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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2R17
Asym. Unit
Info
Asym.Unit (162 KB)
Biol.Unit 1 (82 KB)
Biol.Unit 2 (78 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
FUNCTIONAL ARCHITECTURE OF THE RETROMER CARGO-RECOGNITION COMPLEX
Authors
:
A. Hierro, A. L. Rojas, R. Rojas, N. Murthy, G. Effantin, A. V. Kajava, A. J. S. Bonifacino, J. H. Hurley
Date
:
22 Aug 07 (Deposition) - 30 Oct 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Protein Transport, Membrane, Phosphorylation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Hierro, A. L. Rojas, R. Rojas, N. Murthy, G. Effantin, A. V. Kajava, A. C. Steven, J. S. Bonifacino, J. H. Hurley
Functional Architecture Of The Retromer Cargo-Recognition Complex.
Nature V. 449 1063 2007
[
close entry info
]
Hetero Components
(2, 18)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
2a: SELENOMETHIONINE (MSEa)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
2
Ligand/Ion
GLYCEROL
2
MSE
16
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA D:577 , GLU D:578 , LEU D:579
BINDING SITE FOR RESIDUE GOL D 1
2
AC2
SOFTWARE
HOH C:787 , ASN D:744
BINDING SITE FOR RESIDUE GOL D 2
[
close Site info
]
SAPs(SNPs)/Variants
(5, 9)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_066658 (R524W, chain C/D, )
2: VAR_054046 (V602D, chain C/D, )
3: VAR_066659 (D620N, chain C/D, )
4: VAR_066660 (A737V, chain C, )
5: VAR_066661 (L774M, chain C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_066658
R
524
W
VPS35_HUMAN
Unclassified
---
C/D
R
524
W
2
UniProt
VAR_054046
V
602
D
VPS35_HUMAN
Polymorphism
34687100
C/D
V
602
D
3
UniProt
VAR_066659
D
620
N
VPS35_HUMAN
Disease (PARK17)
---
C/D
D
620
N
4
UniProt
VAR_066660
A
737
V
VPS35_HUMAN
Polymorphism
---
C
A
737
V
5
UniProt
VAR_066661
L
774
M
VPS35_HUMAN
Polymorphism
---
C/D
L
774
M
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
(6, 12)
Info
All Exons
Exon 1.12 (C:483-508 | D:484-508)
Exon 1.13 (C:509-549 | D:509-549)
Exon 1.14 (C:550-609 | D:550-609)
Exon 1.15 (C:610-689 | D:610-678)
Exon 1.16 (C:690-737 | D:695-733)
Exon 1.17 (C:738-780 | D:739-780)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.11/1.12
2: Boundary 1.12/1.13
3: Boundary 1.13/1.14
4: Boundary 1.14/1.15
5: Boundary 1.15/1.16
6: Boundary 1.16/1.17
7: Boundary 1.17/-
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
1.1
ENST00000299138
1
ENSE00001370884
chr16:
46723104-46723043
62
VPS35_HUMAN
1-1
1
0
-
-
1.2
ENST00000299138
2
ENSE00001203286
chr16:
46717518-46717420
99
VPS35_HUMAN
2-34
33
0
-
-
1.3
ENST00000299138
3
ENSE00001300680
chr16:
46716087-46715991
97
VPS35_HUMAN
35-67
33
0
-
-
1.4
ENST00000299138
4
ENSE00001301097
chr16:
46715412-46715289
124
VPS35_HUMAN
67-108
42
0
-
-
1.5
ENST00000299138
5
ENSE00001324372
chr16:
46714765-46714583
183
VPS35_HUMAN
108-169
62
0
-
-
1.6
ENST00000299138
6
ENSE00001304859
chr16:
46713068-46712855
214
VPS35_HUMAN
169-240
72
0
-
-
1.7
ENST00000299138
7
ENSE00001328477
chr16:
46711310-46711227
84
VPS35_HUMAN
241-268
28
0
-
-
1.8
ENST00000299138
8
ENSE00001308709
chr16:
46710604-46710495
110
VPS35_HUMAN
269-305
37
0
-
-
1.9
ENST00000299138
9
ENSE00001322169
chr16:
46708572-46708476
97
VPS35_HUMAN
305-337
33
0
-
-
1.10
ENST00000299138
10
ENSE00001303884
chr16:
46708374-46708226
149
VPS35_HUMAN
338-387
50
0
-
-
1.11
ENST00000299138
11
ENSE00001325496
chr16:
46706384-46706177
208
VPS35_HUMAN
387-456
70
0
-
-
1.12
ENST00000299138
12
ENSE00001307618
chr16:
46705772-46705617
156
VPS35_HUMAN
457-508
52
2
C:483-508
D:484-508
26
25
1.13
ENST00000299138
13
ENSE00001316290
chr16:
46702964-46702842
123
VPS35_HUMAN
509-549
41
2
C:509-549
D:509-549
41
41
1.14
ENST00000299138
14
ENSE00001299009
chr16:
46697074-46696895
180
VPS35_HUMAN
550-609
60
2
C:550-609
D:550-609
60
60
1.15
ENST00000299138
15
ENSE00001320388
chr16:
46696394-46696155
240
VPS35_HUMAN
610-689
80
2
C:610-689
D:610-678
80
69
1.16
ENST00000299138
16
ENSE00000945117
chr16:
46695773-46695630
144
VPS35_HUMAN
690-737
48
2
C:690-737
D:695-733
48
39
1.17
ENST00000299138
17
ENSE00001324467
chr16:
46694563-46691891
2673
VPS35_HUMAN
738-796
59
2
C:738-780
D:739-780
43
42
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2r17a_ (A:)
1b: SCOP_d2r17b_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Metallo-dependent phosphatases
(115)
Superfamily
:
Metallo-dependent phosphatases
(115)
Family
:
YfcE-like
(12)
Protein domain
:
Vacuolar protein sorting 29, VPS29
(6)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d2r17a_
A:
1b
d2r17b_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Metallophos_2_2r17B01 (B:1-158)
1b: PFAM_Metallophos_2_2r17B02 (B:1-158)
2a: PFAM_Vps35_2r17D01 (D:484-754)
2b: PFAM_Vps35_2r17D02 (D:484-754)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Calcineurin
(56)
Family
:
Metallophos_2
(10)
Homo sapiens (Human)
(2)
1a
Metallophos_2-2r17B01
B:1-158
1b
Metallophos_2-2r17B02
B:1-158
Clan
:
no clan defined [family: Vps35]
(1)
Family
:
Vps35
(1)
Homo sapiens (Human)
(1)
2a
Vps35-2r17D01
D:484-754
2b
Vps35-2r17D02
D:484-754
[
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 C
Chain D
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 (162 KB)
Header - Asym.Unit
Biol.Unit 1 (82 KB)
Header - Biol.Unit 1
Biol.Unit 2 (78 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
2R17
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help