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3D12
Biol. Unit 1
Info
Asym.Unit (207 KB)
Biol.Unit 1 (196 KB)
Biol.Unit 2 (100 KB)
Biol.Unit 3 (101 KB)
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(1)
Title
:
CRYSTAL STRUCTURES OF NIPAH VIRUS G ATTACHMENT GLYCOPROTEIN IN COMPLEX WITH ITS RECEPTOR EPHRIN-B3
Authors
:
K. Xu, K. R. Rajashankar, Y. P. Chan, P. Himanen, C. C. Broder, D. B. Nikol
Date
:
02 May 08 (Deposition) - 19 Aug 08 (Release) - 12 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,D,E
Biol. Unit 1: A,B,D,E (1x)
Biol. Unit 2: D,E (1x)
Biol. Unit 3: A,B (1x)
Keywords
:
Beta Propeller, Protein-Receptor Complex, Envelope Protein, Glycoprotein, Hemagglutinin, Hydrolase, Membrane, Signal-Anchor, Transmembrane, Virion, Developmental Protein, Differentiation, Neurogenesis, Hydrolase-Membrane Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Xu, K. R. Rajashankar, Y. P. Chan, J. P. Himanen, C. C. Broder, D. B. Nikolov
Host Cell Recognition By The Henipaviruses: Crystal Structures Of The Nipah G Attachment Glycoprotein And Its Complex With Ephrin-B3.
Proc. Natl. Acad. Sci. Usa V. 105 9953 2008
[
close entry info
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Hetero Components
(9, 26)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
1b: BETA-D-GLUCOSE (BGCb)
1c: BETA-D-GLUCOSE (BGCc)
1d: BETA-D-GLUCOSE (BGCd)
1e: BETA-D-GLUCOSE (BGCe)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
2c: BETA-D-MANNOSE (BMAc)
3a: BETA-D-GULOPYRANOSE (GL0a)
3b: BETA-D-GULOPYRANOSE (GL0b)
4a: ALPHA-D-GLUCOSE (GLCa)
4b: ALPHA-D-GLUCOSE (GLCb)
4c: ALPHA-D-GLUCOSE (GLCc)
5a: ALPHA-L-GALACTOPYRANOSE (GXLa)
6a: 2-(ACETYLAMINO)-2-DEOXY-BETA-D-GUL... (LXBa)
7a: 2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-ID... (LXZa)
8a: ALPHA-D-MANNOSE (MANa)
8b: ALPHA-D-MANNOSE (MANb)
9a: N-ACETYL-D-GLUCOSAMINE (NAGa)
9b: N-ACETYL-D-GLUCOSAMINE (NAGb)
9c: N-ACETYL-D-GLUCOSAMINE (NAGc)
9d: N-ACETYL-D-GLUCOSAMINE (NAGd)
9e: N-ACETYL-D-GLUCOSAMINE (NAGe)
9f: N-ACETYL-D-GLUCOSAMINE (NAGf)
9g: N-ACETYL-D-GLUCOSAMINE (NAGg)
9h: N-ACETYL-D-GLUCOSAMINE (NAGh)
9i: N-ACETYL-D-GLUCOSAMINE (NAGi)
9j: N-ACETYL-D-GLUCOSAMINE (NAGj)
10a: N-ACETYL-D-GALACTOSAMINE (NGAa)
11a: 2-(ACETYLAMINO)-2-DEOXY-ALPHA-L-GL... (NGZa)
12a: SULFATE ION (SO4a)
12b: SULFATE ION (SO4b)
12c: SULFATE ION (SO4c)
12d: SULFATE ION (SO4d)
12e: SULFATE ION (SO4e)
12f: SULFATE ION (SO4f)
12g: SULFATE ION (SO4g)
12h: SULFATE ION (SO4h)
12i: SULFATE ION (SO4i)
12j: SULFATE ION (SO4j)
12k: SULFATE ION (SO4k)
12l: SULFATE ION (SO4l)
12m: SULFATE ION (SO4m)
12n: SULFATE ION (SO4n)
12o: SULFATE ION (SO4o)
12p: SULFATE ION (SO4p)
12q: SULFATE ION (SO4q)
12r: SULFATE ION (SO4r)
12s: SULFATE ION (SO4s)
12t: SULFATE ION (SO4t)
12u: SULFATE ION (SO4u)
12v: SULFATE ION (SO4v)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGC
2
Ligand/Ion
BETA-D-GLUCOSE
2
BMA
2
Ligand/Ion
BETA-D-MANNOSE
3
GL0
1
Ligand/Ion
BETA-D-GULOPYRANOSE
4
GLC
2
Ligand/Ion
ALPHA-D-GLUCOSE
5
GXL
-1
Ligand/Ion
