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.
3J6E
Asym. Unit
Info
Asym.Unit (1.0 MB)
Biol.Unit 1, α-C (1.0 MB)
Biol.Unit 1 (1.0 MB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ENERGY MINIMIZED AVERAGE STRUCTURE OF MICROTUBULES STABILIZED BY GMPCPP
Authors
:
G. M. Alushin, G. C. Lander, E. H. Kellogg, R. Zhang, D. Baker, E. Nogales
Date
:
18 Feb 14 (Deposition) - 04 Jun 14 (Release) - 04 Jun 14 (Revision)
Method
:
ELECTRON MICROSCOPY
Resolution
:
4.70
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R (1x)
Keywords
:
Microtubule, Gmpcpp, Structural Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. M. Alushin, G. C. Lander, E. H. Kellogg, R. Zhang, D. Baker, E. Nogale
High-Resolution Microtubule Structures Reveal The Structura Transitions In Alpha Beta-Tubulin Upon Gtp Hydrolysis.
Cell(Cambridge, Mass. ) V. 157 1117 2014
[
close entry info
]
Hetero Components
(3, 36)
Info
All Hetero Components
1a: PHOSPHOMETHYLPHOSPHONIC ACID GUANY... (G2Pa)
1b: PHOSPHOMETHYLPHOSPHONIC ACID GUANY... (G2Pb)
1c: PHOSPHOMETHYLPHOSPHONIC ACID GUANY... (G2Pc)
1d: PHOSPHOMETHYLPHOSPHONIC ACID GUANY... (G2Pd)
1e: PHOSPHOMETHYLPHOSPHONIC ACID GUANY... (G2Pe)
1f: PHOSPHOMETHYLPHOSPHONIC ACID GUANY... (G2Pf)
1g: PHOSPHOMETHYLPHOSPHONIC ACID GUANY... (G2Pg)
1h: PHOSPHOMETHYLPHOSPHONIC ACID GUANY... (G2Ph)
1i: PHOSPHOMETHYLPHOSPHONIC ACID GUANY... (G2Pi)
2a: GUANOSINE-5'-TRIPHOSPHATE (GTPa)
2b: GUANOSINE-5'-TRIPHOSPHATE (GTPb)
2c: GUANOSINE-5'-TRIPHOSPHATE (GTPc)
2d: GUANOSINE-5'-TRIPHOSPHATE (GTPd)
2e: GUANOSINE-5'-TRIPHOSPHATE (GTPe)
2f: GUANOSINE-5'-TRIPHOSPHATE (GTPf)
2g: GUANOSINE-5'-TRIPHOSPHATE (GTPg)
2h: GUANOSINE-5'-TRIPHOSPHATE (GTPh)
2i: GUANOSINE-5'-TRIPHOSPHATE (GTPi)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
3j: MAGNESIUM ION (MGj)
3k: MAGNESIUM ION (MGk)
3l: MAGNESIUM ION (MGl)
3m: MAGNESIUM ION (MGm)
3n: MAGNESIUM ION (MGn)
3o: MAGNESIUM ION (MGo)
3p: MAGNESIUM ION (MGp)
3q: MAGNESIUM ION (MGq)
3r: MAGNESIUM ION (MGr)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
G2P
9
Ligand/Ion
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
2
GTP
9
Ligand/Ion
GUANOSINE-5'-TRIPHOSPHATE
3
MG
18
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(36, 36)
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)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:10 , GLN A:11 , ALA A:12 , GLN A:15 , ALA A:99 , ASN A:101 , SER A:140 , GLY A:143 , GLY A:144 , THR A:145 , GLY A:146 , ASN A:206 , TYR A:224 , ASN A:228 , MG A:502 , HOH A:601 , HOH A:602 , HOH A:603
BINDING SITE FOR RESIDUE GTP A 501
02
AC2
SOFTWARE
GTP A:501 , HOH A:601 , HOH A:602 , HOH A:603 , HOH A:604
