9LUE: Nipah G head domain

Cryo-EM structure of the Nipah G head domain in complex with three Fabs. Determined by electron microscopy at 3.03 Å resolution. Released 26 Nov 2025.

Method: Electron microscopy
Resolution: 3.03 Å
Organisms: Henipavirus nipahense, Mesocricetus auratus
Chains: 7
Atoms: 8,693
Mol. weight: 124.87 kDa
Ligands: NAG
Released: 26 Nov 2025

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

Secondary structure: helices and β-sheets

9LUE contains 16 α-helices and 105 β-strands across 7 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: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	11-12	2	14
β-strand	17-25	9	13
β-strand	33-39	7	15
β-strand	45-52	8	15
β-strand	57-59	3	15
β-strand	67-72	6	13
β-strand	77-82A	7	13
α-helix	84-86	3
β-strand	88-95	8	15
β-strand	100B-103	4	15
β-strand	107-109	3	15
β-strand	110-111	2	14

Chain B: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	19-25	7	16
β-strand	30	1	17
β-strand	31	1	17
β-strand	33-38	6	18
β-strand	44-49	6	18
β-strand	53-54	2	18
α-helix	55	1
β-strand	62-67	6	16
β-strand	70-75	6	16
β-strand	85-90	6	18

Chain C: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	11-12	2	20
β-strand	18-25	8	19
β-strand	33-40	8	21
β-strand	45-51	7	21
β-strand	57-59	3	21
β-strand	67-72	6	19
β-strand	77-82	6	19
α-helix	84-86	3
β-strand	88-95	8	21
β-strand	102-103	2	21
β-strand	107-109	3	21
β-strand	110-111	2	20

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	22
β-strand	19-24	6	22
β-strand	34-38	5	23
β-strand	45-49	5	23
β-strand	53-54	2	23
β-strand	62-67	6	22
β-strand	70-75	6	22
α-helix	80-82	3
β-strand	85-89	5	23
β-strand	90	1	24
α-helix	96	1
β-strand	97	1	24
β-strand	102	1	23

Chain G: 6 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	178-179	2	1
β-strand	200-203	4	1
α-helix	207-209	3
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
α-helix	307-309	3
β-strand	314-320	7	3
β-strand	332-335	4	3
α-helix	336-337	2
β-strand	339-341	3	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	394-397	4
β-strand	407-417	11	4
β-strand	425-430	6	4
β-strand	431	1	5
α-helix	432	1
β-strand	442-447	6	6
β-strand	450-455	6	6
β-strand	463	1	7
β-strand	465-471	7	6
β-strand	475	1	5
β-strand	476-479	4	6
β-strand	486	1	7
β-strand	490	1	8
β-strand	493	1	8
β-strand	509	1	1
β-strand	512-515	4	9
β-strand	520-526	7	9
β-strand	533	1	1
β-strand	535-540	6	9
β-strand	545-550	6	9
β-strand	557-568	12	1
β-strand	571-581	11	1
β-strand	588	1	2
β-strand	591-596	6	1
α-helix	597-598	2

Chain H: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	25
α-helix	7-8	2
β-strand	12	1	26
β-strand	17-25	9	25
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	45-52	8	12
β-strand	56-59	4	12
β-strand	67-72	6	25
β-strand	77-82A	7	25
α-helix	84-86	3
β-strand	88-96	9	12
β-strand	100A-103	5	12
β-strand	107-109	3	12
β-strand	111	1	26

Chain L: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	10
β-strand	19-29	11	10
β-strand	33-38	6	11
β-strand	45-49	5	11
β-strand	53-54	2	11
β-strand	63-66	4	10
β-strand	68-75	8	10
α-helix	80-82	3
β-strand	85-90	6	11
β-strand	97	1	12
β-strand	98	1	11
β-strand	102	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein G	G	protein	426	Henipavirus nipahense	Q9IH62 (AlphaFold model)
NIV LN3D3 Fab Light Chain	L	protein	107	Mesocricetus auratus
NiV S2B10 Fab Heavy Chain	A	protein	119	Mesocricetus auratus
NiV S2B10 Fab Light Chain	B	protein	111	Mesocricetus auratus
NiV S1E2 Fab Heavy Chain	C	protein	120	Mesocricetus auratus
NiV S1E2 Fab Light Chain	D	protein	106	Mesocricetus auratus
NIV LN3D3 Fab Heavy Chain	H	protein	119	Mesocricetus auratus

