9LU3: LN1F9 Fab

LN1F9 Fab bound to Nipah Virus attachment (G) glycoprotein head domain. Determined by X-ray diffraction at 3.0 Å resolution. Released 26 Nov 2025.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Henipavirus nipahense, Mus musculus
Chains: 6
Atoms: 13,333
Mol. weight: 198.64 kDa
Ligands: NAG
Released: 26 Nov 2025

Explore 9LU3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9LU3 contains 55 α-helices and 156 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: 10 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	178-179	2	1
α-helix	185-187	3
β-strand	201-202	2	1
α-helix	204-206	3
β-strand	216-225	10	2
β-strand	228-237	10	2
β-strand	244-257	14	2
β-strand	263-271	9	2
α-helix	276-278	3
β-strand	279-286	8	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
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	424-425	2
β-strand	426-430	5	4
β-strand	431	1	5
β-strand	442-447	6	6
β-strand	450-455	6	6
β-strand	463	1	7
β-strand	465-468	4	6
β-strand	469-471	3	8
β-strand	475	1	5
β-strand	476-477	2	8
β-strand	486	1	7
β-strand	509	1	1
β-strand	511-515	5	9
β-strand	520-526	7	9
β-strand	535-540	6	9
β-strand	545-550	6	9
β-strand	561-568	8	1
β-strand	571-579	9	1
β-strand	590-596	7	1
α-helix	597-598	2

Chain B: 11 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	178-180	3	21
α-helix	185-187	3
β-strand	201-202	2	21
α-helix	204-206	3
β-strand	217-225	9	22
β-strand	228-237	10	22
β-strand	244-257	14	22
β-strand	263-271	9	22
α-helix	276-278	3
β-strand	279-286	8	23
β-strand	290-297	8	23
α-helix	307-309	3
β-strand	314-320	7	23
α-helix	328-331	4
β-strand	332-335	4	23
β-strand	340-341	2	24
β-strand	347-350	4	24
β-strand	354	1	23
β-strand	356-357	2	24
β-strand	361-371	11	24
α-helix	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	24
α-helix	424-425	2
β-strand	426-430	5	24
β-strand	431	1	25
α-helix	432	1
β-strand	442-447	6	26
β-strand	450-455	6	26
β-strand	465-471	7	26
β-strand	475	1	25
β-strand	476-479	4	26
β-strand	509	1	21
β-strand	511-515	5	27
β-strand	520-526	7	27
β-strand	533	1	28
β-strand	535-540	6	27
β-strand	545-550	6	27
β-strand	557	1	28
β-strand	561-568	8	21
β-strand	571-579	9	21
β-strand	590-596	7	21
α-helix	597-598	2

Chain D: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	29
β-strand	11-12	2	30
β-strand	18-25	8	29
α-helix	29-31	3
β-strand	34-39	6	31
β-strand	45-51	7	31
β-strand	57-58	2	31
α-helix	61-63	3
β-strand	67-72	6	29
β-strand	77-82	6	29
α-helix	84-86	3
β-strand	88-94	7	31
β-strand	102-103	2	31
β-strand	107-109	3	31
β-strand	110-111	2	30
β-strand	117	1	32
α-helix	118-119	2
β-strand	120-124	5	33
α-helix	125-127	3
α-helix	132-134	3
β-strand	135-145	11	33
β-strand	146	1	32
β-strand	151-154	4	34
α-helix	155-157	3
β-strand	163-165	3	33
α-helix	166-168	3
β-strand	169-170	2	33
β-strand	176-185	10	33
α-helix	186-188	3
β-strand	194-200	7	34
β-strand	205-211	7	34

Chain E: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	35
β-strand	10-14	5	36
β-strand	19-25	7	35
β-strand	33-38	6	36
β-strand	45-49	5	36
β-strand	53-54	2	36
α-helix	55	1
β-strand	62-67	6	35
β-strand	70-75	6	35
α-helix	80-82	3
β-strand	84-90	7	36
α-helix	96	1
β-strand	97	1	31
β-strand	98	1	36
β-strand	102-107	6	36
β-strand	111	1	37
α-helix	112-113	2
β-strand	114-118	5	38
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	38
β-strand	140	1	37
β-strand	145-150	6	39
β-strand	154	1	39
β-strand	159-163	5	38
α-helix	164-167	4
β-strand	173-182	10	38
α-helix	183-187	5
β-strand	192-197	6	39
β-strand	205-208	4	39

