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.
3S9M
Asym. Unit
Info
Asym.Unit (328 KB)
Biol.Unit 1 (325 KB)
Biol.Unit 2 (306 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
COMPLEX BETWEEN TRANSFERRIN RECEPTOR 1 AND TRANSFERRIN WITH IRON IN THE N-LOBE, CRYOCOOLED 1
Authors
:
B. E. Eckenroth, A. N. Steere, A. B. Mason, S. J. Everse
Date
:
01 Jun 11 (Deposition) - 10 Aug 11 (Release) - 14 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.32
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (2x)
Biol. Unit 2: B,D (2x)
Keywords
:
Transferrin Receptor Complex, Transferrin Superfamily, Carboxypeptidase Like, Transport Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. E. Eckenroth, A. N. Steere, N. D. Chasteen, S. J. Everse, A. B. Mason
How The Binding Of Human Transferrin Primes The Transferrin Receptor Potentiating Iron Release At Endosomal Ph.
Proc. Natl. Acad. Sci. Usa V. 108 13089 2011
[
close entry info
]
Hetero Components
(4, 8)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: CARBONATE ION (CO3a)
2b: CARBONATE ION (CO3b)
3a: FE (III) ION (FEa)
3b: FE (III) ION (FEb)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
CO3
2
Ligand/Ion
CARBONATE ION
3
FE
2
Ligand/Ion
FE (III) ION
4
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:317 , GLU A:383
BINDING SITE FOR RESIDUE NAG A 903
2
AC2
SOFTWARE
THR A:310 , PHE A:313 , GLU A:465 , GLU A:468
BINDING SITE FOR RESIDUE CA A 900
3
AC3
SOFTWARE
ASN B:317 , GLU B:383 , TRP B:641
BINDING SITE FOR RESIDUE NAG B 903
4
AC4
SOFTWARE
THR B:310 , PHE B:313 , GLU B:465 , GLU B:468
BINDING SITE FOR RESIDUE CA B 900
5
AC5
SOFTWARE
ASP C:63 , TYR C:95 , THR C:120 , ARG C:124 , ALA C:126 , GLY C:127 , TYR C:188 , HIS C:249 , FE C:901
BINDING SITE FOR RESIDUE CO3 C 905
6
AC6
SOFTWARE
ASP C:63 , TYR C:95 , TYR C:188 , HIS C:249 , CO3 C:905
BINDING SITE FOR RESIDUE FE C 901
7
AC7
SOFTWARE
ASP D:63 , THR D:120 , ARG D:124 , SER D:125 , ALA D:126 , TYR D:188 , HIS D:249 , FE D:901
BINDING SITE FOR RESIDUE CO3 D 905
8
AC8
SOFTWARE
ASP D:63 , TYR D:188 , HIS D:249 , CO3 D:905
BINDING SITE FOR RESIDUE FE D 901
[
close Site info
]
SAPs(SNPs)/Variants
(16, 32)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_034569 (R23L, chain C/D, )
02: VAR_029280 (S36R, chain C/D, )
03: VAR_034570 (A57V, chain C/D, )
04: VAR_038810 (D58N, chain C/D, )
05: VAR_011997 (G123S, chain C/D, )
06: VAR_012737 (S142S, chain A/B, )
07: VAR_051806 (L212V, chain A/B, )
08: VAR_011998 (G258S, chain C/D, )
09: VAR_007544 (D277G, chain C/D, )
10: VAR_007545 (H300R, chain C/D, )
11: VAR_011999 (W358C, chain C/D, )
12: VAR_051807 (G420S, chain A/B, )
13: VAR_012001 (T626P, chain C/D, )
14: VAR_012998 (K627E, chain C/D, )
15: VAR_012999 (G652E, chain C/D, )
16: VAR_051808 (R677H, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_034569
