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.
5FLX
Asym. Unit
Info
Asym.Unit (1.4 MB)
Biol.Unit 1, α-C (1.3 MB)
Biol.Unit 1 (1.3 MB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
MAMMALIAN 40S HCV-IRES COMPLEX
Authors
:
H. Yamamoto, M. Collier, J. Loerke, J. Ismer, A. Schmidt, T. Hilal, T. Sp K. Yamamoto, T. Mielke, J. Burger, T. R. Shaikh, M. Dabrowski, P. W. Hil P. Scheerer, C. M. T. Spahn
Date
:
28 Oct 15 (Deposition) - 23 Dec 15 (Release) - 13 Jan 16 (Revision)
Method
:
ELECTRON MICROSCOPY
Resolution
:
3.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d,e,f,g,z,1
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d,e,f,g,z,1 (1x)
Keywords
:
Ribosome, Translation Initiation, Hepatitis C Virus Internal Ribosome Entry Site
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Yamamoto, M. Collier, J. Loerke, J. Ismer, A. Schmidt, T. Hilal, T. Sprink, K. Yamamoto, T. Mielke, J. Burger, T. R. Shaikh, M. Dabrowski, P. W. Hildebrand, P. Scheerer, C. M. Spahn
Molecular Architecture Of The Ribosome-Bound Hepatitis C Virus Internal Ribosomal Entry Site Rna.
Embo J. V. 34 3042 2015
[
close entry info
]
Hetero Components
(2, 76)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1aa: MAGNESIUM ION (MGaa)
1ab: MAGNESIUM ION (MGab)
1ac: MAGNESIUM ION (MGac)
1ad: MAGNESIUM ION (MGad)
1ae: MAGNESIUM ION (MGae)
1af: MAGNESIUM ION (MGaf)
1ag: MAGNESIUM ION (MGag)
1ah: MAGNESIUM ION (MGah)
1ai: MAGNESIUM ION (MGai)
1aj: MAGNESIUM ION (MGaj)
1ak: MAGNESIUM ION (MGak)
1al: MAGNESIUM ION (MGal)
1am: MAGNESIUM ION (MGam)
1an: MAGNESIUM ION (MGan)
1ao: MAGNESIUM ION (MGao)
1ap: MAGNESIUM ION (MGap)
1aq: MAGNESIUM ION (MGaq)
1ar: MAGNESIUM ION (MGar)
1as: MAGNESIUM ION (MGas)
1at: MAGNESIUM ION (MGat)
1au: MAGNESIUM ION (MGau)
1av: MAGNESIUM ION (MGav)
1aw: MAGNESIUM ION (MGaw)
1ax: MAGNESIUM ION (MGax)
1ay: MAGNESIUM ION (MGay)
1az: MAGNESIUM ION (MGaz)
1b: MAGNESIUM ION (MGb)
1ba: MAGNESIUM ION (MGba)
1bb: MAGNESIUM ION (MGbb)
1bc: MAGNESIUM ION (MGbc)
1bd: MAGNESIUM ION (MGbd)
1be: MAGNESIUM ION (MGbe)
1bf: MAGNESIUM ION (MGbf)
1bg: MAGNESIUM ION (MGbg)
1bh: MAGNESIUM ION (MGbh)
1bi: MAGNESIUM ION (MGbi)
1bj: MAGNESIUM ION (MGbj)
1bk: MAGNESIUM ION (MGbk)
1bl: MAGNESIUM ION (MGbl)
1bm: MAGNESIUM ION (MGbm)
1bn: MAGNESIUM ION (MGbn)
1bo: MAGNESIUM ION (MGbo)
1bp: MAGNESIUM ION (MGbp)
1bq: MAGNESIUM ION (MGbq)
1br: MAGNESIUM ION (MGbr)
1bs: MAGNESIUM ION (MGbs)
1bt: MAGNESIUM ION (MGbt)
1bu: MAGNESIUM ION (MGbu)
1bv: MAGNESIUM ION (MGbv)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
1g: MAGNESIUM ION (MGg)
1h: MAGNESIUM ION (MGh)
1i: MAGNESIUM ION (MGi)
1j: MAGNESIUM ION (MGj)
1k: MAGNESIUM ION (MGk)
1l: MAGNESIUM ION (MGl)
1m: MAGNESIUM ION (MGm)
1n: MAGNESIUM ION (MGn)
1o: MAGNESIUM ION (MGo)
1p: MAGNESIUM ION (MGp)
1q: MAGNESIUM ION (MGq)
1r: MAGNESIUM ION (MGr)
1s: MAGNESIUM ION (MGs)
1t: MAGNESIUM ION (MGt)
1u: MAGNESIUM ION (MGu)
1v: MAGNESIUM ION (MGv)
1w: MAGNESIUM ION (MGw)
