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.
1MFQ
Asym. Unit
Info
Asym.Unit (98 KB)
Biol.Unit 1 (92 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 ANALYSIS OF A TERNARY S-DOMAIN COMPLEX OF HUMAN SIGNAL RECOGNITION PARTICLE
Authors
:
A. Kuglstatter, C. Oubridge, K. Nagai
Date
:
13 Aug 02 (Deposition) - 20 Sep 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Rna-Protein Complex, A-Minor Motif, 3-Helix Junction, Signaling Protein/Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Kuglstatter, C. Oubridge, K. Nagai
Induced Structural Changes Of 7Sl Rna During The Assembly Of Human Signal Recognition Particle
Nat. Struct. Biol. V. 9 740 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 8)
Info
All Hetero Components
1a: CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC... (CCCa)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CCC
1
Mod. Nucleotide
CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2
CL
2
Ligand/Ion
CHLORIDE ION
3
MG
5
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
A A:192 , G A:193 , G A:194
BINDING SITE FOR RESIDUE MG A 501
2
AC2
SOFTWARE
A A:183 , C A:185
BINDING SITE FOR RESIDUE MG A 502
3
AC3
SOFTWARE
A A:205
BINDING SITE FOR RESIDUE MG A 503
4
AC4
SOFTWARE
A A:183
BINDING SITE FOR RESIDUE MG A 504
5
AC5
SOFTWARE
C A:116 , U A:117
BINDING SITE FOR RESIDUE MG A 505
[
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
(4, 4)
Info
All Exons
Exon 1.11 (C:323-325)
Exon 1.12 (C:325-349)
Exon 1.13 (C:350-386 (gaps))
Exon 1.14 (C:386-438)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.10/1.11
2: Boundary 1.11/1.12
3: Boundary 1.12/1.13
4: Boundary 1.13/1.14
5: Boundary 1.14/1.15
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
ENST00000216774
1
ENSE00001359255
chr14:
35452231-35452421
191
SRP54_HUMAN
-
0
0
-
-
1.2
ENST00000216774
2
ENSE00000889679
chr14:
35465883-35465993
111
SRP54_HUMAN
1-26
26
0
-
-
1.3
ENST00000216774
3
ENSE00000655760
chr14:
35468764-35468855
92
SRP54_HUMAN
27-57
31
0
-
-
1.4
ENST00000216774
4
ENSE00000655761
chr14:
35470142-35470226
85
SRP54_HUMAN
57-85
29
0
-
-
1.5
ENST00000216774
5
ENSE00000655764
chr14:
35476489-35476593
105
SRP54_HUMAN
86-120
35
0
-
-
1.6
ENST00000216774
6
ENSE00000655766
chr14:
35477833-35477899
67
SRP54_HUMAN
121-143
23
0
-
-
1.7
ENST00000216774
7
ENSE00000655768
chr14:
35477980-35478037
58
SRP54_HUMAN
143-162
20
0
-
-
1.8
ENST00000216774
8
ENSE00000655770
chr14:
35480715-35480865
151
SRP54_HUMAN
162-212
51
0
-
-
1.9
ENST00000216774
9
ENSE00000655772
chr14:
35482552-35482700
149
SRP54_HUMAN
213-262
50
0
-
-
1.10
ENST00000216774
10
ENSE00000655775
chr14:
35483008-35483108
101
SRP54_HUMAN
262-296
35
0
-
-
1.11
ENST00000216774
11
ENSE00000655777
chr14:
35483950-35484036
87
SRP54_HUMAN
296-325
30
1
C:323-325
3
1.12
ENST00000216774
12
ENSE00000655779
chr14:
35487898-35487971
74
SRP54_HUMAN
325-349
25
1
C:325-349
25
1.13
ENST00000216774
13
ENSE00000655781
chr14:
35488172-35488280
109
SRP54_HUMAN
350-386
37
1
C:350-386 (gaps)
37
1.14
ENST00000216774
14
ENSE00000655783
chr14:
35492116-35492286
171
SRP54_HUMAN
386-443
58
1
C:386-438
53
1.15
ENST00000216774
15
ENSE00000655785
chr14:
35497294-35497389
96
SRP54_HUMAN
443-475
33
0
-
-
1.16
ENST00000216774
16
ENSE00000889680
chr14:
35498267-35498773
507
SRP54_HUMAN
475-504
30
0
-
-
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1mfqc_ (C:)
2a: SCOP_d1mfqb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Signal peptide-binding domain
(20)
Superfamily
:
Signal peptide-binding domain
(20)
Family
:
Signal peptide-binding domain
(20)
Protein domain
:
SRP54M
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d1mfqc_
C:
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
SRP19
(11)
Superfamily
:
SRP19
(11)
Family
:
SRP19
(9)
Protein domain
:
SRP19
(9)
Human (Homo sapiens) [TaxId: 9606]
(4)
2a
d1mfqb_
B:
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1mfqB00 (B:14-120)
2a: CATH_1mfqC00 (C:323-438)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Phenylalanyl-tRNA Synthetase; Chain B, domain 1
(22)
Homologous Superfamily
:
SRP19
(8)
Human (Homo sapiens)
(2)
1a
1mfqB00
B:14-120
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
434 Repressor (Amino-terminal Domain)
(116)
Homologous Superfamily
:
[code=1.10.260.30, no name defined]
(16)
Human (Homo sapiens)
(2)
2a
1mfqC00
C:323-438
[
close CATH info
]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_SRP19_1mfqB01 (B:16-116)
2a: PFAM_SRP_SPB_1mfqC01 (C:326-431)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: SRP19]
(9)
Family
:
SRP19
(9)
Homo sapiens (Human)
(3)
1a
SRP19-1mfqB01
B:16-116
Clan
:
no clan defined [family: SRP_SPB]
(20)
Family
:
SRP_SPB
(20)
Homo sapiens (Human)
(2)
2a
SRP_SPB-1mfqC01
C:326-431
[
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 (98 KB)
Header - Asym.Unit
Biol.Unit 1 (92 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
1MFQ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help