R
42
L
TRFE_HUMAN
Polymorphism
41298293
C/D
R
23
L
02
UniProt
VAR_029280
S
55
R
TRFE_HUMAN
Polymorphism
8177318
C/D
S
36
R
03
UniProt
VAR_034570
A
76
V
TRFE_HUMAN
Polymorphism
41298977
C/D
A
57
V
04
UniProt
VAR_038810
D
77
N
TRFE_HUMAN
Disease (ATRAF)
---
C/D
D
58
N
05
UniProt
VAR_011997
G
142
S
TRFE_HUMAN
Polymorphism
1799830
C/D
G
123
S
06
UniProt
VAR_012737
G
142
S
TFR1_HUMAN
Polymorphism
3817672
A/B
S
142
S
07
UniProt
VAR_051806
L
212
V
TFR1_HUMAN
Polymorphism
41301381
A/B
L
212
V
08
UniProt
VAR_011998
G
277
S
TRFE_HUMAN
Polymorphism
1799899
C/D
G
258
S
09
UniProt
VAR_007544
D
296
G
TRFE_HUMAN
Polymorphism
8177238
C/D
D
277
G
10
UniProt
VAR_007545
H
319
R
TRFE_HUMAN
Polymorphism
41295774
C/D
H
300
R
11
UniProt
VAR_011999
W
377
C
TRFE_HUMAN
Polymorphism
1804498
C/D
W
358
C
12
UniProt
VAR_051807
G
420
S
TFR1_HUMAN
Polymorphism
41295879
A/B
G
420
S
13
UniProt
VAR_012001
T
645
P
TRFE_HUMAN
Polymorphism
1130537
C/D
T
626
P
14
UniProt
VAR_012998
K
646
E
TRFE_HUMAN
Polymorphism
---
C/D
K
627
E
15
UniProt
VAR_012999
G
671
E
TRFE_HUMAN
Polymorphism
121918677
C/D
G
652
E
16
UniProt
VAR_051808
R
677
H
TFR1_HUMAN
Polymorphism
41298067
A/B
R
677
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 12)
Info
All PROSITE Patterns/Profiles
1: TRANSFERRIN_LIKE_4 (C:6-328,D:6-328|C:342-664,D:342-66...)
2: TRANSFERRIN_LIKE_1 (C:95-104,D:95-97)
3: TRANSFERRIN_LIKE_2 (C:188-204,D:188-204|-)
4: TRANSFERRIN_LIKE_3 (C:222-252,D:222-252|C:583-588,D:58...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRANSFERRIN_LIKE_4
PS51408
Transferrin-like domain profile.
TRFE_HUMAN
25-347
361-683
4
C:6-328
D:6-328
C:342-664
D:342-664
2
TRANSFERRIN_LIKE_1
PS00205
Transferrin-like domain signature 1.
TRFE_HUMAN
114-123
2
C:95-104
D:95-97
3
TRANSFERRIN_LIKE_2
PS00206
Transferrin-like domain signature 2.
TRFE_HUMAN
207-223
536-551
2
C:188-204
D:188-204
-
4
TRANSFERRIN_LIKE_3
PS00207
Transferrin-like domain signature 3.
TRFE_HUMAN
241-271
577-607
4
C:222-252
D:222-252
C:583-588
D:583-588
[
close PROSITE info
]
Exons
(16, 32)
Info
All Exons
Exon 1.5 (A:121-145 | B:121-145)
Exon 1.6 (A:145-195 | B:145-195)
Exon 1.7b (A:195-229 | B:195-229)
Exon 1.8b (A:230-267 | B:230-267)
Exon 1.9 (A:268-300 | B:268-300)
Exon 1.10b (A:301-347 | B:301-347)
Exon 1.11a (A:347-400 | B:347-400)
Exon 1.12 (A:400-440 | B:400-440)
Exon 1.14c (A:440-468 | B:440-468)
Exon 1.14d (A:469-490 | B:469-490)
Exon 1.15c (A:490-512 | B:490-512)
Exon 1.16b (A:513-532 | B:513-532)
Exon 1.17b (A:532-559 | B:532-559)
Exon 1.18c (A:560-633 | B:560-633)
Exon 1.19c (A:634-680 | B:634-680)
Exon 1.20a (A:681-758 | B:681-759)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.3/1.5
02: Boundary 1.5/1.6
03: Boundary 1.6/1.7b
04: Boundary 1.7b/1.8b
05: Boundary 1.8b/1.9
06: Boundary 1.9/1.10b
07: Boundary 1.10b/1.11a
08: Boundary 1.11a/1.12