ALPHA-L-GALACTOPYRANOSE
6
LXB
-1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-BETA-D-GULOPYRANOSE
7
LXZ
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-IDOPYRANOSE
8
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
9
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
10
NGA
1
Ligand/Ion
N-ACETYL-D-GALACTOSAMINE
11
NGZ
-1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-ALPHA-L-GLUCOPYRANOSE
12
SO4
11
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(32, 32)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:402 , SER A:405 , HIS A:406 , ARG E:90 , ARG E:91
BINDING SITE FOR RESIDUE SO4 A 1368
02
AC2
SOFTWARE
ASN A:404 , ALA B:97 , ALA E:87 , ARG E:90
BINDING SITE FOR RESIDUE SO4 A 1369
03
AC3
SOFTWARE
NAG A:1210
BINDING SITE FOR RESIDUE SO4 A 1370
04
AC4
SOFTWARE
NAG A:1313 , NAG A:1314
BINDING SITE FOR RESIDUE SO4 A 1371
05
AC5
SOFTWARE
HOH A:46 , HOH A:47 , LYS A:541 , ASN A:543 , GLU A:544
BINDING SITE FOR RESIDUE SO4 A 1372
06
AC6
SOFTWARE
ARG A:480
BINDING SITE FOR RESIDUE SO4 A 1373
07
AC7
SOFTWARE
GLN A:434 , ARG A:435 , SO4 A:1375
BINDING SITE FOR RESIDUE SO4 A 1374
08
AC8
SOFTWARE
TYR A:377 , ASP A:433 , ARG A:435 , LEU A:436 , SO4 A:1374
BINDING SITE FOR RESIDUE SO4 A 1375
09
AC9
SOFTWARE
LYS A:596 , PRO A:598 , GLU A:599 , GLN A:600
BINDING SITE FOR RESIDUE SO4 A 1376
10
BC1
SOFTWARE
GLU B:85 , ALA B:87 , ARG B:90 , HIS B:133 , ASP B:134
BINDING SITE FOR RESIDUE SO4 B 202
11
BC2
SOFTWARE
ARG B:90 , ARG B:91
BINDING SITE FOR RESIDUE SO4 B 203
12
BC3
SOFTWARE
ASN D:497 , LXB D:1461
BINDING SITE FOR RESIDUE GXL D 1467
13
BC4
SOFTWARE
ARG D:402 , SER D:405 , HIS D:406
BINDING SITE FOR RESIDUE SO4 D 1468
14
BC5
SOFTWARE
NAG D:1310
BINDING SITE FOR RESIDUE SO4 D 1469
15
BC6
SOFTWARE
NAG D:1413 , NAG D:1414
BINDING SITE FOR RESIDUE SO4 D 1470
16
BC7
SOFTWARE
LYS D:541 , ASN D:543 , GLU D:544
BINDING SITE FOR RESIDUE SO4 D 1471
17
BC8
SOFTWARE
ARG D:480 , NAG D:1413
BINDING SITE FOR RESIDUE SO4 D 1472
18
BC9
SOFTWARE
GLN D:434 , ARG D:435 , SO4 D:1474
BINDING SITE FOR RESIDUE SO4 D 1473
19
CC1
SOFTWARE
TYR D:377 , ARG D:435 , LEU D:436 , TRP D:460 , SO4 D:1473
BINDING SITE FOR RESIDUE SO4 D 1474
20
CC2
SOFTWARE
LYS D:596 , GLU D:599 , GLN D:600
BINDING SITE FOR RESIDUE SO4 D 1475
21
CC3
SOFTWARE
GLY D:327 , GLY D:328 , GLY D:329 , ASN D:331 , GLN D:332 , HOH D:1520
BINDING SITE FOR RESIDUE SO4 D 1476
22
CC4
SOFTWARE
ARG D:318 , GLY D:329
BINDING SITE FOR RESIDUE SO4 D 1477
23
CC5
SOFTWARE
MAN A:1142 , THR E:158 , ARG E:159
BINDING SITE FOR RESIDUE SO4 E 190
24
CC6
SOFTWARE
VAL A:300 , ASN A:306 , GLN E:43 , LEU E:157 , THR E:158 , SO4 E:190
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 306 RESIDUES 1138 TO 1142
25
CC7
SOFTWARE
HOH A:25 , HOH A:26 , HOH A:27 , ASN A:378 , SER A:380 , SO4 A:1370 , MAN D:1242
BINDING SITE FOR MONO-SACCHARIDE NAG A1210 BOUND TO ASN A 378
26
CC8
SOFTWARE
HOH A:34 , HOH A:36 , GLN A:434 , ASN A:478 , TRP A:479 , ARG A:480 , ASN A:481 , SO4 A:1371