BINDING SITE FOR RESIDUE MG A 502
03
AC3
SOFTWARE
GLY B:10 , GLN B:11 , CYS B:12 , GLN B:15 , ALA B:99 , ASN B:101 , SER B:140 , GLY B:144 , THR B:145 , GLY B:146 , GLU B:183 , ASN B:206 , TYR B:224 , ASN B:228 , MG B:502 , HOH B:601 , HOH B:602
BINDING SITE FOR RESIDUE G2P B 501
04
AC4
SOFTWARE
G2P B:501 , HOH B:601 , HOH B:602 , HOH B:603 , HOH B:604
BINDING SITE FOR RESIDUE MG B 502
05
AC5
SOFTWARE
GLY C:10 , GLN C:11 , ALA C:12 , GLN C:15 , ALA C:99 , ASN C:101 , SER C:140 , GLY C:143 , GLY C:144 , THR C:145 , GLY C:146 , ASN C:206 , TYR C:224 , ASN C:228 , MG C:502 , HOH C:601 , HOH C:602 , HOH C:603
BINDING SITE FOR RESIDUE GTP C 501
06
AC6
SOFTWARE
GTP C:501 , HOH C:601 , HOH C:602 , HOH C:603 , HOH C:604
BINDING SITE FOR RESIDUE MG C 502
07
AC7
SOFTWARE
GLY D:10 , GLN D:11 , CYS D:12 , GLN D:15 , ALA D:99 , ASN D:101 , SER D:140 , GLY D:144 , THR D:145 , GLY D:146 , GLU D:183 , ASN D:206 , TYR D:224 , ASN D:228 , MG D:502 , HOH D:601 , HOH D:602
BINDING SITE FOR RESIDUE G2P D 501
08
AC8
SOFTWARE
G2P D:501 , HOH D:601 , HOH D:602 , HOH D:603 , HOH D:604
BINDING SITE FOR RESIDUE MG D 502
09
AC9
SOFTWARE
GLY E:10 , GLN E:11 , ALA E:12 , GLN E:15 , ALA E:99 , ASN E:101 , SER E:140 , GLY E:143 , GLY E:144 , THR E:145 , GLY E:146 , ASN E:206 , TYR E:224 , ASN E:228 , MG E:502 , HOH E:601 , HOH E:602 , HOH E:603
BINDING SITE FOR RESIDUE GTP E 501
10
BC1
SOFTWARE
GTP E:501 , HOH E:601 , HOH E:602 , HOH E:603 , HOH E:604
BINDING SITE FOR RESIDUE MG E 502
11
BC2
SOFTWARE
GLY F:10 , GLN F:11 , CYS F:12 , GLN F:15 , ALA F:99 , ASN F:101 , SER F:140 , GLY F:144 , THR F:145 , GLY F:146 , GLU F:183 , ASN F:206 , TYR F:224 , ASN F:228 , MG F:502 , HOH F:601 , HOH F:602
BINDING SITE FOR RESIDUE G2P F 501
12
BC3
SOFTWARE
G2P F:501 , HOH F:601 , HOH F:602 , HOH F:603 , HOH F:604
BINDING SITE FOR RESIDUE MG F 502
13
BC4
SOFTWARE
GLY G:10 , GLN G:11 , ALA G:12 , GLN G:15 , ALA G:99 , ASN G:101 , SER G:140 , GLY G:143 , GLY G:144 , THR G:145 , GLY G:146 , ASN G:206 , TYR G:224 , ASN G:228 , MG G:502 , HOH G:601 , HOH G:602 , HOH G:603
BINDING SITE FOR RESIDUE GTP G 501
14
BC5
SOFTWARE
GTP G:501 , HOH G:601 , HOH G:602 , HOH G:603 , HOH G:604
BINDING SITE FOR RESIDUE MG G 502
15
BC6
SOFTWARE
GLY H:10 , GLN H:11 , CYS H:12 , GLN H:15 , ALA H:99 , ASN H:101 , SER H:140 , GLY H:144 , THR H:145 , GLY H:146 , GLU H:183 , ASN H:206 , TYR H:224 , ASN H:228 , MG H:502 , HOH H:901 , HOH H:902
BINDING SITE FOR RESIDUE G2P H 501
16
BC7
SOFTWARE
G2P H:501 , HOH H:901 , HOH H:902 , HOH H:903 , HOH H:904
BINDING SITE FOR RESIDUE MG H 502
17
BC8
SOFTWARE
