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1OZN
Asym. Unit
Info
Asym.Unit (60 KB)
Biol.Unit 1 (55 KB)
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(1)
Title
:
1.5A CRYSTAL STRUCTURE OF THE NOGO RECEPTOR LIGAND BINDING DOMAIN REVEALS A CONVERGENT RECOGNITION SCAFFOLD MEDIATING INHIBITION OF MYELINATION
Authors
:
X. He, J. F. Bazan, J. B. Park, G. Mcdermott, Z. He, K. C. Garcia
Date
:
09 Apr 03 (Deposition) - 20 May 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.52
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Nogo Receptor, Mad, Myelination Inhibition, Omgp, Mag, Nogo-66, P75, Signal Transduction, Neuronal Regeneration, Ligand Binding, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. L. He, J. F. Bazan, G. Mcdermott, J. B. Park, K. Wang, M. Tessier-Lavigne, Z. He, K. C. Garcia
Structure Of The Nogo Receptor Ectodomain. A Recognition Module Implicated In Myelin Inhibition.
Neuron V. 38 177 2003
[
close entry info
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Hetero Components
(5, 10)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
1c: ACETIC ACID (ACYc)
2a: BETA-D-MANNOSE (BMAa)
3a: ALPHA-D-MANNOSE (MANa)
3b: ALPHA-D-MANNOSE (MANb)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
5b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
5c: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
3
Ligand/Ion
ACETIC ACID
2
BMA
1
Ligand/Ion
BETA-D-MANNOSE
3
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
4
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
NDG
3
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:45 , ALA A:58 , ARG A:81 , ASN A:82 , ASN A:304 , NDG A:402 , HOH A:675 , HOH A:702 , HOH A:719
BINDING SITE FOR RESIDUE NDG A 401
02
AC2
SOFTWARE
GLN A:45 , GLN A:46 , NDG A:401 , MAN A:403 , MAN A:404 , HOH A:505
BINDING SITE FOR RESIDUE NDG A 402
03
AC3
SOFTWARE
VAL A:32 , LEU A:289 , NDG A:402 , MAN A:404 , HOH A:573 , HOH A:720
BINDING SITE FOR RESIDUE MAN A 403
04
AC4
SOFTWARE
VAL A:263 , ASP A:265 , LEU A:289 , PRO A:290 , GLN A:307 , NDG A:402 , MAN A:403
BINDING SITE FOR RESIDUE MAN A 404
05
AC5
SOFTWARE
ASP A:122 , ALA A:154 , ALA A:155 , ASN A:179 , NDG A:406 , HOH A:628 , HOH A:689 , HOH A:691 , HOH A:695
BINDING SITE FOR RESIDUE NAG A 405
06
AC6
SOFTWARE
ALA A:98 , ASP A:122 , NAG A:405 , BMA A:407
BINDING SITE FOR RESIDUE NDG A 406
07
AC7
SOFTWARE
ALA A:99 , NDG A:406 , HOH A:651
BINDING SITE FOR RESIDUE BMA A 407
08
AC8
SOFTWARE
PRO A:290 , ARG A:292 , GLN A:307 , HOH A:466
BINDING SITE FOR RESIDUE ACY A 1
09
AC9
SOFTWARE
GLN A:49 , ALA A:50 , ARG A:269 , HOH A:581
BINDING SITE FOR RESIDUE ACY A 2
10
BC1
SOFTWARE
GLN A:49 , ARG A:68 , GLY A:308 , HOH A:572 , HOH A:701
BINDING SITE FOR RESIDUE ACY A 3
[
close Site info
]
SAPs(SNPs)/Variants
(10, 10)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_079224 (V53M, chain A, )
02: VAR_079225 (R68H, chain A, )
03: VAR_079154 (R119W, chain A, )
04: VAR_079226 (G141S, chain A, )
05: VAR_079155 (R196H, chain A, )
06: VAR_079227 (R227C, chain A, )
07: VAR_079228 (R227H, chain A, )
08: VAR_079229 (D259N, chain A, )
09: VAR_079230 (V263M, chain A, )
10: VAR_079231 (R292H, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_079224
V
53
M
RTN4R_HUMAN
---
145292678
A
V
53
M
02
UniProt
VAR_079225
R
68
H
RTN4R_HUMAN
---
145773589
A
R
68
H
03
UniProt
VAR_079154
R
119
W
RTN4R_HUMAN
---
74315508
A
R
119
W
04
UniProt
VAR_079226
G
141
S
RTN4R_HUMAN
---
760855779
A
G
141
S
05
UniProt
VAR_079155
R
196
H
RTN4R_HUMAN
---
74315509
A
R
196
H
06
UniProt
VAR_079227
R
227
C
RTN4R_HUMAN
---
754793885
A
R
227
C
07
UniProt
VAR_079228
R
227
H
RTN4R_HUMAN
---
576939822
A
R
227
H
08
UniProt
VAR_079229
D
259
N
RTN4R_HUMAN
---
3747073
A
D
259
N
09
UniProt
VAR_079230
V
263
M
RTN4R_HUMAN
---
752810777
A
V
263
M
10
UniProt
VAR_079231
R
292
H
RTN4R_HUMAN
---
---
A
R
292
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: LRR (A:82-103|A:106-128|A:155-176|A:179...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LRR
PS51450
Leucine-rich repeat profile.
RTN4R_HUMAN
82-103
106-128
155-176
179-200
203-224
227-248
6
A:82-103
A:106-128
A:155-176
A:179-200
A:203-224
A:227-248
[
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]
Exons
(1, 1)
Info
All Exons
Exon 1.8e (A:26-309)
View:
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All Exon Boundaries
1: Boundary 1.5a/1.8e
2: Boundary 1.8e/-
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
1.5a
ENST00000043402
5a
ENSE00001358408
chr22:
20256054-20255594
461
RTN4R_HUMAN
1-8
8
0
-
-
1.8e
ENST00000043402
8e
ENSE00001557601
chr22:
20230633-20228938
1696
RTN4R_HUMAN
8-473
466
1
A:26-309
284
[
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]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1ozna_ (A:)
View:
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)
(
)
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(
)
Superfamilies
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
(112)
Superfamily
:
L domain-like
(93)
Family
:
Ngr ectodomain-like
(21)
Protein domain
:
Reticulon 4 receptor (Nogo-66 receptor, Ngr)
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1ozna_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1oznA00 (A:26-309)
View:
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Classes
(
)
(
)
Architectures
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Horseshoe
(92)
Topology
:
Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
(73)
Homologous Superfamily
:
Ribonuclease Inhibitor
(73)
Human (Homo sapiens)
(26)
1a
1oznA00
A:26-309
[
close CATH info
]
Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_LRR_8_1oznA01 (A:202-261)
1b: PFAM_LRR_8_1oznA02 (A:202-261)
1c: PFAM_LRR_8_1oznA03 (A:202-261)
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Clans
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)
(
)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
LRR
(77)
Family
:
LRR_8
(41)
Homo sapiens (Human)
(24)
1a
LRR_8-1oznA01
A:202-261
1b
LRR_8-1oznA02
A:202-261
1c
LRR_8-1oznA03
A:202-261
[
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]
Atom Selection
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Protein
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Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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