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 481 RESIDUES 1313 TO 1314
27
CC9
SOFTWARE
ASN A:497 , ASN A:529
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 529 RESIDUES 1361 TO 1367
28
DC1
SOFTWARE
ASP A:379 , NAG A:1210 , VAL D:300 , ASN D:306 , TYR D:309
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 306 RESIDUES 1238 TO 1242
29
DC2
SOFTWARE
ASN D:378 , SER D:380 , SO4 D:1469 , HOH D:1500 , HOH D:1501
BINDING SITE FOR MONO-SACCHARIDE NAG D1310 BOUND TO ASN D 378
30
DC3
SOFTWARE
ASN D:478 , TRP D:479 , ASN D:481 , SO4 D:1470 , SO4 D:1472 , HOH D:1479
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 481 RESIDUES 1413 TO 1414
31
DC4
SOFTWARE
PHE D:496 , ASN D:529 , GXL D:1467 , HOH D:1511 , HOH D:1512 , ARG E:112
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 529 RESIDUES 1461 TO 1466
32
DC5
SOFTWARE
LXB D:1461 , BGC D:1466
BINDING SITE FOR CHAIN D OF POLYSACCHARIDE RESIDUES 1462 TO 1465
[
close Site info
]
SAPs(SNPs)/Variants
(8, 16)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_GLYCP_NIPAV_004 (R248K, chain A/D, )
2: VAR_GLYCP_NIPAV_005 (T272A, chain A/D, )
3: VAR_GLYCP_NIPAV_006 (G327D, chain A/D, )
4: VAR_GLYCP_NIPAV_007 (I408V, chain A/D, )
5: VAR_GLYCP_NIPAV_008 (V426I, chain A/D, )
6: VAR_GLYCP_NIPAV_009 (L470Q, chain A/D, )
7: VAR_GLYCP_NIPAV_010 (N478S, chain A/D, )
8: VAR_GLYCP_NIPAV_011 (N481D, chain A/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_GLYCP_NIPAV_004
*
R
248
K
GLYCP_NIPAV
---
---
A/D
R
248
K
2
UniProt
VAR_GLYCP_NIPAV_005
*
T
272
A
GLYCP_NIPAV
---
---
A/D
T
272
A
3
UniProt
VAR_GLYCP_NIPAV_006
*
G
327
D
GLYCP_NIPAV
---
---
A/D
G
327
D
4
UniProt
VAR_GLYCP_NIPAV_007
*
I
408
V
GLYCP_NIPAV
---
---
A/D
I
408
V
5
UniProt
VAR_GLYCP_NIPAV_008
*
V
426
I
GLYCP_NIPAV
---
---
A/D
V
426
I
6
UniProt
VAR_GLYCP_NIPAV_009
*
L
470
Q
GLYCP_NIPAV
---
---
A/D
L
470
Q
7
UniProt
VAR_GLYCP_NIPAV_010
*
N
478
S
GLYCP_NIPAV
---
---
A/D
N
478
S
8
UniProt
VAR_GLYCP_NIPAV_011
*
N
481
D
GLYCP_NIPAV
---
---
A/D
N
481
D
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: EPHRIN_RBD_1 (B:112-139,E:112-139)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EPHRIN_RBD_1
PS01299
Ephrin receptor-binding (ephrin RBD) domain signature.
EFNB3_MOUSE
112-139
2
B:112-139
E:112-139
[
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]
Exons
(0, 0)
Info
All Exons
View:
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Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3d12b_ (B:)
1b: SCOP_d3d12e_ (E:)
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Protein Domains
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Organisms
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)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
automated matches
(57)
Protein domain
:
automated matches
(57)
Mouse (Mus musculus) [TaxId: 10090]
(1)
1a
d3d12b_
B:
1b
d3d12e_
E:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
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)
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