GLY I:10 , GLN I:11 , ALA I:12 , GLN I:15 , ALA I:99 , ASN I:101 , SER I:140 , GLY I:143 , GLY I:144 , THR I:145 , GLY I:146 , ASN I:206 , TYR I:224 , ASN I:228 , MG I:502 , HOH I:601 , HOH I:602 , HOH I:603
BINDING SITE FOR RESIDUE GTP I 501
18
BC9
SOFTWARE
GTP I:501 , HOH I:601 , HOH I:602 , HOH I:603 , HOH I:604
BINDING SITE FOR RESIDUE MG I 502
19
CC1
SOFTWARE
GLY J:10 , GLN J:11 , CYS J:12 , GLN J:15 , ALA J:99 , ASN J:101 , SER J:140 , GLY J:144 , THR J:145 , GLY J:146 , GLU J:183 , ASN J:206 , TYR J:224 , ASN J:228 , MG J:502 , HOH J:601 , HOH J:602
BINDING SITE FOR RESIDUE G2P J 501
20
CC2
SOFTWARE
G2P J:501 , HOH J:601 , HOH J:602 , HOH J:603 , HOH J:604
BINDING SITE FOR RESIDUE MG J 502
21
CC3
SOFTWARE
GLY K:10 , GLN K:11 , ALA K:12 , GLN K:15 , ALA K:99 , ASN K:101 , SER K:140 , GLY K:143 , GLY K:144 , THR K:145 , GLY K:146 , ASN K:206 , TYR K:224 , ASN K:228 , MG K:502 , HOH K:601 , HOH K:602 , HOH K:603
BINDING SITE FOR RESIDUE GTP K 501
22
CC4
SOFTWARE
GTP K:501 , HOH K:601 , HOH K:602 , HOH K:603 , HOH K:604
BINDING SITE FOR RESIDUE MG K 502
23
CC5
SOFTWARE
GLY L:10 , GLN L:11 , CYS L:12 , GLN L:15 , ALA L:99 , ASN L:101 , SER L:140 , GLY L:144 , THR L:145 , GLY L:146 , GLU L:183 , ASN L:206 , TYR L:224 , ASN L:228 , MG L:502 , HOH L:601 , HOH L:602
BINDING SITE FOR RESIDUE G2P L 501
24
CC6
SOFTWARE
G2P L:501 , HOH L:601 , HOH L:602 , HOH L:603 , HOH L:604
BINDING SITE FOR RESIDUE MG L 502
25
CC7
SOFTWARE
GLY M:10 , GLN M:11 , ALA M:12 , GLN M:15 , ALA M:99 , ASN M:101 , SER M:140 , GLY M:143 , GLY M:144 , THR M:145 , GLY M:146 , ASN M:206 , TYR M:224 , ASN M:228 , MG M:502 , HOH M:601 , HOH M:602 , HOH M:603
BINDING SITE FOR RESIDUE GTP M 501
26
CC8
SOFTWARE
GTP M:501 , HOH M:601 , HOH M:602 , HOH M:603 , HOH M:604
BINDING SITE FOR RESIDUE MG M 502
27
CC9
SOFTWARE
GLY N:10 , GLN N:11 , CYS N:12 , GLN N:15 , ALA N:99 , ASN N:101 , SER N:140 , GLY N:144 , THR N:145 , GLY N:146 , GLU N:183 , ASN N:206 , TYR N:224 , ASN N:228 , MG N:502 , HOH N:601 , HOH N:602
BINDING SITE FOR RESIDUE G2P N 501
28
DC1
SOFTWARE
G2P N:501 , HOH N:601 , HOH N:602 , HOH N:603 , HOH N:604
BINDING SITE FOR RESIDUE MG N 502
29
DC2
SOFTWARE
GLY O:10 , GLN O:11 , ALA O:12 , GLN O:15 , ALA O:99 , ASN O:101 , SER O:140 , GLY O:143 , GLY O:144 , THR O:145 , GLY O:146 , ASN O:206 , TYR O:224 , ASN O:228 , MG O:502 , HOH O:601 , HOH O:602 , HOH O:603
BINDING SITE FOR RESIDUE GTP O 501
30
DC3
SOFTWARE
GTP O:501 , HOH O:601 , HOH O:602 , HOH O:603 , HOH O:604
BINDING SITE FOR RESIDUE MG O 502
31
DC4
SOFTWARE
GLY P:10 , GLN P:11 , CYS P:12 , GLN P:15 , ALA P:99 , ASN P:101 , SER P:140 , GLY P:144 , THR P:145 , GLY P:146 , GLU P:183 , ASN P:206 , TYR P:224 , ASN P:228 , MG P:502 , HOH P:601 , HOH P:602
