2VWD: Nipah Virus Attachment Glycoprotein

Nipah Virus Attachment Glycoprotein. Determined by X-ray diffraction at 2.25 Å resolution. Released 7 Oct 2008.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Nipah virus
Chains: 2
Atoms: 7,278
Mol. weight: 97.37 kDa
Ligands: NAG, GBL
Released: 7 Oct 2008

Explore 2VWD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VWD contains 17 α-helices and 63 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	201-202	2	1
β-strand	215-225	11	2
β-strand	228-237	10	2
β-strand	245-257	13	2
β-strand	263-271	9	2
α-helix	276-278	3
β-strand	279-287	9	3
β-strand	290-297	8	3
α-helix	307-309	3
β-strand	314-320	7	3
α-helix	328-330	3
β-strand	332-335	4	3
α-helix	336	1
β-strand	340-341	2	4
β-strand	347-350	4	4
β-strand	354	1	3
β-strand	356-358	3	4
β-strand	361-371	11	4
α-helix	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	4
β-strand	426-430	5	4
β-strand	431	1	5
α-helix	432	1
β-strand	442-447	6	6
β-strand	450-455	6	6
β-strand	465-471	7	6
β-strand	475	1	5
β-strand	476-479	4	6
β-strand	509	1	1
β-strand	511-515	5	7
β-strand	520-526	7	7
β-strand	533	1	1
β-strand	535-541	7	7
β-strand	544-550	7	7
β-strand	557-568	12	1
β-strand	571-582	12	1
β-strand	587-596	10	1
α-helix	597-598	2

Chain B: 8 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	201-202	2	8
α-helix	204-206	3
β-strand	216-225	10	9
β-strand	228-236	9	9
α-helix	244	1
β-strand	245-257	13	9
β-strand	263-271	9	9
β-strand	279-287	9	10
β-strand	290-297	8	10
β-strand	314-320	7	10
α-helix	328-330	3
β-strand	332-335	4	10
β-strand	340-341	2	11
β-strand	347-350	4	11
β-strand	354	1	10
β-strand	356-358	3	11
β-strand	361-371	11	11
α-helix	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	11
β-strand	426-430	5	11
β-strand	431	1	12
α-helix	432	1
β-strand	442-447	6	13
β-strand	450-455	6	13
β-strand	465-471	7	13
β-strand	475	1	12
β-strand	476-479	4	13
β-strand	509	1	8
β-strand	511-515	5	14
β-strand	520-526	7	14
β-strand	533	1	15
β-strand	535-541	7	14
β-strand	544-550	7	14
β-strand	557	1	15
β-strand	558-568	11	8
β-strand	571-582	12	8
β-strand	587-596	10	8
α-helix	597-598	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin-neuraminidase	A, B	protein	420	Nipah virus	Q9IH62 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2VWD_1 HEMAGGLUTININ-NEURAMINIDASE (chains A, B)
GLPNNICLQKTSNQILKPKLISYTLPVVGQSGTCITDPLLAMDEGYFAYSHLERIGSCSR
GVSKQRIIGVGEVLDRGDEVPSLFMTNVWTPPNPNTVYHCSAVYNNEFYYVLCAVSTVGD
PILNSTYWSGSLMMTRLAVKPKSNGGGYNQHQLALRSIEKGRYDKVMPYGPSGIKQGDTL
YFPAVGFLVRTEFKYNDSNCPITKCQYSKPENCRLSMGIRPNSHYILRSGLLKYNLSDGE
NPKVVFIEISDQRLSIGSPSKIYDSLGQPVFYQASFSWDTMIKFGDVLTVNPLVVNWRNN
TVISRPGQSQCPRFNTCPEICWEGVYNDAFLIDRINWISAGVFLDSNQTAENPVFTVFKD
NEILYRAQLASEDTNAQKTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAVKIPEQCT

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10
GBL	Gamma-butyrolactone	C4 H6 O2	8

Water and common crystallization additives (CL) are not listed.

Primary citation

Crystal Structure and Carbohydrate Analysis of Nipah Virus Attachment Glycoprotein: A Template for Antiviral and Vaccine Design. Bowden, T.A., Crispin, M., Harvey, D.J. et al. J Virol (2008) 82:11628. DOI 10.1128/JVI.01344-08 · PubMed

Other PDB entries of the same protein (UniProt Q9IH62 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2VSM 1.8 Å, Nipah virus attachment glycoprotein in complex with human cell surface receptor ephrinB2
3D11 2.31 Å, Crystal Structures of the Nipah G Attachment Glycoprotein
8JA5 2.79 Å, Crystal structure of Nipah Virus attachment (G) glycoprotein in complex with…
8K3C 2.88 Å, Nipah virus Attachment glycoprotein with 41-6 antibody fragment
8K0D 2.94 Å, Cryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5…
9LU3 3.0 Å, LN1F9 Fab bound to Nipah Virus attachment (G) glycoprotein head domain
3D12 3.0 Å, Crystal Structures of Nipah Virus G Attachment Glycoprotein in Complex with its Receptor…
9LUE 3.03 Å, Cryo-EM structure of the Nipah G head domain in complex with three Fabs
8K0C 3.18 Å, Cryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G…
7TXZ 3.2 Å, Nipah Virus attachment (G) glycoprotein ectodomain in complex with nAH1.3 neutralizing…
6VY5 3.4 Å, Crystal structure of Nipah receptor binding protein head domain in complex with human…
7TY0 3.5 Å, Nipah Virus attachment (G) glycoprotein ectodomain in complex with nAH1.3 neutralizing…

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