1x: MAGNESIUM ION (MGx)
1y: MAGNESIUM ION (MGy)
1z: MAGNESIUM ION (MGz)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
74
Ligand/Ion
MAGNESIUM ION
2
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(68, 68)
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)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (SOFTWARE)
52: FC7 (SOFTWARE)
53: FC8 (SOFTWARE)
54: FC9 (SOFTWARE)
55: GC1 (SOFTWARE)
56: GC2 (SOFTWARE)
57: GC3 (SOFTWARE)
58: GC4 (SOFTWARE)
59: GC5 (SOFTWARE)
60: GC6 (SOFTWARE)
61: GC7 (SOFTWARE)
62: GC8 (SOFTWARE)
63: GC9 (SOFTWARE)
64: HC1 (SOFTWARE)
65: HC2 (SOFTWARE)
66: HC3 (SOFTWARE)
67: HC4 (SOFTWARE)
68: HC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
A z:342
BINDING SITE FOR RESIDUE MG 11902
02
AC2
SOFTWARE
G 1:598
BINDING SITE FOR RESIDUE MG 11904
03
AC3
SOFTWARE
U 1:1243
BINDING SITE FOR RESIDUE MG 11906
04
AC4
SOFTWARE
G 1:1089
BINDING SITE FOR RESIDUE MG 11907
05
AC5
SOFTWARE
G 1:1104
BINDING SITE FOR RESIDUE MG 11909
06
AC6
SOFTWARE
G 1:1071
BINDING SITE FOR RESIDUE MG 11911
07
AC7
SOFTWARE
A 1:19
BINDING SITE FOR RESIDUE MG 11912
08
AC8
SOFTWARE
G 1:975
BINDING SITE FOR RESIDUE MG 11913
09
AC9
SOFTWARE
U 1:416 , C 1:417
BINDING SITE FOR RESIDUE MG 11914
10
BC1
SOFTWARE
C 1:350
BINDING SITE FOR RESIDUE MG 11915
11
BC2
SOFTWARE
U 1:968
BINDING SITE FOR RESIDUE MG 11917
12
BC3
SOFTWARE
G 1:94
BINDING SITE FOR RESIDUE MG 11918
13
BC4
SOFTWARE
U 1:1360 , G 1:1361 , U 1:1362
BINDING SITE FOR RESIDUE MG 11919
14
BC5
SOFTWARE
C 1:1219
BINDING SITE FOR RESIDUE MG 11920
15
BC6
SOFTWARE
A 1:1831 , A 1:1832 , G 1:1836 , G 1:1837
BINDING SITE FOR RESIDUE MG 11921
16
BC7
SOFTWARE
G 1:1226 , G 1:1227
BINDING SITE FOR RESIDUE MG 11922
17
BC8
SOFTWARE
A 1:1832 , G 1:1836 , G 1:1837 , U 1:1838 , U 1:1839 , U 1:1840
BINDING SITE FOR RESIDUE MG 11923
18
BC9
SOFTWARE
C 1:1518 , U 1:1519
BINDING SITE FOR RESIDUE MG 11924
19
CC1
SOFTWARE
A 1:679
BINDING SITE FOR RESIDUE MG 11925
20
CC2
SOFTWARE
C 1:676 , U 1:1025
BINDING SITE FOR RESIDUE MG 11926
21
CC3
SOFTWARE
A 1:672 , C 1:674
BINDING SITE FOR RESIDUE MG 11927
22
CC4
SOFTWARE
A 1:1035
BINDING SITE FOR RESIDUE MG 11928
23
CC5
SOFTWARE
C 1:1331 , G 1:1490 , G 1:1491
BINDING SITE FOR RESIDUE MG 11929
24
CC6
SOFTWARE
G 1:1330 , G 1:1334 , G 1:1335 , C 1:1336 , U 1:1492
BINDING SITE FOR RESIDUE MG 11930
25
CC7
SOFTWARE
G 1:1245 , A 1:1246 , U 1:1492
BINDING SITE FOR RESIDUE MG 11931
26
CC8
SOFTWARE
U 1:667 , A 1:668 , A 1:669 , A 1:670
BINDING SITE FOR RESIDUE MG 11932
27
CC9
SOFTWARE
A 1:668
BINDING SITE FOR RESIDUE MG 11933
28
DC1
SOFTWARE
G 1:1652 , U 1:1653
BINDING SITE FOR RESIDUE MG 11935
29
DC2
SOFTWARE
A 1:1223 , G 1:1224
BINDING SITE FOR RESIDUE MG 11936
30
DC3
SOFTWARE
G 1:1224 , U 1:1225
BINDING SITE FOR RESIDUE MG 11937
31
DC4
SOFTWARE
G 1:1330 , C 1:1331
BINDING SITE FOR RESIDUE MG 11938
32
DC5
SOFTWARE
G 1:385 , A 1:389
BINDING SITE FOR RESIDUE MG 11939
33
DC6
SOFTWARE
A 1:449 , C 1:450