09: Boundary 1.12/1.14c
10: Boundary 1.14c/1.14d
11: Boundary 1.14d/1.15c
12: Boundary 1.15c/1.16b
13: Boundary 1.16b/1.17b
14: Boundary 1.17b/1.18c
15: Boundary 1.18c/1.19c
16: Boundary 1.19c/1.20a
17: Boundary 1.20a/-
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
1.1e
ENST00000392396
1e
ENSE00001511658
chr3:
195808961-195808702
260
TFR1_HUMAN
-
0
0
-
-
1.2
ENST00000392396
2
ENSE00002184017
chr3:
195803993-195803935
59
TFR1_HUMAN
1-12
12
0
-
-
1.3
ENST00000392396
3
ENSE00000336901
chr3:
195802231-195802030
202
TFR1_HUMAN
13-80
68
0
-
-
1.5
ENST00000392396
5
ENSE00001645063
chr3:
195800996-195800801
196
TFR1_HUMAN
80-145
66
2
A:121-145
B:121-145
25
25
1.6
ENST00000392396
6
ENSE00001615518
chr3:
195799023-195798874
150
TFR1_HUMAN
145-195
51
2
A:145-195
B:145-195
51
51
1.7b
ENST00000392396
7b
ENSE00000781814
chr3:
195798369-195798267
103
TFR1_HUMAN
195-229
35
2
A:195-229
B:195-229
35
35
1.8b
ENST00000392396
8b
ENSE00000336905
chr3:
195796439-195796326
114
TFR1_HUMAN
230-267
38
2
A:230-267
B:230-267
38
38
1.9
ENST00000392396
9
ENSE00000781817
chr3:
195795001-195794903
99
TFR1_HUMAN
268-300
33
2
A:268-300
B:268-300
33
33
1.10b
ENST00000392396
10b
ENSE00000781818
chr3:
195794528-195794389
140
TFR1_HUMAN
301-347
47
2
A:301-347
B:301-347
47
47
1.11a
ENST00000392396
11a
ENSE00000781819
chr3:
195792471-195792314
158
TFR1_HUMAN
347-400
54
2
A:347-400
B:347-400
54
54
1.12
ENST00000392396
12
ENSE00000781821
chr3:
195791299-195791180
120
TFR1_HUMAN
400-440
41
2
A:400-440
B:400-440
41
41
1.14c
ENST00000392396
14c
ENSE00001189905
chr3:
195789810-195789725
86
TFR1_HUMAN
440-468
29
2
A:440-468
B:440-468
29
29
1.14d
ENST00000392396
14d
ENSE00000781823
chr3:
195789516-195789453
64
TFR1_HUMAN
469-490
22
2
A:469-490
B:469-490
22
22
1.15c
ENST00000392396
15c
ENSE00000781824
chr3:
195787118-195787051
68
TFR1_HUMAN
490-512
23
2
A:490-512
B:490-512
23
23
1.16b
ENST00000392396
16b
ENSE00000781826
chr3:
195785503-195785445
59
TFR1_HUMAN
513-532
20
2
A:513-532
B:513-532
20
20
1.17b
ENST00000392396
17b
ENSE00000781827
chr3:
195785236-195785155
82
TFR1_HUMAN
532-559
28
2
A:532-559
B:532-559
28
28
1.18c
ENST00000392396
18c
ENSE00000781828
chr3:
195782172-195781951
222
TFR1_HUMAN
560-633
74
2
A:560-633
B:560-633
74
74
1.19c
ENST00000392396
19c
ENSE00000781829
chr3:
195780429-195780289
141
TFR1_HUMAN
634-680
47
2
A:634-680
B:634-680
47
47
1.20a
ENST00000392396
20a
ENSE00001405345
chr3:
195779055-195776347
2709
TFR1_HUMAN
681-760
80
2
A:681-758
B:681-759
78
79
[
close EXON info
]
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
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 (328 KB)
Header - Asym.Unit
Biol.Unit 1 (325 KB)
Header - Biol.Unit 1
Biol.Unit 2 (306 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
3S9M
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help