Sequence of entity 1 (G), FASTA

>9LUE_1 Glycoprotein G (chains G)
GVSNLVGLPNNICLQKTSNQILKPKLISYTLPVVGQSGTCITDPLLAMDEGYFAYSHLER
IGSCSRGVSKQRIIGVGEVLDRGDEVPSLFMTNVWTPPNPNTVYHCSAVYNNEFYYVLCA
VSTVGDPILNSTYWSGSLMMTRLAVKPKSNGGGYNQHQLALRSIEKGRYDKVMPYGPSGI
KQGDTLYFPAVGFLVRTEFKYNDSNCPITKCQYSKPENCRLSMGIRPNSHYILRSGLLKY
NLSDGENPKVVFIEISDQRLSIGSPSKIYDSLGQPVFYQASFSWDTMIKFGDVLTVNPLV
VNWRNNTVISRPGQSQCPRFNTCPEICWEGVYNDAFLIDRINWISAGVFLDSNQTAENPV
FTVFKDNEILYRAQLASEDTNAQKTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAVK
IPEQCT

Sequence of entity 2 (L), FASTA

>9LUE_2 NIV LN3D3 Fab Light Chain (chains L)
EIQMTQSPATLSVTPGDSVSLSCRASQSISNNLHWYQQKSHESPRLLIKYASQSISGIPS
RFSGSGSGTDFTLSINNLETEDFGMYFCQHSDSWPFTFGSGTKLEIK

Sequence of entity 3 (A), FASTA

>9LUE_3 NiV S2B10 Fab Heavy Chain (chains A)
QMQLQESGPGLVKPSQSLSLTCTVTGYSITSDYAWNWIRQFPRNKLEWMGFITYSGSTSY
NPSLKSRISLTRDTSKNQFFLQLSSVTTEDTATYYCARSGANWDWFAYWGQGTLVTVSA

Sequence of entity 4 (B), FASTA

>9LUE_4 NiV S2B10 Fab Light Chain (chains B)
DIQMTQSPASLAVSLGQRATISCRASESVDNYGNSFMHWYQQKPGQPPKLLIYRASKLES
GIPARFSGSGSRTDFTLTINPVEADDVATYHCQQSNEDPWTFGGGTKLEIK

Sequence of entity 5 (C), FASTA

>9LUE_5 NiV S1E2 Fab Heavy Chain (chains C)
QMQLQESGPGLVKPSQSLSLTCSVTGYSITSGYYWNWIRQFSGNKLEWMGYINHDGSKNY
NPSLKNRISITRDTSKNQFFLKLNSVTTEDTATYYCARDYGSYYYPMDYWGQGTSVTVSS

Sequence of entity 6 (D), FASTA

>9LUE_6 NiV S1E2 Fab Light Chain (chains D)
EIVLTQSPPIMSASPGEKVTITCSASSSVTFMHWFQQKPGTSPKLWIFSTSNLASGVPAR
FSGSGSGTSYSLTISRMEAEDAATYYCQQRSSYPFTFGSGTKLEIK

Sequence of entity 7 (H), FASTA

>9LUE_7 NIV LN3D3 Fab Heavy Chain (chains H)
EVKLEESGPELVKPGASVKMSCKASGYTFTNYVMHWVKQKPGQGLEWIGYVNPYNDGTQY
NEKFRDKATLTSDKSSSTVYMELNSLTSEDSAVYYCTRGDYPYWVFEVWGAGTTVTVSS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

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…
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…
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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