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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2WJV
Asym. Unit
Info
Asym.Unit (274 KB)
Biol.Unit 1 (135 KB)
Biol.Unit 2 (135 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 COMPLEX BETWEEN HUMAN NONSENSE MEDIATED DECAY FACTORS UPF1 AND UPF2
Authors
:
M. Clerici, A. Mourao, I. Gutsche, N. H. Gehring, M. W. Hentze, A. Kulozi J. Kadlec, M. Sattler, S. Cusack
Date
:
01 Jun 09 (Deposition) - 07 Jul 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.85
Chains
:
Asym. Unit : A,B,D,E
Biol. Unit 1: A,D (1x)
Biol. Unit 2: B,E (1x)
Keywords
:
Hydrolase, Zinc-Finger, Atp-Binding, Rna-Binding, Nonsense-Mediated Mrna Decay, Nucleotide-Binding, Metal-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Clerici, A. Mourao, I. Gutsche, N. H. Gehring, M. W. Hentze, A. Kulozik, J. Kadlec, M. Sattler, S. Cusack
Unusual Bipartite Mode Of Interaction Between The Nonsense-Mediated Decay Factors, Upf1 And Upf2.
Embo J. V. 28 2293 2009
[
close entry info
]
Hetero Components
(2, 29)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
1e: SULFATE ION (SO4e)
1f: SULFATE ION (SO4f)
1g: SULFATE ION (SO4g)
1h: SULFATE ION (SO4h)
1i: SULFATE ION (SO4i)
1j: SULFATE ION (SO4j)
1k: SULFATE ION (SO4k)
1l: SULFATE ION (SO4l)
1m: SULFATE ION (SO4m)
1n: SULFATE ION (SO4n)
1o: SULFATE ION (SO4o)
1p: SULFATE ION (SO4p)
1q: SULFATE ION (SO4q)
1r: SULFATE ION (SO4r)
1s: SULFATE ION (SO4s)
1t: SULFATE ION (SO4t)
1u: SULFATE ION (SO4u)
1v: SULFATE ION (SO4v)
1w: SULFATE ION (SO4w)
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
SO4
23
Ligand/Ion
SULFATE ION
2
ZN
6
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(29, 29)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:123 , CYS A:126 , CYS A:145 , HIS A:155
BINDING SITE FOR RESIDUE ZN A 1
02
AC2
SOFTWARE
CYS A:137 , SER A:140 , HIS A:159 , CYS A:165
BINDING SITE FOR RESIDUE ZN A 2
03
AC3
SOFTWARE
CYS A:183 , CYS A:186 , CYS A:209 , CYS A:213
BINDING SITE FOR RESIDUE ZN A 3
04
AC4
SOFTWARE
GLY A:497 , LYS A:498 , THR A:499 , VAL A:500
BINDING SITE FOR RESIDUE SO4 A 987
05
AC5
SOFTWARE
GLY A:901 , PRO A:902 , ARG A:907
BINDING SITE FOR RESIDUE SO4 A 988
06
AC6
SOFTWARE
MET A:357 , SER A:523 , ASN A:524 , ILE A:525 , ARG A:549
BINDING SITE FOR RESIDUE SO4 A 989
07
AC7
SOFTWARE
PRO A:494 , GLN A:665 , ARG A:703 , GLY A:831 , ARG A:865
BINDING SITE FOR RESIDUE SO4 A 990
08
AC8
SOFTWARE
TYR A:764 , ARG A:843 , HIS A:847 , GLN A:848 , GLY A:849
BINDING SITE FOR RESIDUE SO4 A 991
09
AC9
SOFTWARE
ARG A:767
BINDING SITE FOR RESIDUE SO4 A 992
10
BC1
SOFTWARE
ARG A:832
BINDING SITE FOR RESIDUE SO4 A 993
11
BC2
SOFTWARE
ASN A:472 , HIS A:473
BINDING SITE FOR RESIDUE SO4 A 994
12
BC3
SOFTWARE
ARG A:462 , PHE A:463 , THR A:464
BINDING SITE FOR RESIDUE SO4 A 995
13
BC4
SOFTWARE
