2VSM: Nipah virus attachment glycoprotein

Nipah virus attachment glycoprotein in complex with human cell surface receptor ephrinB2. Determined by X-ray diffraction at 1.8 Å resolution. Released 20 May 2008.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Nipah virus, Homo sapiens
Chains: 2
Atoms: 5,272
Mol. weight: 63.83 kDa
Ligands: NAG, IPA
Released: 20 May 2008

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

Secondary structure: helices and β-sheets

2VSM contains 14 α-helices and 48 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: 7 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	201-203	3	1
β-strand	215-225	11	2
β-strand	228-237	10	2
β-strand	244-257	14	2
β-strand	263-271	9	2
β-strand	279-287	9	3
β-strand	290-297	8	3
β-strand	314-320	7	3
α-helix	328-331	4
β-strand	332-336	5	3
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
α-helix	418-420	3
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	571-581	11	1
β-strand	587-588	2	2
β-strand	591-596	6	1
α-helix	597-598	2

Chain B: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	32	1	8
α-helix	33-35	3
β-strand	36-37	2	8
β-strand	46	1	9
β-strand	50	1	9
β-strand	51-53	3	10
α-helix	55-56	2
β-strand	60-65	6	8
α-helix	66-68	3
α-helix	75-77	3
β-strand	78	1	11
β-strand	79-81	3	12
β-strand	82-84	3	10
α-helix	86-91	6
β-strand	93	1	13
β-strand	102-104	3	12
β-strand	111-116	6	8
β-strand	133-138	6	10
β-strand	143	1	11
α-helix	145-147	3
β-strand	152	1	13
α-helix	154-158	5
β-strand	162-167	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin-neuraminidase	A	protein	416	Nipah virus	Q9IH62 (AlphaFold model)
Ephrin-B2	B	protein	140	Homo sapiens	P52799 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2VSM_1 HEMAGGLUTININ-NEURAMINIDASE (chains A)
ICLQKTSNQILKPKLISYTLPVVGQSGTCITDPLLAMDEGYFAYSHLERIGSCSRGVSKQ
RIIGVGEVLDRGDEVPSLFMTNVWTPPNPNTVYHCSAVYNNEFYYVLCAVSTVGDPILNS
TYWSGSLMMTRLAVKPKSNGGGYNQHQLALRSIEKGRYDKVMPYGPSGIKQGDTLYFPAV
GFLVRTEFKYNDSNCPITKCQYSKPENCRLSMGIRPNSHYILRSGLLKYNLSDGENPKVV
FIEISDQRLSIGSPSKIYDSLGQPVFYQASFSWDTMIKFGDVLTVNPLVVNWRNNTVISR
PGQSQCPRFNTCPEICWEGVYNDAFLIDRINWISAGVFLDSNQTAENPVFTVFKDNEILY
RAQLASEDTNAQKTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAVKIPEQCTH

Sequence of entity 2 (B), FASTA

>2VSM_2 EPHRIN-B2 (chains B)
IVLEPIYWNSSNSKFLPGQGLVLYPQIGDKLDIICPKVDSKTVGQYEYYKVYMVDKDQAD
RCTIKKENTPLLNCAKPDQDIKFTIKFQEFSPNLWGLEFQKNKDYYIISTSNGSLEGLDN
QEGGVCQTRAMKILMKVGHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
IPA	Isopropyl alcohol	C3 H8 O	1

Primary citation

Structural Basis of Nipah and Hendra Virus Attachment to Their Cell-Surface Receptor Ephrin-B2. Bowden, T.A., Aricescu, A.R., Gilbert, R.J. et al. Nat Struct Mol Biol (2008) 15:567. DOI 10.1038/NSMB.1435 · PubMed

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

2VWD 2.25 Å, Nipah Virus Attachment Glycoprotein
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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