8JA5: Nipah Virus attachment (G) glycoprotein

Crystal structure of Nipah Virus attachment (G) glycoprotein in complex with neutralizing antibody 14F8. Determined by X-ray diffraction at 2.79 Å resolution. Released 8 May 2024.

Method: X-ray diffraction
Resolution: 2.79 Å
Organisms: Mus musculus, Nipah henipavirus
Chains: 6
Atoms: 13,483
Mol. weight: 197.54 kDa
Ligands: NAG
Released: 8 May 2024

Explore 8JA5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JA5 contains 45 α-helices and 159 β-strands across 6 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: 8 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	201-202	2	12
α-helix	204-206	3
β-strand	216-225	10	13
β-strand	228-237	10	13
β-strand	244-257	14	13
β-strand	263-271	9	13
α-helix	276-278	3
β-strand	279-287	9	14
β-strand	290-297	8	14
β-strand	314-320	7	14
β-strand	332-335	4	14
β-strand	340-341	2	15
β-strand	347-350	4	15
β-strand	354	1	14
β-strand	356-358	3	15
β-strand	361-371	11	15
α-helix	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	15
α-helix	424-425	2
β-strand	426-430	5	15
β-strand	431	1	16
α-helix	432	1
β-strand	442-447	6	17
β-strand	450-455	6	17
β-strand	463	1	18
β-strand	465-471	7	17
β-strand	475	1	16
β-strand	476-479	4	17
β-strand	486	1	18
β-strand	509	1	12
β-strand	511-515	5	19
β-strand	520-526	7	19
β-strand	533	1	20
β-strand	535-541	7	19
β-strand	544-550	7	19
β-strand	557	1	20
β-strand	558-567	10	12
β-strand	572-582	11	12
β-strand	587-596	10	12
α-helix	597-598	2

Chain B: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	21
β-strand	11-12	2	22
β-strand	18-25	8	21
β-strand	33-39	7	23
α-helix	44-45	2
β-strand	46-51	6	23
β-strand	57-59	3	23
α-helix	61-63	3
β-strand	67-72	6	21
β-strand	77-82	6	21
α-helix	87-89	3
β-strand	91-99	9	23
β-strand	102-106	5	23
β-strand	110-112	3	23
β-strand	113-114	2	22
α-helix	118-119	2
α-helix	121-122	2
β-strand	123-127	5	24
β-strand	134-135	2	24
β-strand	138-148	11	24
β-strand	154-157	4	25
α-helix	158-160	3
β-strand	162	1	25
β-strand	166-168	3	24
α-helix	169-171	3
β-strand	172	1	26
β-strand	179	1	24
β-strand	180	1	26
β-strand	181-188	8	24
β-strand	192	1	27
β-strand	195	1	27
β-strand	198-203	6	25
α-helix	204-206	3
β-strand	208-213	6	25

Chain C: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-6	3	28
β-strand	10-14	5	29
β-strand	19-25	7	28
β-strand	30	1	30
β-strand	36	1	30
β-strand	38-43	6	29
β-strand	50-54	5	29
β-strand	58-59	2	29
α-helix	60	1
β-strand	67-72	6	28
β-strand	75-80	6	28
α-helix	85-87	3
β-strand	89-95	7	29
α-helix	101	1
β-strand	102-103	2	29
β-strand	107-112	6	29
β-strand	119-123	5	31
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	31
β-strand	149-155	7	32
β-strand	158-159	2	32
β-strand	164-168	5	31
α-helix	169-172	4
β-strand	178-187	10	31
α-helix	188-192	5
β-strand	196-203	8	32
β-strand	210-214	5	32

Chain D: 8 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	200-202	3	33
α-helix	204-206	3
β-strand	216-225	10	34
β-strand	228-237	10	34
β-strand	244-257	14	34
β-strand	263-271	9	34
α-helix	276-278	3
β-strand	279-287	9	35
β-strand	290-297	8	35
β-strand	314-320	7	35
β-strand	332-335	4	35
α-helix	336-337	2
β-strand	339-341	3	36
β-strand	347-350	4	36
β-strand	354	1	35
β-strand	356-358	3	36
β-strand	361-371	11	36
α-helix	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	36
β-strand	425-430	6	36
β-strand	431	1	37
α-helix	432	1
β-strand	442-447	6	38
β-strand	450-455	6	38
β-strand	465-471	7	38
β-strand	475	1	37
β-strand	476-479	4	38
β-strand	509	1	33
β-strand	511-515	5	39
β-strand	520-526	7	39
β-strand	533	1	40
β-strand	535-541	7	39
β-strand	544-550	7	39
β-strand	557	1	40
β-strand	558-568	11	33
β-strand	571-582	12	33
β-strand	587-596	10	33
α-helix	597-598	2