BINDING SITE FOR RESIDUE MG 11940
34
DC7
SOFTWARE
U 1:1120 , G 1:1121
BINDING SITE FOR RESIDUE MG 11941
35
DC8
SOFTWARE
G 1:601 , A 1:604 , A 1:605
BINDING SITE FOR RESIDUE MG 11942
36
DC9
SOFTWARE
A 1:99 , U 1:100 , G 1:407 , C 1:409
BINDING SITE FOR RESIDUE MG 11943
37
EC1
SOFTWARE
C 1:1660
BINDING SITE FOR RESIDUE MG 11944
38
EC2
SOFTWARE
U 1:1659 , A 1:1664
BINDING SITE FOR RESIDUE MG 11945
39
EC3
SOFTWARE
G 1:1227 , C 1:1525
BINDING SITE FOR RESIDUE MG 11946
40
EC4
SOFTWARE
G 1:1526 , C 1:1527
BINDING SITE FOR RESIDUE MG 11947
41
EC5
SOFTWARE
G 1:1604 , G 1:1605 , G 1:1606
BINDING SITE FOR RESIDUE MG 11948
42
EC6
SOFTWARE
G 1:673 , A 1:1082
BINDING SITE FOR RESIDUE MG 11949
43
EC7
SOFTWARE
G 1:16
BINDING SITE FOR RESIDUE MG 11950
44
EC8
SOFTWARE
G 1:684 , A 1:685
BINDING SITE FOR RESIDUE MG 11951
45
EC9
SOFTWARE
G 1:1352 , A 1:1353
BINDING SITE FOR RESIDUE MG 11952
46
FC1
SOFTWARE
C 1:472
BINDING SITE FOR RESIDUE MG 11954
47
FC2
SOFTWARE
C 1:48 , A 1:473
BINDING SITE FOR RESIDUE MG 11955
48
FC3
SOFTWARE
G 1:421
BINDING SITE FOR RESIDUE MG 11956
49
FC4
SOFTWARE
G 1:7 , G 1:16
BINDING SITE FOR RESIDUE MG 11957
50
FC5
SOFTWARE
G 1:1048 , C 1:1067 , G 1:1068
BINDING SITE FOR RESIDUE MG 11958
51
FC6
SOFTWARE
U 1:1441 , U 1:1442 , C 1:1443
BINDING SITE FOR RESIDUE MG 11959
52
FC7
SOFTWARE
G 1:1497
BINDING SITE FOR RESIDUE MG 11960
53
FC8
SOFTWARE
A 1:619 , G 1:620
BINDING SITE FOR RESIDUE MG 11961
54
FC9
SOFTWARE
G 1:1256 , A 1:1258
BINDING SITE FOR RESIDUE MG 11962
55
GC1
SOFTWARE
C 1:1341
BINDING SITE FOR RESIDUE MG 11963
56
GC2
SOFTWARE
U 1:1602 , G 1:1603 , G 1:1605
BINDING SITE FOR RESIDUE MG 11964
57
GC3
SOFTWARE
G 1:94 , C 1:450 , G 1:451
BINDING SITE FOR RESIDUE MG 11965
58
GC4
SOFTWARE
G 1:1702 , G z:344 , A z:345
BINDING SITE FOR RESIDUE MG 11966
59
GC5
SOFTWARE
U 1:1694 , G 1:1862
BINDING SITE FOR RESIDUE MG 11967
60
GC6
SOFTWARE
A 1:349 , G 1:432
BINDING SITE FOR RESIDUE MG 11968
61
GC7
SOFTWARE
G 1:1041
BINDING SITE FOR RESIDUE MG 11969
62
GC8
SOFTWARE
G 1:1040
BINDING SITE FOR RESIDUE MG 11970
63
GC9
SOFTWARE
U 1:1038
BINDING SITE FOR RESIDUE MG 11971
64
HC1
SOFTWARE
U 1:1721
BINDING SITE FOR RESIDUE MG 11972
65
HC2
SOFTWARE
SER D:139
BINDING SITE FOR RESIDUE MG D 301
66
HC3
SOFTWARE
C 1:621 , HIS X:110 , ALA X:111
BINDING SITE FOR RESIDUE MG X 201
67
HC4
SOFTWARE
THR a:24 , ASN a:25 , ALA a:27
BINDING SITE FOR RESIDUE ZN a 201
68
HC5
SOFTWARE
VAL d:23 , CYS d:24 , CYS d:39 , CYS d:42
BINDING SITE FOR RESIDUE ZN d 101
[
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
(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
Chain S
Chain T
Chain U
Chain V
Chain W
Chain X
Chain Y
Chain Z
Chain a
Chain b
Chain c
Chain d
Chain e
Chain f
Chain g
Chain z
Chain 1
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 (1.4 MB)
Header - Asym.Unit
Biol.Unit 1 (1.3 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
5FLX
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
