chain D/H/L/O/E/I/M/Q/W/X, )
6: VAR_025705 (C623R, chain D/H/L/O/S/T/E/I/M/Q/W/X, )
7: VAR_022312 (I634T, chain A/F/J/N/R/U/B/G/K/P/V/Y, )
8: VAR_022313 (E642Q, chain A/F/J/N/R/U/B/G/K/P/V/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/F/J/N/R/U
B/G/K/P/V/Y
S
12
512
C
2
UniProt
VAR_038790
A
14
T
NHEJ1_HUMAN
Polymorphism
34689457
D/H/L/O/S/T
E/I/M/Q/W/X
A
14
514
T
3
UniProt
VAR_022311
A
56
T
XRCC4_HUMAN
Polymorphism
28383151
A/F/J/N/R/U
B/G/K/P/V/Y
A
56
556
T
4
UniProt
VAR_025704
R
57
G
NHEJ1_HUMAN
Disease (NHEJ1-SCID)
---
D/H/L/O/S/T
E/I/M/Q/W/X
R
57
557
G
5
UniProt
VAR_038791
H
89
R
NHEJ1_HUMAN
Polymorphism
1056296
D/H/L/O
E/I/M/Q/W/X
H
89
589
R
6
UniProt
VAR_025705
C
123
R
NHEJ1_HUMAN
Disease (NHEJ1-SCID)
---
D/H/L/O/S/T
E/I/M/Q/W/X
C
123
623
R
7
UniProt
VAR_022312
I
134
T
XRCC4_HUMAN
Polymorphism
28360135
A/F/J/N/R/U
B/G/K/P/V/Y
I
134
634
T
8
UniProt
VAR_022313
E
142
Q
XRCC4_HUMAN
Polymorphism
28360136
A/F/J/N/R/U
B/G/K/P/V/Y
E
142
642
Q
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(8, 96)
Info
All Exons
Exon 1.2b (A:1-47 | B:501-547 | F:1-47 | G:50...)
Exon 1.3a (A:47-105 | B:547-605 (gaps) | F:47...)
Exon 1.4 (A:106-147 | B:606-657 | F:106-157 ...)
Exon 2.4b (D:1-59 | E:501-559 | H:1-59 | I:50...)
Exon 2.5a (D:60-130 | E:560-630 | H:60-130 | ...)
Exon 2.6 (D:131-177 | E:631-677 | H:131-177 ...)
Exon 2.7b (D:177-196 | E:677-696 | H:177-196 ...)
Exon 2.11b (D:197-227 | E:697-727 | H:197-227 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1b/1.2b
02: Boundary 1.2b/1.3a
03: Boundary 1.3a/1.4
04: Boundary 1.4/1.5
05: Boundary 2.1b/2.4b
06: Boundary 2.4b/2.5a
07: Boundary 2.5a/2.6
08: Boundary 2.6/2.7b
09: Boundary 2.7b/2.11b
10: Boundary 2.11b/2.12
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
12
A:1-47
B:501-547
F:1-47
G:501-547
J:1-47
K:501-547
N:1-47
P:501-547
R:1-47
U:1-47
V:501-547
Y:501-547
47
47
47
47
47
47
47
47
47
47
47
47
1.3a
ENST00000338635
3a
ENSE00000971597
chr5:
82406847-82407022
176
XRCC4_HUMAN
47-105
59
12
A:47-105
B:547-605 (gaps)
F:47-105
G:547-605
J:47-105
K:547-605
N:47-105
P:547-605
R:47-105
U:47-105
V:547-605
Y:547-605
59
59
59
59
59
59
59
59
59
59
59
59
1.4
ENST00000338635
4
ENSE00001005114
chr5:
82491589-82491755
167
XRCC4_HUMAN
106-161
56
12
A:106-147
B:606-657
F:106-157
G:606-657
J:106-157
K:606-657
N:106-157
P:606-657
R:106-157
U:106-157
V:606-657
Y:606-657
42
52
52
52
52
52
52
52
52
52
52
52
1.5
ENST00000338635
5
ENSE00001005109
chr5:
82499371-82499526
156
XRCC4_HUMAN
161-213
53
0
-
-
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
-
-
2.1b
ENST00000356853
1b
ENSE00001869065
chr2:
220025575-220025442
134
NHEJ1_HUMAN
-
0
0
-
-
2.4b
ENST00000356853
4b
ENSE00002167216
chr2:
220023084-220022908
177
NHEJ1_HUMAN
1-59
59
12
D:1-59
E:501-559
H:1-59
I:501-559
L:1-59
M:501-559
O:1-59
Q:501-559
S:1-59
T:1-59
W:501-559
X:501-559
59
59
59
59
59
59
59
59
59
59
59
59
2.5a
ENST00000356853
5a
ENSE00001708572
chr2:
220022406-220022194
213
NHEJ1_HUMAN
60-130
71
12
D:60-130
E:560-630
H:60-130
I:560-630
L:60-130
M:560-630
O:60-130
Q:560-630
S:60-130 (gaps)
T:60-130 (gaps)
W:560-630
X:560-630
71
71
71
71
71
71
71
71
71
71
71
71
2.6
ENST00000356853
6
ENSE00001664826
chr2:
220012517-220012379
139
NHEJ1_HUMAN
131-177
47
12
D:131-177
E:631-677
H:131-177
I:631-677
L:131-177
M:631-677
O:131-177
Q:631-677
S:131-177
T:131-177
W:631-677
X:631-677
47
47
47
47
47
47
47
47
47
47
47
47
2.7b
ENST00000356853
7b
ENSE00001631569
chr2:
220011460-220011402
59
NHEJ1_HUMAN
177-196
20
12
D:177-196
E:677-696
H:177-196
I:677-696
L:177-196
M:677-696
O:177-196
Q:677-696
S:177-196
T:177-196
W:677-696
X:677-696
20
20
20
20
20
20
20
20
20
20
20
20
2.11b
ENST00000356853
11b
ENSE00001776599
chr2:
219942928-219942811
118
NHEJ1_HUMAN
197-236
40
12
D:197-227
E:697-727
H:197-227
I:697-727
L:197-227
M:697-727
O:197-227
Q:697-727
S:197-227
T:197-227
W:697-727
X:697-727
31
31
31
31
31
31
31
31
31
31
31
31
2.12
ENST00000356853
12
ENSE00001706214
chr2:
219942086-219941968
119
NHEJ1_HUMAN
236-275
40
0
-
-
2.13f
ENST00000356853
13f
ENSE00001781266
chr2:
219941177-219940043
1135
NHEJ1_HUMAN
276-299
24
0
-
-
[
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SCOP Domains
(0, 0)
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all CATH domains
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Pfam Domains
(0, 0)
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all PFAM domains
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Sorry, no Info available
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