Chain H: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
β-strand	34-39	6	3
α-helix	44-45	2
β-strand	46-51	6	3
β-strand	57-59	3	3
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	87-89	3
β-strand	91-99	9	3
β-strand	102-106	5	3
β-strand	110-112	3	3
β-strand	113-114	2	2
α-helix	118-119	2
β-strand	123-127	5	4
β-strand	134-135	2	4
β-strand	138-148	11	4
β-strand	154-157	4	5
α-helix	158-160	3
β-strand	162	1	5
β-strand	166-168	3	4
α-helix	169-171	3
β-strand	172-173	2	4
β-strand	179-188	10	4
β-strand	192	1	6
β-strand	195	1	6
β-strand	197-203	7	5
α-helix	204-206	3
β-strand	208-214	7	5

Chain L: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	7
β-strand	10-14	5	8
β-strand	19-25	7	7
β-strand	30	1	9
β-strand	36	1	9
β-strand	38-43	6	8
β-strand	50-54	5	8
β-strand	58-59	2	8
α-helix	60	1
β-strand	67-72	6	7
β-strand	75-80	6	7
α-helix	85-87	3
β-strand	89-95	7	8
α-helix	101	1
β-strand	102-103	2	8
β-strand	104	1	7
β-strand	107-112	6	8
β-strand	119-123	5	10
α-helix	124-126	3
α-helix	127-132	6
β-strand	134-144	11	10
β-strand	149-155	7	11
β-strand	158-159	2	11
β-strand	164-168	5	10
α-helix	169-172	4
β-strand	178-187	10	10
β-strand	197-203	7	11
β-strand	210-213	4	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
14F8 antibody heavy chain	B, H	protein	233	Mus musculus
14F8 antibody light chain	L	protein	216	Mus musculus
Glycoprotein G	A, D	protein	423	Nipah henipavirus	Q9IH62 (AlphaFold model)
14F8 antibody light chain	C	protein	219	Mus musculus

Sequence of entity 1 (B, H), FASTA

>8JA5_1 14F8 antibody heavy chain (chains B, H)
QVQLKESGPGLVAPSQSLSITCTVSGFSLTSYDISWIRQPPGKGLEWLGVIWTGGVTNYN
SAFLSRLSISKDNSKSQVFLKMNSLQTDDTAIYYCVREGDWFFDVWGAGTTVTVSSASTK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPHHHHHH

Sequence of entity 2 (L), FASTA

>8JA5_2 14F8 antibody light chain (chains L)
DVLMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPQLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKINRVEAEDLGLYYCFQASHVPYTFGGGTKLEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKLYACEVTHQGLSSPVTKSAAA

Sequence of entity 3 (A, D), FASTA

>8JA5_3 Glycoprotein G (chains A, D)
NNICLQKTSNQILKPKLISYTLPVVGQSGTCITDPLLAMDEGYFAYSHLERIGSCSRGVS
KQRIIGVGEVLDRGDEVPSLFMTNVWTPPNPNTVYHCSAVYNNEFYYVLCAVSTVGDPIL
NSTYWSGSLMMTRLAVKPKSNGGGYNQHQLALRSIEKGRYDKVMPYGPSGIKQGDTLYFP
AVGFLVRTEFKYNDSNCPITKCQYSKPENCRLSMGIRPNSHYILRSGLLKYNLSDGENPK
VVFIEISDQRLSIGSPSKIYDSLGQPVFYQASFSWDTMIKFGDVLTVNPLVVNWRNNTVI
SRPGQSQCPRFNTCPEICWEGVYNDAFLIDRINWISAGVFLDSNQTAENPVFTVFKDNEI
LYRAQLASEDTNAQKTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAVKIPEQCTHHH
HHH

Sequence of entity 4 (C), FASTA

>8JA5_4 14F8 antibody light chain (chains C)
DVLMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPQLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKINRVEAEDLGLYYCFQASHVPYTFGGGTKLEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKLYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Single amino acid substitution in Hendra virus attachment glycoprotein induces cross-neutralizing antibodies against Nipah virus. Li, Y., Huang, X., Li, R. et al. Signal Transduct Target Ther (2025) 10:276-276. DOI 10.1038/s41392-025-02370-0 · 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
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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