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3D12
Asym. Unit
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
]
Hetero Components
(12, 52)
Info
All Hetero Components
01a: BETA-D-GLUCOSE (BGCa)
01b: BETA-D-GLUCOSE (BGCb)
01c: BETA-D-GLUCOSE (BGCc)
01d: BETA-D-GLUCOSE (BGCd)
01e: BETA-D-GLUCOSE (BGCe)
02a: BETA-D-MANNOSE (BMAa)
02b: BETA-D-MANNOSE (BMAb)
02c: BETA-D-MANNOSE (BMAc)
03a: BETA-D-GULOPYRANOSE (GL0a)
03b: BETA-D-GULOPYRANOSE (GL0b)
04a: ALPHA-D-GLUCOSE (GLCa)
04b: ALPHA-D-GLUCOSE (GLCb)
04c: ALPHA-D-GLUCOSE (GLCc)
05a: ALPHA-L-GALACTOPYRANOSE (GXLa)
06a: 2-(ACETYLAMINO)-2-DEOXY-BETA-D-GUL... (LXBa)
07a: 2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-ID... (LXZa)
08a: ALPHA-D-MANNOSE (MANa)
08b: ALPHA-D-MANNOSE (MANb)
09a: N-ACETYL-D-GLUCOSAMINE (NAGa)
09b: N-ACETYL-D-GLUCOSAMINE (NAGb)
09c: N-ACETYL-D-GLUCOSAMINE (NAGc)
09d: N-ACETYL-D-GLUCOSAMINE (NAGd)
09e: N-ACETYL-D-GLUCOSAMINE (NAGe)
09f: N-ACETYL-D-GLUCOSAMINE (NAGf)
09g: N-ACETYL-D-GLUCOSAMINE (NAGg)
09h: N-ACETYL-D-GLUCOSAMINE (NAGh)
09i: N-ACETYL-D-GLUCOSAMINE (NAGi)
09j: 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
5
Ligand/Ion
BETA-D-GLUCOSE
2
BMA
3
Ligand/Ion
BETA-D-MANNOSE
3
GL0
2
Ligand/Ion
BETA-D-GULOPYRANOSE
4
GLC
3
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
2
Ligand/Ion
ALPHA-D-MANNOSE
9
NAG
10
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
22
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 not available)
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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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.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3d12b_ (B:)
1b: SCOP_d3d12e_ (E:)
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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:
[
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]
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:
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Label:
Sorry, no Info available
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Asym.Unit (207 KB)
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