8XPY: Glycoprotein G

Structure of Nipah virus Malaysia string G protein ectodomain monomer bound to single-domain antibody n425 at 3.63 Angstroms overall resolution. Determined by electron microscopy at 3.63 Å resolution. Released 18 Sept 2024.

Method: Electron microscopy
Resolution: 3.63 Å
Organisms: Henipavirus nipahense, Homo sapiens
Chains: 2
Atoms: 4,568
Mol. weight: 84.42 kDa
Released: 18 Sept 2024

Explore 8XPY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8XPY contains 9 α-helices and 50 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, 33 β-strands

Element	Residues	Length	Sheet
β-strand	179	1	1
β-strand	201-202	2	1
β-strand	216-218	3	2
β-strand	222-225	4	2
β-strand	228-238	11	2
β-strand	243-257	15	2
β-strand	263-271	9	2
α-helix	276-278	3
β-strand	279-280	2	3
β-strand	285-286	2	3
β-strand	290-297	8	3
β-strand	314-320	7	3
β-strand	334-336	3	3
β-strand	340-341	2	4
β-strand	347-350	4	4
β-strand	356-357	2	4
β-strand	362-371	10	4
α-helix	372-374	3
α-helix	392-394	3
α-helix	396-398	3
β-strand	400	1	4
β-strand	407-416	10	4
β-strand	426-430	5	4
α-helix	431-432	2
β-strand	442-446	5	5
β-strand	451-455	5	5
β-strand	465-471	7	5
β-strand	476-479	4	5
α-helix	480	1
β-strand	509	1	1
β-strand	512-515	4	6
β-strand	520-526	7	6
β-strand	533	1	7
β-strand	535-540	6	6
β-strand	547-550	4	6
β-strand	557	1	7
β-strand	561-567	7	1
β-strand	572-582	11	1
β-strand	587-596	10	1
α-helix	597-598	2

Chain B: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	8
β-strand	6	1	9
β-strand	12	1	10
β-strand	17-18	2	11
β-strand	22	1	9
β-strand	25	1	8
β-strand	35-39	5	12
β-strand	45-49	5	12
β-strand	50-51	2	13
β-strand	58-59	2	13
α-helix	62-64	3
β-strand	68	1	11
β-strand	71	1	14
β-strand	80	1	14
β-strand	83-84	2	11
α-helix	88-90	3
β-strand	92-97	6	12
β-strand	113-115	3	12
β-strand	117	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein G	A	protein	602	Henipavirus nipahense	Q9IH62 (AlphaFold model)
single-domain antibody n425	B	protein	119	Homo sapiens

Sequence of entity 1 (A), FASTA

>8XPY_1 Glycoprotein G (chains A)
MPAENKKVRFENTTSDKGKIPSKVIKSYYGTMDIKKINEGLLDSKILSAFNTVIALLGSI
VIIVMNIMIIQNYTRSTDNQAVIKDALQGIQQQIKGLADKIGTEIGPKVSLIDTSSTITI
PANIGLLGSKISQSTASINENVNEKCKFTLPPLKIHECNISCPNPLPFREYRPQTEGVSN
LVGLPNNICLQKTSNQILKPKLISYTLPVVGQSGTCITDPLLAMDEGYFAYSHLERIGSC
SRGVSKQRIIGVGEVLDRGDEVPSLFMTNVWTPPNPNTVYHCSAVYNNEFYYVLCAVSTV
GDPILNSTYWSGSLMMTRLAVKPKSNGGGYNQHQLALRSIEKGRYDKVMPYGPSGIKQGD
TLYFPAVGFLVRTEFKYNDSNCPITKCQYSKPENCRLSMGIRPNSHYILRSGLLKYNLSD
GENPKVVFIEISDQRLSIGSPSKIYDSLGQPVFYQASFSWDTMIKFGDVLTVNPLVVNWR
NNTVISRPGQSQCPRFNTCPEICWEGVYNDAFLIDRINWISAGVFLDSNQTAENPVFTVF
KDNEILYRAQLASEDTNAQKTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAVKIPEQ
CT

Sequence of entity 2 (B), FASTA

>8XPY_2 single-domain antibody n425 (chains B)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSYISSSSSYTNY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTASYYCARGLAGVWGIDVWGQGTLVTVSS

Primary citation

Fully human single-domain antibody targeting a highly conserved cryptic epitope on the Nipah virus G protein. Wang, Y., Sun, Y., Shen, Z. et al. Nat Commun (2024) 15:6892-6892. DOI 10.1038/s41467-024-51066-6 · 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
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…

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