BINDING SITE FOR RESIDUE G2P P 501
32
DC5
SOFTWARE
G2P P:501 , HOH P:601 , HOH P:602 , HOH P:603 , HOH P:604
BINDING SITE FOR RESIDUE MG P 502
33
DC6
SOFTWARE
GLY Q:10 , GLN Q:11 , ALA Q:12 , GLN Q:15 , ALA Q:99 , ASN Q:101 , SER Q:140 , GLY Q:143 , GLY Q:144 , THR Q:145 , GLY Q:146 , ASN Q:206 , TYR Q:224 , ASN Q:228 , MG Q:502 , HOH Q:601 , HOH Q:602 , HOH Q:603
BINDING SITE FOR RESIDUE GTP Q 501
34
DC7
SOFTWARE
GTP Q:501 , HOH Q:601 , HOH Q:602 , HOH Q:603 , HOH Q:604
BINDING SITE FOR RESIDUE MG Q 502
35
DC8
SOFTWARE
GLY R:10 , GLN R:11 , CYS R:12 , GLN R:15 , ALA R:99 , ASN R:101 , SER R:140 , GLY R:144 , THR R:145 , GLY R:146 , GLU R:183 , ASN R:206 , TYR R:224 , ASN R:228 , MG R:502 , HOH R:601 , HOH R:602
BINDING SITE FOR RESIDUE G2P R 501
36
DC9
SOFTWARE
G2P R:501 , HOH R:601 , HOH R:602 , HOH R:603 , HOH R:604
BINDING SITE FOR RESIDUE MG R 502
[
close Site info
]
SAPs(SNPs)/Variants
(6, 54)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_TBB_PIG_001 (H37V, chain B/D/F/H/J/L/N/P/R, )
2: VAR_TBB_PIG_002 (N50S, chain B/D/F/H/J/L/N/P/R, )
3: VAR_TBA1A_PIG_001 (G265G, chain A/C/E/G/I/K/M/O/Q, )
4: VAR_TBA1A_PIG_002 (G265I, chain A/C/E/G/I/K/M/O/Q, )
5: VAR_TBA1A_PIG_003 (H266I, chain A/C/E/G/I/K/M/O/Q, )
6: VAR_TBB_PIG_003 (S277A, chain B/D/F/H/J/L/N/P/R, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_TBB_PIG_001
*
H
37
V
TBB_PIG
---
---
B/D/F/H/J/L/N/P/R
H
37
V
2
UniProt
VAR_TBB_PIG_002
*
N
48
S
TBB_PIG
---
---
B/D/F/H/J/L/N/P/R
N
50
S
3
UniProt
VAR_TBA1A_PIG_001
*
A
265
G
TBA1A_PIG
---
---
A/C/E/G/I/K/M/O/Q
G
265
G
4
UniProt
VAR_TBA1A_PIG_002
*
A
265
I
TBA1A_PIG
---
---
A/C/E/G/I/K/M/O/Q
G
265
I
5
UniProt
VAR_TBA1A_PIG_003
*
H
266
I
TBA1A_PIG
---
---
A/C/E/G/I/K/M/O/Q
H
266
I
6
UniProt
VAR_TBB_PIG_003
*
S
275
A
TBB_PIG
---
---
B/D/F/H/J/L/N/P/R
S
277
A
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 18)
Info
All PROSITE Patterns/Profiles
1: TUBULIN (B:142-148,D:142-148,F:142-148,H:14...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TUBULIN
PS00227
Tubulin subunits alpha, beta, and gamma signature.
TBB_PIG
140-146
9
B:142-148
D:142-148
F:142-148
H:142-148
J:142-148
L:142-148
N:142-148
P:142-148
R:142-148
TBA1A_PIG
142-148
9
A:142-148
C:142-148
E:142-148
G:142-148
I:142-148
K:142-148
M:142-148
O:142-148
Q:142-148
[
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
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
Chain Q
Chain R
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 (1.0 MB)
Header - Asym.Unit
Biol.Unit 1 (1.0 MB)
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
3J6E
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help