Chain H: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	57-58	2	12
α-helix	61-63	3
β-strand	67-72	6	10
β-strand	77-82	6	10
α-helix	84-86	3
β-strand	88-94	7	12
β-strand	102-103	2	12
β-strand	107-109	3	12
β-strand	110-111	2	11
β-strand	117	1	13
α-helix	118-119	2
β-strand	120-124	5	14
β-strand	131-132	2	14
β-strand	135-145	11	14
β-strand	146	1	13
β-strand	151-154	4	15
α-helix	155-157	3
β-strand	159	1	15
β-strand	163-165	3	14
α-helix	166-168	3
β-strand	169-170	2	14
β-strand	176-185	10	14
α-helix	186-189	4
β-strand	194-200	7	15
β-strand	205-211	7	15

Chain L: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-14	5	17
β-strand	19-25	7	16
β-strand	33-38	6	17
α-helix	43-44	2
β-strand	45-49	5	17
β-strand	53-54	2	17
α-helix	55	1
β-strand	62-67	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	84-90	7	17
α-helix	96	1
β-strand	97-98	2	17
β-strand	102-107	6	17
β-strand	111	1	18
α-helix	112-113	2
β-strand	114-118	5	19
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	19
β-strand	140	1	18
β-strand	144-150	7	20
β-strand	153-154	2	20
α-helix	155	1
β-strand	159-163	5	19
α-helix	165-167	3
β-strand	173-182	10	19
α-helix	183-188	6
β-strand	191-198	8	20
β-strand	205-210	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein G	A, B	protein	441	Henipavirus nipahense	Q9IH62 (AlphaFold model)
mAb LN1F9 Fab heavy chain	D, H	protein	234	Mus musculus
mAb LN1F9 Fab light chain	E, L	protein	214	Mus musculus

Sequence of entity 1 (A, B), FASTA

>9LU3_1 Glycoprotein G (chains A, B)
HHHHHHLEVLFQGPEGVSNLVGLPNNICLQKTSNQILKPKLISYTLPVVGQSGTCITDPL
LAMDEGYFAYSHLERIGSCSRGVSKQRIIGVGEVLDRGDEVPSLFMTNVWTPPNPNTVYH
CSAVYNNEFYYVLCAVSTVGDPILNSTYWSGSLMMTRLAVKPKSNGGGYNQHQLALRSIE
KGRYDKVMPYGPSGIKQGDTLYFPAVGFLVRTEFKYNDSNCPITKCQYSKPENCRLSMGI
RPNSHYILRSGLLKYNLSDGENPKVVFIEISDQRLSIGSPSKIYDSLGQPVFYQASFSWD
TMIKFGDVLTVNPLVVNWRNNTVISRPGQSQCPRFNTCPEICWEGVYNDAFLIDRINWIS
AGVFLDSNQTAENPVFTVFKDNEILYRAQLASEDTNAQKTITNCFLLKNKIWCISLVEIY
DTGDNVIRPKLFAVKIPEQCT

Sequence of entity 2 (D, H), FASTA

>9LU3_2 mAb LN1F9 Fab heavy chain (chains D, H)
EVKLVESGGGLVKPGGSLKLSCAASGFSFRNYAMSWVRQSPEKRLEWVAEVSSGGGYTYY
PDTVTGRFTISRDNAKNILYLEMSSLRSEDTAMYYCTRDPDSSGYLAWFAYWGQGTLVTV
SAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH

Sequence of entity 3 (E, L), FASTA

>9LU3_3 mAb LN1F9 Fab light chain (chains E, L)
DILLTQSPASLSASVGETVTITCRASENINSYLAWYQQKQGKSPQLLVYNAKTLAEGVPS
RFSGSGSDTQFSLKINTLQPEDFGTYYCQHHSGTPYTFGGGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10

Primary citation

Antigenic landscape of Nipah virus attachment glycoprotein analysis reveals a protective immunodominant epitope across species. Zhou, D., Wang, Y., Yao, Y. et al. NPJ Vaccines (2025) 11:5-5. DOI 10.1038/s41541-025-01319-2 · 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…
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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