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1V9U
Asym. Unit
Info
Asym.Unit (143 KB)
Biol.Unit 1, α-C (7.5 MB)
Biol.Unit 1 (7.5 MB)
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(1)
Title
:
HUMAN RHINOVIRUS 2 BOUND TO A FRAGMENT OF ITS CELLULAR RECEPTOR PROTEIN
Authors
:
N. Verdaguer, I. Fita, M. Reithmayer, R. Moser, D. Blaas
Date
:
03 Feb 04 (Deposition) - 04 May 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.60
Chains
:
Asym. Unit : 1,2,3,4,5
Biol. Unit 1: 1,2,3,4,5 (60x)
Keywords
:
Human Rhinovirus, Vldl-Receptor, Virus-Protein Complex, Icosahedral Virus, Virus/Receptor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Verdaguer, I. Fita, M. Reithmayer, R. Moser, D. Blaas
X-Ray Structure Of A Minor Group Human Rhinovirus Bound To A Fragment Of Its Cellular Receptor Protein
Nat. Struct. Mol. Biol. V. 11 429 2004
(for further references see the
PDB file header
)
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: LAURIC ACID (DAOa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
DAO
1
Ligand/Ion
LAURIC ACID
[
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TRP 5:132 , ASP 5:135 , GLU 5:137 , ASP 5:139 , ASP 5:145 , GLU 5:146
BINDING SITE FOR RESIDUE CA 5 1
2
AC2
SOFTWARE
ILE 1:99 , ASN 1:100 , LEU 1:101 , GLN 1:102 , ILE 1:123 , ASN 1:211
BINDING SITE FOR RESIDUE DAO 1 290
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: LDLRA_1 (-|-|5:127-149|-|-|-|-|-)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LDLRA_1
PS01209
LDL-receptor class A (LDLRA) domain signature.
VLDLR_HUMAN
45-67
84-108
127-149
166-188
205-229
251-273
290-312
331-355
1
-
-
5:127-149
-
-
-
-
-
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Exons
(2, 2)
Info
All Exons
Exon 1.4 (5:113-150)
Exon 1.5b (5:150-151)
View:
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All Exon Boundaries
1: Boundary 1.3/1.4
2: Boundary 1.4/1.5b
3: Boundary 1.5b/1.6
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
1.1a
ENST00000382100
1a
ENSE00001931208
chr9:
2621834-2622271
438
VLDLR_HUMAN
1-28
28
0
-
-
1.2c
ENST00000382100
2c
ENSE00001257347
chr9:
2635453-2635572
120
VLDLR_HUMAN
28-68
41
0
-
-
1.3
ENST00000382100
3
ENSE00000982061
chr9:
2639859-2639981
123
VLDLR_HUMAN
68-109
42
0
-
-
1.4
ENST00000382100
4
ENSE00000982062
chr9:
2641377-2641499
123
VLDLR_HUMAN
109-150
42
1
5:113-150
38
1.5b
ENST00000382100
5b
ENSE00002174845
chr9:
2643160-2643531
372
VLDLR_HUMAN
150-274
125
1
5:150-151
2
1.6
ENST00000382100
6
ENSE00001735963
chr9:
2643628-2643750
123
VLDLR_HUMAN
274-315
42
0
-
-
1.7
ENST00000382100
7
ENSE00001655382
chr9:
2643837-2643959
123
VLDLR_HUMAN
315-356
42
0
-
-
1.8
ENST00000382100
8
ENSE00001700967
chr9:
2644734-2644853
120
VLDLR_HUMAN
356-396
41
0
-
-
1.9
ENST00000382100
9
ENSE00001803937
chr9:
2644957-2645082
126
VLDLR_HUMAN
396-438
43
0
-
-
1.10
ENST00000382100
10
ENSE00001626953
chr9:
2645574-2645745
172
VLDLR_HUMAN
438-495
58
0
-
-
1.11a
ENST00000382100
11a
ENSE00001738995
chr9:
2646334-2646552
219
VLDLR_HUMAN
495-568
74
0
-
-
1.12a
ENST00000382100
12a
ENSE00001798149
chr9:
2647474-2647592
119
VLDLR_HUMAN
568-608
41
0
-
-
1.13
ENST00000382100
13
ENSE00001638697
chr9:
2648208-2648347
140
VLDLR_HUMAN
608-654
47
0
-
-
1.14
ENST00000382100
14
ENSE00001687844
chr9:
2648669-2648810
142
VLDLR_HUMAN
655-702
48
0
-
-
1.15
ENST00000382100
15
ENSE00001696031
chr9:
2650370-2650516
147
VLDLR_HUMAN
702-751
50
0
-
-
1.16
ENST00000382100
16
ENSE00001740203
chr9:
2651415-2651498
84
VLDLR_HUMAN
751-779
29
0
-
-
1.17
ENST00000382100
17
ENSE00001673529
chr9:
2651874-2651954
81
VLDLR_HUMAN
779-806
28
0
-
-
1.18
ENST00000382100
18
ENSE00001715686
chr9:
2652780-2652949
170
VLDLR_HUMAN
806-862
57
0
-
-
1.19a
ENST00000382100
19a
ENSE00001257470
chr9:
2653833-2654480
648
VLDLR_HUMAN
863-873
11
0
-
-
[
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SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1v9u_1 (4:,2:)
1b: SCOP_d1v9u1_ (1:)
1c: SCOP_d1v9u3_ (3:)
2a: SCOP_d1v9u5_ (5:)
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Protein Domains
(
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(
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Organisms
(
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(
)
Class
:
All beta proteins
(24004)
Fold
:
Nucleoplasmin-like/VP (viral coat and capsid proteins)
(278)
Superfamily
:
Positive stranded ssRNA viruses
(163)
Family
:
Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
(103)
Protein domain
:
Rhinovirus coat proteins
(46)
Human rhinovirus A 2 (HRV-2) [TaxId: 12130]
(2)
1a
d1v9u.1
4:,2:
1b
d1v9u1_
1:
1c
d1v9u3_
3:
Class
:
Small proteins
(3458)
Fold
:
LDL receptor-like module
(20)
Superfamily
:
LDL receptor-like module
(20)
Family
:
LDL receptor-like module
(19)
Protein domain
:
Very low-density lipoprotein receptor
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d1v9u5_
5:
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_1v9u300 (3:1-237)
1b: CATH_1v9u200 (2:12-261)
1c: CATH_1v9u100 (1:15-283)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.20, no name defined]
(133)
Human rhinovirus 2. Organism_taxid: 12130. Strain: serotype 2. Human rhinovirus 2. Organism_taxid: 12130. Strain: serotype 2. Human rhinovirus 2. Organism_taxid: 12130. Strain: serotype 2. Human rhinovirus 2. Organism_taxid: 12130. Strain: serotype 2.
(1)
1a
1v9u300
3:1-237
1b
1v9u200
2:12-261
1c
1v9u100
1:15-283
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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Asym.Unit (143 KB)
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