THR A:794 , PRO A:795 , SER A:825 , VAL A:826 , ASP A:827 , GLY A:851 , PHE A:852 , ARG A:858
BINDING SITE FOR RESIDUE SO4 A 996
14
BC5
SOFTWARE
SER A:763 , PRO A:795 , TYR A:796 , GLU A:797 , ILE A:850
BINDING SITE FOR RESIDUE SO4 A 997
15
BC6
SOFTWARE
THR A:418 , ARG A:422 , PRO A:623
BINDING SITE FOR RESIDUE SO4 A 998
16
BC7
SOFTWARE
LEU A:544 , CYS A:545 , ALA A:546 , GLU A:550 , LEU A:561 , HIS A:562 , ARG A:624
BINDING SITE FOR RESIDUE SO4 A 999
17
BC8
SOFTWARE
CYS B:123 , CYS B:126 , CYS B:145 , HIS B:155
BINDING SITE FOR RESIDUE ZN B 1
18
BC9
SOFTWARE
CYS B:137 , SER B:140 , HIS B:159 , CYS B:165
BINDING SITE FOR RESIDUE ZN B 2
19
CC1
SOFTWARE
CYS B:183 , CYS B:186 , CYS B:209 , CYS B:213
BINDING SITE FOR RESIDUE ZN B 3
20
CC2
SOFTWARE
ASN B:472 , HIS B:473
BINDING SITE FOR RESIDUE SO4 B 989
21
CC3
SOFTWARE
GLY B:497 , THR B:499 , VAL B:500
BINDING SITE FOR RESIDUE SO4 B 990
22
CC4
SOFTWARE
TYR B:764 , ARG B:843 , HIS B:847 , GLN B:848 , GLY B:849
BINDING SITE FOR RESIDUE SO4 B 991
23
CC5
SOFTWARE
ARG B:767
BINDING SITE FOR RESIDUE SO4 B 992
24
CC6
SOFTWARE
ARG B:832
BINDING SITE FOR RESIDUE SO4 B 993
25
CC7
SOFTWARE
ARG B:462 , PHE B:463 , THR B:464
BINDING SITE FOR RESIDUE SO4 B 995
26
CC8
SOFTWARE
THR B:794 , PRO B:795 , SER B:825 , VAL B:826 , ASP B:827 , GLY B:851 , PHE B:852 , ARG B:858
BINDING SITE FOR RESIDUE SO4 B 996
27
CC9
SOFTWARE
SER B:763 , PRO B:795 , TYR B:796 , GLU B:797 , ILE B:850
BINDING SITE FOR RESIDUE SO4 B 997
28
DC1
SOFTWARE
SER B:523 , ASN B:524 , ILE B:525 , ARG B:549
BINDING SITE FOR RESIDUE SO4 B 998
29
DC2
SOFTWARE
PRO B:494 , GLN B:665 , ARG B:703 , GLY B:831 , ARG B:865
BINDING SITE FOR RESIDUE SO4 B 999
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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
(3, 6)
Info
All Exons
Exon 1.19 (D:1102-1126 (gaps) | E:1102-1126 (...)
Exon 1.20 (D:1127-1182 (gaps) | E:1127-1182 (...)
Exon 1.21b (D:1183-1198 | E:1183-1198)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.18/1.19
2: Boundary 1.19/1.20
3: Boundary 1.20/1.21b
4: Boundary 1.21b/1.22
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
ENST00000397053
1b
ENSE00001402467
chr10:
12085023-12084913
111
RENT2_HUMAN
-
0
0
-
-
1.3c
ENST00000397053
3c
ENSE00002187710
chr10:
12077440-12077058
383
RENT2_HUMAN
1-122
122
0
-
-
1.4
ENST00000397053
4
ENSE00000999707
chr10:
12071523-12070744
780
RENT2_HUMAN
122-382
261
0
-
-
1.5
ENST00000397053
5
ENSE00001349465
chr10:
12056183-12056023
161
RENT2_HUMAN
382-436
55
0
-
-
1.6
ENST00000397053
6
ENSE00001213473
chr10:
12046726-12046529
198
RENT2_HUMAN
436-502
67
0
-
-
1.7
ENST00000397053
7
ENSE00001213468
chr10:
12043824-12043675
150
RENT2_HUMAN
502-552
51
0
-
-
1.8b
ENST00000397053
8b
ENSE00001213463
chr10:
12042008-12041905
104
RENT2_HUMAN
552-586
35
0
-
-
1.9
ENST00000397053
9
ENSE00001754391
