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2W9E
Asym. Unit
Info
Asym.Unit (91 KB)
Biol.Unit 1 (84 KB)
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(1)
Title
:
STRUCTURE OF ICSM 18 (ANTI-PRP THERAPEUTIC ANTIBODY) FAB FRAGMENT COMPLEXED WITH HUMAN PRP FRAGMENT 119-231
Authors
:
S. V. Antonyuk, C. R. Trevitt, R. W. Strange, G. S. Jackson, D. Sangar, M. Batchelor, S. Jones, T. Georgiou, S. Cooper, C. Fraser, A. Khalili- A. R. Clarke, S. S. Hasnain, J. Collinge
Date
:
23 Jan 09 (Deposition) - 03 Feb 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,H,L
Biol. Unit 1: A,H,L (1x)
Keywords
:
Fab, Prp, Prion, Membrane, Gpi-Anchor, Lipoprotein, Golgi Apparatus, Disease Mutation, Immune System, Glycoprotein, Cell Membrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. V. Antonyuk, C. R. Trevitt, R. W. Strange, G. S. Jackson, D. Sangar, M. Batchelor, S. Cooper, C. Fraser, S. Jones, T. Georgiou, A. Khalili-Shirazi, A. R. Clarke, S. S. Hasnain, J. Collinge
Crystal Structure Of Human Prion Protein Bound To A Therapeutic Antibody.
Proc. Natl. Acad. Sci. Usa V. 106 2554 2009
[
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:136 , TYR H:60 , ARG H:65
BINDING SITE FOR RESIDUE SO4 A 300
[
close Site info
]
SAPs(SNPs)/Variants
(20, 20)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_006467 (M129V, chain A, )
02: VAR_014264 (G131V, chain A, )
03: VAR_006468 (N171S, chain A, )
04: VAR_006469 (D178N, chain A, )
05: VAR_006470 (V180I, chain A, )
06: VAR_006471 (T183A, chain A, )
07: VAR_008746 (H187R, chain A, )
08: VAR_008748 (T188K, chain A, )
09: VAR_008747 (T188R, chain A, )
10: VAR_008749 (E196K, chain A, )
11: VAR_006472 (F198S, chain A, )
12: VAR_006473 (E200K, chain A, )
13: VAR_008750 (D202N, chain A, )
14: VAR_008751 (V203I, chain A, )
15: VAR_006474 (R208H, chain A, )
16: VAR_006475 (V210I, chain A, )
17: VAR_008752 (E211Q, chain A, )
18: VAR_008753 (Q212P, chain A, )
19: VAR_006476 (Q217R, chain A, )
20: VAR_006477 (E219K, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_006467
M
129
V
PRIO_HUMAN
Polymorphism
1799990
A
M
129
V
02
UniProt
VAR_014264
G
131
V
PRIO_HUMAN
Disease (GSD)
---
A
G
131
V
03
UniProt
VAR_006468
N
171
S
PRIO_HUMAN
Polymorphism
16990018
A
N
171
S
04
UniProt
VAR_006469
D
178
N
PRIO_HUMAN
Disease (FFI)
---
A
D
178
N
05
UniProt
VAR_006470
V
180
I
PRIO_HUMAN
Disease (CJD)
---
A
V
180
I
06
UniProt
VAR_006471
T
183
A
PRIO_HUMAN
Unclassified
---
A
T
183
A
07
UniProt
VAR_008746
H
187
R
PRIO_HUMAN
Disease (GSD)
---
A
H
187
R
08
UniProt
VAR_008748
T
188
K
PRIO_HUMAN
Unclassified
---
A
T
188
K
09
UniProt
VAR_008747
T
188
R
PRIO_HUMAN
Polymorphism
---
A
T
188
R
10
UniProt
VAR_008749
E
196
K
PRIO_HUMAN
Disease (CJD)
---
A
E
196
K
11
UniProt
VAR_006472
F
198
S
PRIO_HUMAN
Disease (GSD)
---
A
F
198
S
12
UniProt
VAR_006473
E
200
K
PRIO_HUMAN
Disease (CJD)
---
A
E
200
K
13
UniProt
VAR_008750
D
202
N
PRIO_HUMAN
Disease (GSD)
---
A
D
202
N
14
UniProt
VAR_008751
V
203
I
PRIO_HUMAN
Disease (CJD)
---
A
V
203
I
15
UniProt
VAR_006474
R
208
H
PRIO_HUMAN
Disease (CJD)
---
A
R
208
H
16
UniProt
VAR_006475
V
210
I
PRIO_HUMAN
Disease (CJD)
---
A
V
210
I
17
UniProt
VAR_008752
E
211
Q
PRIO_HUMAN
Disease (CJD)
---
A
E
211
Q
18
UniProt
VAR_008753
Q
212
P
PRIO_HUMAN
Disease (GSD)
---
A
Q
212
P
19
UniProt
VAR_006476
Q
217
R
PRIO_HUMAN
Disease (GSD)
---
A
Q
217
R
20
UniProt
VAR_006477
E
219
K
PRIO_HUMAN
Polymorphism
1800014
A
E
219
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (L:191-197)
2: PRION_2 (A:200-218)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
IGKC_MOUSE
84-90
1
L:191-197
2
PRION_2
PS00706
Prion protein signature 2.
PRIO_HUMAN
200-218
1
A:200-218
[
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]
Exons
(1, 1)
Info
All Exons
Exon 1.2e (A:125-223)
View:
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All Exon Boundaries
1: Boundary 1.1c/1.2e
2: Boundary 1.2e/-
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
1.1c
ENST00000379440
1c
ENSE00001957346
chr20:
4666882-4667158
277
PRIO_HUMAN
-
0
0
-
-
1.2e
ENST00000379440
2e
ENSE00001928116
chr20:
4679857-4682236
2380
PRIO_HUMAN
1-257
257
1
A:125-223
99
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d2w9el1 (L:1-109)
2a: SCOP_d2w9el2 (L:110-212)
3a: SCOP_d2w9ea_ (A:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Mouse (Mus musculus) [TaxId: 10090]
(360)
1a
d2w9el1
L:1-109
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Mouse (Mus musculus) [TaxId: 10090]
(309)
2a
d2w9el2
L:110-212
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Prion-like
(73)
Superfamily
:
Prion-like
(73)
Family
:
Prion-like
(73)
Protein domain
:
automated matches
(29)
Human (Homo sapiens) [TaxId: 9606]
(8)
3a
d2w9ea_
A:
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2w9eA00 (A:125-223)
2a: CATH_2w9eL02 (L:108-210)
2b: CATH_2w9eH02 (H:117-215)
2c: CATH_2w9eH01 (H:1-116)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Major Prion Protein
(62)
Homologous Superfamily
:
Major Prion Protein
(62)
Human (Homo sapiens)
(28)
1a
2w9eA00
A:125-223
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
2w9eL02
L:108-210
2b
2w9eH02
H:117-215
2c
2w9eH01
H:1-116
[
close CATH info
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Prion_2w9eA01 (A:134-223)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Prion]
(32)
Family
:
Prion
(32)
Homo sapiens (Human)
(7)
1a
Prion-2w9eA01
A:134-223
[
close Pfam info
]
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Backbone
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Protein & NOT PROSITE
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Chain L
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