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.
4ADJ
Asym. Unit
Info
Asym.Unit (443 KB)
Biol.Unit 1 (432 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 RUBELLA VIRUS GLYCOPROTEIN E1 IN ITS POST-FUSION FORM CRYSTALLIZED IN PRESENCE OF 1MM OF CALCIUM ACETATE
Authors
:
R. M. Dubois, M. C. Vaney, M. A. Tortorici, R. Al Kurdi, G. Barba-Spaeth
Date
:
26 Dec 11 (Deposition) - 09 Jan 13 (Release) - 23 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.94
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Viral Protein, Membrane Fusion
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. M. Dubois, M. C. Vaney, M. A. Tortorici, R. A. Kurdi, G. Barba-Spaeth T. Krey, F. A. Rey
Functional And Evolutionary Insight From The Crystal Structure Of Rubella Virus Protein E1.
Nature V. 493 552 2013
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 17)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
4
Ligand/Ion
ACETATE ION
2
CA
3
Ligand/Ion
CALCIUM ION
3
GOL
4
Ligand/Ion
GLYCEROL
4
NA
2
Ligand/Ion
SODIUM ION
5
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:79 , ARG A:252 , HOH A:2096 , HOH A:2099 , HOH A:2380 , ALA B:268 , HIS B:298
BINDING SITE FOR RESIDUE GOL A1437
02
AC2
SOFTWARE
THR A:277 , HIS A:290 , ARG A:292
BINDING SITE FOR RESIDUE GOL A1438
03
AC3
SOFTWARE
ASN A:88 , ALA A:89 , ASP A:136 , THR A:137 , HOH A:2114
BINDING SITE FOR RESIDUE NA A1439
04
AC4
SOFTWARE
ASN A:88 , ALA A:89 , ASP A:136 , THR A:137 , HOH A:2114
BINDING SITE FOR RESIDUE CA A1440
05
AC5
SOFTWARE
SER A:91 , SER A:92 , ASP A:136
BINDING SITE FOR RESIDUE ACT A1441
06
AC6
SOFTWARE
SER B:100 , TYR B:101
BINDING SITE FOR RESIDUE GOL B1437
07
AC7
SOFTWARE
ASN B:88 , ALA B:89 , ASP B:136 , THR B:137 , ACT B:1439 , HOH B:2094
BINDING SITE FOR RESIDUE CA B1438
08
AC8
SOFTWARE
ASN B:88 , THR B:135 , ASP B:136 , THR B:137 , CA B:1438
BINDING SITE FOR RESIDUE ACT B1439
09
AC9
SOFTWARE
SER B:92 , ASP B:136
BINDING SITE FOR RESIDUE ACT B1440
10
BC1
SOFTWARE
SER C:100 , TYR C:101 , TYR C:108
BINDING SITE FOR RESIDUE GOL C1437
11
BC2
SOFTWARE
ASP C:314 , HOH C:2255 , HOH C:2258
BINDING SITE FOR RESIDUE ACT C1438
12
BC3
SOFTWARE
ASN C:88 , ALA C:89 , ASP C:136 , THR C:137 , HOH C:2084
BINDING SITE FOR RESIDUE NA C1439
13
BC4
SOFTWARE
ASN C:88 , ALA C:89 , ASP C:136 , THR C:137 , HOH C:2084
BINDING SITE FOR RESIDUE CA C1440
14
BC5
SOFTWARE
GLN A:168 , SER A:175 , ASN A:177
BINDING SITE FOR MONO-SACCHARIDE NAG A1001 BOUND TO ASN A 177
15
BC6
SOFTWARE
GLN B:168 , SER B:175 , ASN B:177
BINDING SITE FOR MONO-SACCHARIDE NAG B1001 BOUND TO ASN B 177
16
BC7
SOFTWARE
HOH B:2311 , TYR C:6 , LEU C:7 , CYS C:8 , ASN C:76
BINDING SITE FOR MONO-SACCHARIDE NAG C2001 BOUND TO ASN C 76
17
BC8
SOFTWARE
GLN C:168 , SER C:175 , ASN C:177 , HOH C:2314
BINDING SITE FOR MONO-SACCHARIDE NAG C1001 BOUND TO ASN C 177
[
close Site info
]
SAPs(SNPs)/Variants
(1, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_POLS_RUBVM_005 (R27G, chain A/B/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_POLS_RUBVM_005
*
R
609
G
POLS_RUBVM
---
---
A/B/C
R
27
G
* ID not provided by source
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
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (443 KB)
Header - Asym.Unit
Biol.Unit 1 (432 KB)
Header - Biol.Unit 1
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
4ADJ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