chr10:
12039756-12039671
86
RENT2_HUMAN
587-615
29
0
-
-
1.10
ENST00000397053
10
ENSE00001649308
chr10:
12021164-12021056
109
RENT2_HUMAN
615-651
37
0
-
-
1.11
ENST00000397053
11
ENSE00001649100
chr10:
12009453-12009340
114
RENT2_HUMAN
652-689
38
0
-
-
1.12
ENST00000397053
12
ENSE00001742008
chr10:
12006124-12006008
117
RENT2_HUMAN
690-728
39
0
-
-
1.13
ENST00000397053
13
ENSE00001617394
chr10:
12001355-12001170
186
RENT2_HUMAN
729-790
62
0
-
-
1.14
ENST00000397053
14
ENSE00001724518
chr10:
11998522-11998319
204
RENT2_HUMAN
791-858
68
0
-
-
1.15
ENST00000397053
15
ENSE00001595330
chr10:
11997506-11997231
276
RENT2_HUMAN
859-950
92
0
-
-
1.16
ENST00000397053
16
ENSE00001647744
chr10:
11994248-11994065
184
RENT2_HUMAN
951-1012
62
0
-
-
1.17
ENST00000397053
17
ENSE00001662463
chr10:
11990507-11990368
140
RENT2_HUMAN
1012-1058
47
0
-
-
1.18
ENST00000397053
18
ENSE00001754512
chr10:
11985167-11985063
105
RENT2_HUMAN
1059-1093
35
0
-
-
1.19
ENST00000397053
19
ENSE00001760455
chr10:
11984762-11984664
99
RENT2_HUMAN
1094-1126
33
2
D:1102-1126 (gaps)
E:1102-1126 (gaps)
30
30
1.20
ENST00000397053
20
ENSE00001094605
chr10:
11978711-11978544
168
RENT2_HUMAN
1127-1182
56
2
D:1127-1182 (gaps)
E:1127-1182 (gaps)
56
56
1.21b
ENST00000397053
21b
ENSE00001094602
chr10:
11973781-11973640
142
RENT2_HUMAN
1183-1230
48
2
D:1183-1198
E:1183-1198
16
16
1.22
ENST00000397053
22
ENSE00001094595
chr10:
11971984-11971864
121
RENT2_HUMAN
1230-1270
41
0
-
-
1.23a
ENST00000397053
23a
ENSE00001213550
chr10:
11963306-11962022
1285
RENT2_HUMAN
1270-1272
3
0
-
-
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(4, 8)
Info
all PFAM domains
1a: PFAM_AAA_11_2wjvB01 (B:470-673)
1b: PFAM_AAA_11_2wjvB02 (B:470-673)
2a: PFAM_AAA_12_2wjvB03 (B:680-877)
2b: PFAM_AAA_12_2wjvB04 (B:680-877)
3a: PFAM_Upf2_2wjvE01 (E:1105-1198)
3b: PFAM_Upf2_2wjvE02 (E:1105-1198)
4a: PFAM_UPF1_Zn_bind_2wjvB05 (B:121-272)
4b: PFAM_UPF1_Zn_bind_2wjvB06 (B:121-272)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
AAA_11
(5)
Homo sapiens (Human)
(4)
1a
AAA_11-2wjvB01
B:470-673
1b
AAA_11-2wjvB02
B:470-673
Family
:
AAA_12
(5)
Homo sapiens (Human)
(4)
2a
AAA_12-2wjvB03
B:680-877
2b
AAA_12-2wjvB04
B:680-877
Clan
:
TPR
(230)
Family
:
Upf2
(1)
Homo sapiens (Human)
(1)
3a
Upf2-2wjvE01
E:1105-1198
3b
Upf2-2wjvE02
E:1105-1198
Clan
:
no clan defined [family: UPF1_Zn_bind]
(3)
Family
:
UPF1_Zn_bind
(3)
Homo sapiens (Human)
(2)
4a
UPF1_Zn_bind-2wjvB05
B:121-272
4b
UPF1_Zn_bind-2wjvB06
B:121-272
[
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 D
Chain E
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 (274 KB)
Header - Asym.Unit
Biol.Unit 1 (135 KB)
Header - Biol.Unit 1
Biol.Unit 2 (135 KB)
Header - Biol.Unit 2
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
2WJV
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help